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@article{DBLP:journals/bib/AbdellahFGGBFCKPCK24, author = {Marwan Abdellah and Alessandro Foni and Juan Jose Garcia{-}Cantero and Nadir Rom{\'{a}}n Guerrero and Elvis Boci and Adrien Fleury and Jay S. Coggan and Daniel Keller and Judit Planas and Jean{-}Denis Courcol and Georges Khazen}, title = {Synthesis of geometrically realistic and watertight neuronal ultrastructure manifolds for \emph{in silico} modeling}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae393}, doi = {10.1093/BIB/BBAE393}, timestamp = {Sat, 31 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/AbdellahFGGBFCKPCK24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AhammadLBJACHDKS24, author = {Ishtiaque Ahammad and Anika Bushra Lamisa and Arittra Bhattacharjee and Tabassum Binte Jamal and Md Shamsul Arefin and Zeshan Mahmud Chowdhury and Mohammad Uzzal Hossain and Keshob Chandra Das and Chaman Ara Keya and Md. Salimullah}, title = {AITeQ: a machine learning framework for Alzheimer's prediction using a distinctive five-gene signature}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae291}, doi = {10.1093/BIB/BBAE291}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/AhammadLBJACHDKS24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AherrahrouTA24, author = {Noura Aherrahrou and Hamid Tairi and Zouhair Aherrahrou}, title = {Genomic privacy preservation in genome-wide association studies: taxonomy, limitations, challenges, and vision}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae356}, doi = {10.1093/BIB/BBAE356}, timestamp = {Sat, 31 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/AherrahrouTA24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AllersOCBK24, author = {Steven Allers and Kyle A. O'Connell and Thad B. Carlson and David Belardo and Benjamin L. King}, title = {Reusable tutorials for using cloud-based computing environments for the analysis of bacterial gene expression data from bulk {RNA} sequencing}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae301}, doi = {10.1093/BIB/BBAE301}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/AllersOCBK24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/Amisaki24, author = {Takashi Amisaki}, title = {Multilevel superposition for deciphering the conformational variability of protein ensembles}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae137}, doi = {10.1093/BIB/BBAE137}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/Amisaki24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AnthonyS24, author = {Harrison Anthony and Cathal Seoighe}, title = {Performance assessment of computational tools to detect microsatellite instability}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae390}, doi = {10.1093/BIB/BBAE390}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/AnthonyS24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ArulrajWIZFP24, author = {Theinmozhi Arulraj and Hanwen Wang and Alberto Ippolito and Shuming Zhang and Elana J. Fertig and Aleksander S. Popel}, title = {Leveraging multi-omics data to empower quantitative systems pharmacology in immuno-oncology}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae131}, doi = {10.1093/BIB/BBAE131}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ArulrajWIZFP24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BadaczewskaDawidWKK24, author = {Aleksandra E. Badaczewska{-}Dawid and Karol Wroblewski and Mateusz Kurcinski and Sebastian Kmiecik}, title = {Structure prediction of linear and cyclic peptides using CABS-flex}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae003}, doi = {10.1093/BIB/BBAE003}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/BadaczewskaDawidWKK24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BarbitoffULNGP24, author = {Yury A Barbitoff and Mikhail O. Ushakov and Tatyana E. Lazareva and Yulia A Nasykhova and Andrey S. Glotov and Alexander V. Predeus}, title = {Bioinformatics of germline variant discovery for rare disease diagnostics: current approaches and remaining challenges}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbad508}, doi = {10.1093/BIB/BBAD508}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BarbitoffULNGP24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BattuelloCBLSRNBC24, author = {Paolo Battuello and Giorgio Corti and Alice Bartolini and Annalisa Lorenzato and Alberto Sogari and Mariangela Russo and Federica Di Nicolantonio and Alberto Bardelli and Giovanni Crisafulli}, title = {Mutational signatures of colorectal cancers according to distinct computational workflows}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae249}, doi = {10.1093/BIB/BBAE249}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BattuelloCBLSRNBC24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BaulAJWLYZ24, author = {Sudipto Baul and Khandakar Tanvir Ahmed and Qibing Jiang and Guangyu Wang and Qian Li and Jeongsik Yong and Wei Zhang}, title = {Integrating spatial transcriptomics and bulk RNA-seq: predicting gene expression with enhanced resolution through graph attention networks}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae316}, doi = {10.1093/BIB/BBAE316}, timestamp = {Tue, 13 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BaulAJWLYZ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BealsHL24, author = {Joshua Beals and Haiyan Hu and Xiaoman Li}, title = {A survey of experimental and computational identification of small proteins}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae345}, doi = {10.1093/BIB/BBAE345}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BealsHL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BianLDW24, author = {Jilong Bian and Hao Lu and Guanghui Dong and Guohua Wang}, title = {Hierarchical multimodal self-attention-based graph neural network for {DTI} prediction}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae293}, doi = {10.1093/BIB/BBAE293}, timestamp = {Fri, 26 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BianLDW24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BoettoFHASPBCCSZKQDSA24, author = {Christophe Boetto and Arthur Frouin and L{\'{e}}o Henches and Antoine Auvergne and Yuka Suzuki and Etienne Patin and Marius Bredon and Alec Chiu and Milieu Interieur Consortium and Sriram Sankararaman and Noah Zaitlen and Sean P. Kennedy and Lluis Quintana{-}Murci and Darragh Duffy and Harry Sokol and Hugues Aschard}, title = {{MANOCCA:} a robust and computationally efficient test of covariance in high-dimension multivariate omics data}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae272}, doi = {10.1093/BIB/BBAE272}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BoettoFHASPBCCSZKQDSA24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BrooksLMSNNSCG24, author = {Thomas G. Brooks and Nicholas F. Lahens and Antonijo Mrcela and Dimitra Sarantopoulou and Soumyashant Nayak and Amruta Naik and Shaon Sengupta and Peter S. Choi and Gregory R. Grant}, title = {{BEERS2:} RNA-Seq simulation through high fidelity \emph{in silico} modeling}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae164}, doi = {10.1093/BIB/BBAE164}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BrooksLMSNNSCG24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BrouardMV24, author = {C{\'{e}}line Brouard and Rapha{\"{e}}l Mourad and Nathalie Vialaneix}, title = {Should we really use graph neural networks for transcriptomic prediction?}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae027}, doi = {10.1093/BIB/BBAE027}, timestamp = {Fri, 22 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/BrouardMV24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BrowningTB24, author = {James S. L. Browning Jr. and Daniel R. Tauritz and John Beckmann}, title = {Evolutionary algorithms simulating molecular evolution: a new field proposal}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae360}, doi = {10.1093/BIB/BBAE360}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BrowningTB24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BudhkarTLZSS24, author = {Aishwarya Budhkar and Ziyang Tang and Xiang Liu and Xuhong Zhang and Jing Su and Qianqian Song}, title = {xSiGra: explainable model for single-cell spatial data elucidation}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae388}, doi = {10.1093/BIB/BBAE388}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BudhkarTLZSS24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BugnonPGRPFCASM24, author = {Leandro A Bugnon and Leandro E. Di Persia and Matias Gerard and Jonathan Raad and Santiago Prochetto and Emilio Fenoy and Uciel Chorostecki and Federico Ariel and Georgina Stegmayer and Diego H. Milone}, title = {sincFold: end-to-end learning of short- and long-range interactions in {RNA} secondary structure}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae271}, doi = {10.1093/BIB/BBAE271}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BugnonPGRPFCASM24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/CaiLLHWBZ24, author = {Yantong Cai and Jia Lv and Rui Li and Xiaowen Huang and Shi Wang and Zhenmin Bao and Qifan Zeng}, title = {Deqformer: high-definition and scalable deep learning probe design method}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae007}, doi = {10.1093/BIB/BBAE007}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/CaiLLHWBZ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/CastanhoAM24, author = {Eduardo N. Castanho and Helena Aidos and Sara C. Madeira}, title = {Biclustering data analysis: a comprehensive survey}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae342}, doi = {10.1093/BIB/BBAE342}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/CastanhoAM24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenAZZ24, author = {Zhaojia Chen and Noor ul Ain and Qian Zhao and Xingtan Zhang}, title = {From tradition to innovation: conventional and deep learning frameworks in genome annotation}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae138}, doi = {10.1093/BIB/BBAE138}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenAZZ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenGZ24, author = {Lei Chen and Jiahui Gu and Bo Zhou}, title = {PMiSLocMF: predicting miRNA subcellular localizations by incorporating multi-source features of miRNAs}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae386}, doi = {10.1093/BIB/BBAE386}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenGZ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenH24, author = {Xing Chen and Li Huang}, title = {Computational model for drug research}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae158}, doi = {10.1093/BIB/BBAE158}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenH24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenLDYLR24, author = {Hegang Chen and Yuyin Lu and Zhiming Dai and Yuedong Yang and Qing Li and Yanghui Rao}, title = {Comprehensive single-cell RNA-seq analysis using deep interpretable generative modeling guided by biological hierarchy knowledge}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae314}, doi = {10.1093/BIB/BBAE314}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenLDYLR24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenROXXLGBTXWLBC24, author = {Bijia Chen and Chao Ren and Zhangyi Ouyang and Jingxuan Xu and Kang Xu and Yaru Li and Hejiang Guo and Xuemei Bai and Mengge Tian and Xiang Xu and Yuyang Wang and Hao Li and Xiaochen Bo and Hebing Chen}, title = {Stratifying {TAD} boundaries pinpoints focal genomic regions of regulation, damage, and repair}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae306}, doi = {10.1093/BIB/BBAE306}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenROXXLGBTXWLBC24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenSSTD24, author = {Mingshuai Chen and Mingai Sun and Xi Su and Prayag Tiwari and Yijie Ding}, title = {Fuzzy kernel evidence Random Forest for identifying pseudouridine sites}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae169}, doi = {10.1093/BIB/BBAE169}, timestamp = {Sun, 28 Apr 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenSSTD24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenYLWLW24, author = {Nanjun Chen and Jixiang Yu and Zhe Liu and Fuzhou Wang and Xiangtao Li and Ka{-}Chun Wong}, title = {{TP-LMMSG:} a peptide prediction graph neural network incorporating flexible amino acid property representation}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae308}, doi = {10.1093/BIB/BBAE308}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenYLWLW24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenZDWRY24, author = {Ken Chen and Yue Zhou and Maolin Ding and Yu Wang and Zhixiang Ren and Yuedong Yang}, title = {Self-supervised learning on millions of primary {RNA} sequences from 72 vertebrates improves sequence-based {RNA} splicing prediction}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae163}, doi = {10.1093/BIB/BBAE163}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenZDWRY24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenZLQZ24, author = {Qiuhao Chen and Liyuan Zhang and Yaojia Liu and Zhonghao Qin and Tianyi Zhao}, title = {PUTransGCN: identification of piRNA-disease associations based on attention encoding graph convolutional network and positive unlabelled learning}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae144}, doi = {10.1093/BIB/BBAE144}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenZLQZ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/Cheng24, author = {Liang Cheng}, title = {Attention mechanism models for precision medicine}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae156}, doi = {10.1093/BIB/BBAE156}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/Cheng24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChoBNPN24, author = {Juok Cho and Bukyung Baik and Hai C. T. Nguyen and Daeui Park and Dougu Nam}, title = {Characterizing efficient feature selection for single-cell expression analysis}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae317}, doi = {10.1093/BIB/BBAE317}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChoBNPN24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChuwdhuryGCLKLD24, author = {Gulam Sarwar Chuwdhury and Yunshan Guo and Chi{-}Leung Chiang and Ka{-}On Lam and Ngar{-}Woon Kam and Zhonghua Liu and Wei Dai}, title = {ImmuneMirror: {A} machine learning-based integrative pipeline and web server for neoantigen prediction}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae024}, doi = {10.1093/BIB/BBAE024}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ChuwdhuryGCLKLD24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/Cinquin24, author = {Olivier Cinquin}, title = {ChIP-GPT: a managed large language model for robust data extraction from biomedical database records}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbad535}, doi = {10.1093/BIB/BBAD535}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/Cinquin24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/CuiLXWFLWZ24, author = {Wentao Cui and Qingqing Long and Meng Xiao and Xuezhi Wang and Guihai Feng and Xin Li and Pengfei Wang and Yuanchun Zhou}, title = {Refining computational inference of gene regulatory networks: integrating knockout data within a multi-task framework}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae361}, doi = {10.1093/BIB/BBAE361}, timestamp = {Sat, 31 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/CuiLXWFLWZ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DingXCLFSJ24, author = {Xiao{-}Hong Ding and Yi Xiao and Fenfang Chen and Cheng{-}Lin Liu and Tong Fu and Zhi{-}Ming Shao and Yi{-}Zhou Jiang}, title = {The {HLA-I} landscape confers prognosis and antitumor immunity in breast cancer}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae151}, doi = {10.1093/BIB/BBAE151}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DingXCLFSJ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DingZFL24, author = {Xiaobao Ding and Lin Zhang and Ming Fan and Lihua Li}, title = {{TME-NET:} an interpretable deep neural network for predicting pan-cancer immune checkpoint inhibitor responses}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae410}, doi = {10.1093/BIB/BBAE410}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DingZFL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DongJLDZ24, author = {Zihan Dong and Wei Jiang and Hongyu Li and Andrew T. Dewan and Hongyu Zhao}, title = {{LDER-GE} estimates phenotypic variance component of gene-environment interactions in human complex traits accurately with {GE} interaction summary statistics and full {LD} information}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae335}, doi = {10.1093/BIB/BBAE335}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DongJLDZ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DouYZLD24, author = {Chang Dou and Yijie Yang and Fei Zhu and Bingzhi Li and Yuping Duan}, title = {Explorer: efficient {DNA} coding by De Bruijn graph toward arbitrary local and global biochemical constraints}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae363}, doi = {10.1093/BIB/BBAE363}, timestamp = {Sat, 31 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DouYZLD24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DuanZW24, author = {Junbo Duan and Xinrui Zhao and Xiaoming Wu}, title = {LoRA-TV: read depth profile-based clustering of tumor cells in single-cell sequencing}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae277}, doi = {10.1093/BIB/BBAE277}, timestamp = {Fri, 26 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DuanZW24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/EckhartLRL24, author = {Lea Eckhart and Kerstin Lenhof and Lisa{-}Marie Rolli and Hans{-}Peter Lenhof}, title = {A comprehensive benchmarking of machine learning algorithms and dimensionality reduction methods for drug sensitivity prediction}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae242}, doi = {10.1093/BIB/BBAE242}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/EckhartLRL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FanCCHWLWGZLWM24, author = {Chuiqin Fan and Fuyi Chen and Yuanguo Chen and Liangping Huang and Manna Wang and Yulin Liu and Yu Wang and Huijie Guo and Nanpeng Zheng and Yanbing Liu and Hongwu Wang and Lian Ma}, title = {irGSEA: the integration of single-cell rank-based gene set enrichment analysis}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae243}, doi = {10.1093/BIB/BBAE243}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/FanCCHWLWGZLWM24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FangFLLYYZLSGQ24, author = {Minghao Fang and Jingwen Fang and Songwen Luo and Ke Liu and Qiaoni Yu and Jiaxuan Yang and Youyang Zhou and Zongkai Li and Ruoming Sun and Chuang Guo and Kun Qu}, title = {eccDNA-pipe: an integrated pipeline for identification, analysis and visualization of extrachromosomal circular {DNA} from high-throughput sequencing data}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae034}, doi = {10.1093/BIB/BBAE034}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/FangFLLYYZLSGQ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FiamIN24, author = {Regina N{\'{o}}ra Fiam and Csabai Istv{\'{a}}n and Solymosi Norbert}, title = {Comparing full variation profile analysis with the conventional consensus method in SARS-CoV-2 phylogeny}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae296}, doi = {10.1093/BIB/BBAE296}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/FiamIN24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FuDLXLZL24, author = {Qiqing Fu and Chenyu Dong and Yunhe Liu and Xiaoqiong Xia and Gang Liu and Fan Zhong and Lei Liu}, title = {A comparison of scRNA-seq annotation methods based on experimentally labeled immune cell subtype dataset}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae392}, doi = {10.1093/BIB/BBAE392}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/FuDLXLZL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GaoMXPGGHLJL24, author = {Yuan Gao and Bin Ma and Qianshuai Xu and Yuna Peng and Huimin Gong and Aohan Guan and Kexin Hua and Paul R. Langford and Hui Jin and Rui Luo}, title = {Spatial proximity and gene function: a new dimension in prokaryotic gene association network analysis with 3D-GeneNet}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae320}, doi = {10.1093/BIB/BBAE320}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GaoMXPGGHLJL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GaoSXCDZW24, author = {Zhen Gao and Yansen Su and Junfeng Xia and Rui{-}Fen Cao and Yun Ding and Chun{-}Hou Zheng and Pi{-}Jing Wei}, title = {DeepFGRN: inference of gene regulatory network with regulation type based on directed graph embedding}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae143}, doi = {10.1093/BIB/BBAE143}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GaoSXCDZW24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GayEXYWWYWAL24, author = {Skylar A Gay and Gregory Ellison and Jianing Xu and Jialin Yang and Yiliang Wei and Shaoyuan Wu and Lili Yu and Christopher C. Whalen and Jonathan Arnold and Liang Liu}, title = {Phylogenetic inference of inter-population transmission rates for infectious diseases}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae312}, doi = {10.1093/BIB/BBAE312}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GayEXYWWYWAL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GeraultGCND24, author = {Marc{-}Antoine Gerault and Samuel Granjeaud and Luc Camoin and P{\"{a}}r Nordlund and Lingyun Dai}, title = {{IMPRINTS.CETSA} and IMPRINTS.CETSA.app: an {R} package and a Shiny application for the analysis and interpretation of {IMPRINTS-CETSA} data}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae128}, doi = {10.1093/BIB/BBAE128}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GeraultGCND24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GolesSCSSADPONM24, author = {Montserrat Goles and Anamaria Sanchez{-}Daza and Gabriel Cabas{-}Mora and Lindybeth Sarmiento{-}Var{\'{o}}n and Julieta Sep{\'{u}}lveda{-}Ya{\~{n}}ez and Hoda Anvari{-}Kazemabad and Mehdi D. Davari and Roberto Uribe Paredes and Alvaro Olivera{-}Nappa and Marcelo A. Navarrete and David Medina{-}Ortiz}, title = {Peptide-based drug discovery through artificial intelligence: towards an autonomous design of therapeutic peptides}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae275}, doi = {10.1093/BIB/BBAE275}, timestamp = {Thu, 22 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GolesSCSSADPONM24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GomezRF24, author = {Catalina Gonzalez Gomez and Manuel Rosa{-}Calatrava and Julien Fouret}, title = {Optimizing \emph{in silico} drug discovery: simulation of connected differential expression signatures and applications to benchmarking}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae299}, doi = {10.1093/BIB/BBAE299}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GomezRF24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GuWXHJLGLSY24, author = {Shuang Gu and Chaoliang Wen and Zhen Xiao and Qiang Huang and Zheyi Jiang and Honghong Liu and Jia Gao and Junying Li and Congjiao Sun and Ning Yang}, title = {MyoV: a deep learning-based tool for the automated quantification of muscle fibers}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbad528}, doi = {10.1093/BIB/BBAD528}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/GuWXHJLGLSY24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GuoC24, author = {Xinyu Guo and Liang Chen}, title = {From {G1} to {M:} a comparative study of methods for identifying cell cycle phases}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbad517}, doi = {10.1093/BIB/BBAD517}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/GuoC24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GuoHCYWHHC24, author = {Yue Guo and Haitao Hu and Wenbo Chen and Hao Yin and Jian Wu and Chang{-}Yu Hsieh and Qiaojun He and Ji Cao}, title = {SynergyX: a multi-modality mutual attention network for interpretable drug synergy prediction}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae015}, doi = {10.1093/BIB/BBAE015}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/GuoHCYWHHC24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GuoWWZH24, author = {Zhen{-}Hao Guo and Yan{-}Bin Wang and Siguo Wang and Qinhu Zhang and De{-}Shuang Huang}, title = {scCorrector: a robust method for integrating multi-study single-cell data}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbad525}, doi = {10.1093/BIB/BBAD525}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/GuoWWZH24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GuoWYYHZL24, author = {Lu{-}Xiang Guo and Lei Wang and Zhu{-}Hong You and Chang{-}Qing Yu and Meng{-}Lei Hu and Bo{-}Wei Zhao and Yang Li}, title = {Likelihood-based feature representation learning combined with neighborhood information for predicting circRNA-miRNA associations}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae020}, doi = {10.1093/BIB/BBAE020}, timestamp = {Thu, 08 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GuoWYYHZL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GuoYZD24, author = {Qirui Guo and Musu Yuan and Lei Zhang and Minghua Deng}, title = {scPLAN: a hierarchical computational framework for single transcriptomics data annotation, integration and cell-type label refinement}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae305}, doi = {10.1093/BIB/BBAE305}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GuoYZD24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GuptaKBJS24, author = {Sagar Gupta and Veerbhan Kesarwani and Umesh Bhati and Jyoti and Ravi Shankar}, title = {PTFSpot: deep co-learning on transcription factors and their binding regions attains impeccable universality in plants}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae324}, doi = {10.1093/BIB/BBAE324}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GuptaKBJS24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GyawaliDWC24, author = {Rajan Gyawali and Ashwin Dhakal and Liguo Wang and Jianlin Cheng}, title = {CryoSegNet: accurate cryo-EM protein particle picking by integrating the foundational {AI} image segmentation model and attention-gated U-Net}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae282}, doi = {10.1093/BIB/BBAE282}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GyawaliDWC24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HahnPHLMSHVDTL24, author = {Georg Hahn and Dmitry Prokopenko and Julian Hecker and Sharon Marie Lutz and Kristina Mullin and Leinal Sejour and Winston Hide and Ioannis Vlachos and Stacia Desantis and Rudolph E. Tanzi and Christoph Lange}, title = {Prediction of disease-free survival for precision medicine using cooperative learning on multi-omic data}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae267}, doi = {10.1093/BIB/BBAE267}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HahnPHLMSHVDTL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HanLKSJLBJKL24, author = {Seokjin Han and Ji Eun Lee and Seolhee Kang and Minyoung So and Hee Jin and Jang Ho Lee and Sunghyeob Baek and Hyungjin Jun and Tae Yong Kim and Yun{-}Sil Lee}, title = {Standigm ASK{\texttrademark}: knowledge graph and artificial intelligence platform applied to target discovery in idiopathic pulmonary fibrosis}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae035}, doi = {10.1093/BIB/BBAE035}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HanLKSJLBJKL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HerajyLH24, author = {Mostafa Herajy and Fei Liu and Monika Heiner}, title = {Design patterns for the construction of computational biological models}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae318}, doi = {10.1093/BIB/BBAE318}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HerajyLH24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HernandezGamarraSDSVPCA24, author = {Miguel Hernandez{-}Gamarra and Alba Salgado{-}Roo and Eduardo Dominguez and Elena Mar{\'{\i}}a Goiricelaya Seco and Sara Veiga{-}R{\'{u}}a and Luc{\'{\i}}a F. Pedrera{-}Garbayo and {\'{A}}ngel Carracedo and Catarina Allegue}, title = {{CARTAR:} a comprehensive web tool for identifying potential targets in chimeric antigen receptor therapies using {TCGA} and GTEx data}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae326}, doi = {10.1093/BIB/BBAE326}, timestamp = {Fri, 26 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HernandezGamarraSDSVPCA24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HouXZCZS24, author = {Linlin Hou and Hongxin Xiang and Xiangxiang Zeng and Dongsheng Cao and Li Zeng and Bosheng Song}, title = {Attribute-guided prototype network for few-shot molecular property prediction}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae394}, doi = {10.1093/BIB/BBAE394}, timestamp = {Sat, 31 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HouXZCZS24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuGGGJZWJ24, author = {Heng Hu and Runtian Gao and Wentao Gao and Bo Gao and Zhongjun Jiang and Murong Zhou and Guohua Wang and Tao Jiang}, title = {{SVDF:} enhancing structural variation detect from long-read sequencing via automatic filtering strategies}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae336}, doi = {10.1093/BIB/BBAE336}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HuGGGJZWJ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuXYLZS24, author = {Yaofeng Hu and Kai Xiao and Hengyu Yang and Xiaoping Liu and Chuanchao Zhang and Qianqian Shi}, title = {Spatially contrastive variational autoencoder for deciphering tissue heterogeneity from spatially resolved transcriptomics}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae016}, doi = {10.1093/BIB/BBAE016}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HuXYLZS24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuangFWZLWDS24, author = {Fengjuan Huang and Xinjie Fan and Ying Wang and Yu Zou and Jiangfang Lian and Chuang Wang and Feng Ding and Yunxiang Sun}, title = {Computational insights into the cross-talk between medin and A\emph{{\(\beta\)}}: implications for age-related vascular risk factors in Alzheimer's disease}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbad526}, doi = {10.1093/BIB/BBAD526}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HuangFWZLWDS24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuangHLYTH24, author = {Ming{-}Siang Huang and Jen{-}Chieh Han and Pei{-}Yen Lin and Yu{-}Ting You and Richard Tzong{-}Han Tsai and Wen{-}Lian Hsu}, title = {Surveying biomedical relation extraction: a critical examination of current datasets and the proposal of a new resource}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae132}, doi = {10.1093/BIB/BBAE132}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HuangHLYTH24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuangLLHZ24, author = {Yiran Huang and Yufu Lin and Wei Lan and Cuiyu Huang and Cheng Zhong}, title = {GloEC: a hierarchical-aware global model for predicting enzyme function}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae365}, doi = {10.1093/BIB/BBAE365}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HuangLLHZ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuangYZL24, author = {Weihong Huang and Feng Yang and Qiang Zhang and Juan Liu}, title = {A dual-scale fused hypergraph convolution-based hyperedge prediction model for predicting missing reactions in genome-scale metabolic networks}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae383}, doi = {10.1093/BIB/BBAE383}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HuangYZL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuangZMLWDFAD24, author = {Jinze Huang and Yang Zhao and Bo Meng and Ao Lu and Yaoguang Wei and Lianhua Dong and Xiang Fang and Dong An and Xinhua Dai}, title = {{SEAOP:} a statistical ensemble approach for outlier detection in quantitative proteomics data}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae129}, doi = {10.1093/BIB/BBAE129}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HuangZMLWDFAD24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuynhC24, author = {Tram Huynh and Zixuan Cang}, title = {Topological and geometric analysis of cell states in single-cell transcriptomic data}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae176}, doi = {10.1093/BIB/BBAE176}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HuynhC24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/IanevskiKNMXAT24, author = {Aleksandr Ianevski and Aleksandr Kushnir and Kristen Nader and Mitro Miihkinen and Henri Xhaard and Tero Aittokallio and ZiaurRehman Tanoli}, title = {RepurposeDrugs: an interactive web-portal and predictive platform for repurposing mono- and combination therapies}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae328}, doi = {10.1093/BIB/BBAE328}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/IanevskiKNMXAT24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JainS24, author = {Sarthak Jain and Sandra E. Safo}, title = {DeepIDA-GRU: a deep learning pipeline for integrative discriminant analysis of cross-sectional and longitudinal multiview data with applications to inflammatory bowel disease classification}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae339}, doi = {10.1093/BIB/BBAE339}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JainS24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JiZXXP24, author = {Boya Ji and Haitao Zou and Liwen Xu and Xiaolan Xie and Shaoliang Peng}, title = {{MUSCLE:} multi-view and multi-scale attentional feature fusion for microRNA-disease associations prediction}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae167}, doi = {10.1093/BIB/BBAE167}, timestamp = {Sun, 28 Apr 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JiZXXP24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JiaRLGZ24, author = {Ran Jia and Ying{-}Zan Ren and Po{-}Nian Li and Rui Gao and Yusen Zhang}, title = {{SCSMD:} Single Cell Consistent Clustering based on Spectral Matrix Decomposition}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae273}, doi = {10.1093/BIB/BBAE273}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JiaRLGZ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JiaXDL24, author = {Qitao Jia and Yuanling Xia and Fanglin Dong and Weihua Li}, title = {MetaFluAD: meta-learning for predicting antigenic distances among influenza viruses}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae395}, doi = {10.1093/BIB/BBAE395}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JiaXDL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JiangGMNZHWH24, author = {Feng Jiang and Yuzhi Guo and Hehuan Ma and Saiyang Na and Wenliang Zhong and Yi Han and Tao Wang and Junzhou Huang}, title = {{GTE:} a graph learning framework for prediction of T-cell receptors and epitopes binding specificity}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae343}, doi = {10.1093/BIB/BBAE343}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JiangGMNZHWH24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JiangLHJLXW24, author = {Junyao Jiang and Jinlian Li and Sunan Huang and Fan Jiang and Yanran Liang and Xueli Xu and Jie Wang}, title = {{CACIMAR:} cross-species analysis of cell identities, markers, regulations, and interactions using single-cell {RNA} sequencing data}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae283}, doi = {10.1093/BIB/BBAE283}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JiangLHJLXW24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JiangPLLZL24, author = {Jici Jiang and Hongdi Pei and Jiayu Li and Mingxin Li and Quan Zou and Zhibin Lv}, title = {FEOpti-ACVP: identification of novel anti-coronavirus peptide sequences based on feature engineering and optimization}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae037}, doi = {10.1093/BIB/BBAE037}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/JiangPLLZL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JinYWCJWKXHH24, author = {Ruofan Jin and Qing Ye and Jike Wang and Zheng Cao and Dejun Jiang and Tianyue Wang and Yu Kang and Wanting Xu and Chang{-}Yu Hsieh and Tingjun Hou}, title = {AttABseq: an attention-based deep learning prediction method for antigen-antibody binding affinity changes based on protein sequences}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae304}, doi = {10.1093/BIB/BBAE304}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JinYWCJWKXHH24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JingGXSPHYYLS24, author = {Hongtai Jing and Zhengtao Gao and Sheng Xu and Tao Shen and Zhangzhi Peng and Shwai He and Tao You and Shuang Ye and Wei Lin and Siqi Sun}, title = {Accurate prediction of antibody function and structure using bio-inspired antibody language model}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae245}, doi = {10.1093/BIB/BBAE245}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JingGXSPHYYLS24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JoshiW24, author = {Kandarp Joshi and Dan O. Wang}, title = {epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbad521}, doi = {10.1093/BIB/BBAD521}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/JoshiW24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JoubbiMMMCCM24, author = {Sara Joubbi and Alessio Micheli and Paolo Milazzo and Giuseppe Maccari and Giorgio Ciano and Dario Cardamone and Duccio Medini}, title = {Antibody design using deep learning: from sequence and structure design to affinity maturation}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae307}, doi = {10.1093/BIB/BBAE307}, timestamp = {Fri, 26 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JoubbiMMMCCM24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/KangZG24, author = {Yue Kang and Hongyu Zhang and Jinting Guan}, title = {scINRB: single-cell gene expression imputation with network regularization and bulk RNA-seq data}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae148}, doi = {10.1093/BIB/BBAE148}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/KangZG24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/KatchborianNetoABNFOBMLDSLC24, author = {Albert Katchborian{-}Neto and Matheus F. Alves and Paula C. P. Bueno and Karen de Jesus Nic{\'{a}}cio and Miller S. Ferreira and Tiago B. Oliveira and Henrique Barbosa and Michael Murgu and Ana C. C. de Paula Ladvocat and Danielle F. Dias and Marisi G. Soares and Jo{\~{a}}o Henrique Ghilardi Lago and Daniela A Chagas{-}Paula}, title = {Integrative open workflow for confident annotation and molecular networking of metabolomics {MSE/DIA} data}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae013}, doi = {10.1093/BIB/BBAE013}, timestamp = {Thu, 02 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/KatchborianNetoABNFOBMLDSLC24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/KhanIT24, author = {Asif M. Khan and Esra B{\"{u}}sra Isik and Tin Wee Tan}, title = {A global initiative on addressing bioinformatics' grand challenges}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae278}, doi = {10.1093/BIB/BBAE278}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/KhanIT24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/KimJKKLKYKPWSA24, author = {Yujin Kim and Minwoo Jeong and In Gyeong Koh and Chanhee Kim and Hyeji Lee and Jae Hyun Kim and Ronald Yurko and Il Bin Kim and Jeongbin Park and Donna M. Werling and Stephan J. Sanders and Joon{-}Yong An}, title = {CWAS-Plus: estimating category-wide association of rare noncoding variation from whole-genome sequencing data with cell-type-specific functional data}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae323}, doi = {10.1093/BIB/BBAE323}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/KimJKKLKYKPWSA24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/KimS24, author = {Jaeyoon Kim and Junhee Seok}, title = {ctGAN: combined transformation of gene expression and survival data with generative adversarial network}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae325}, doi = {10.1093/BIB/BBAE325}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/KimS24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/KoKSMK24, author = {Euiseong Ko and Youngsoon Kim and Farhad Shokoohi and Tesfaye B. Mersha and Mingon Kang}, title = {{SPIN:} sex-specific and pathway-based interpretable neural network for sexual dimorphism analysis}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae239}, doi = {10.1093/BIB/BBAE239}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/KoKSMK24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/KoPLW24, author = {Young Su Ko and Jonathan Parkinson and Cong Liu and Wei Wang}, title = {TUnA: an uncertainty-aware transformer model for sequence-based protein-protein interaction prediction}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae359}, doi = {10.1093/BIB/BBAE359}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/KoPLW24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/KoopmanBC24, author = {Jacob J. E. Koopman and Katherine A Buhler and May Y. Choi}, title = {From machine learning to clinical practice: phenotypic clusters of anti-MDA5 antibody-positive dermatomyositis}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae303}, doi = {10.1093/BIB/BBAE303}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/KoopmanBC24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/KrishnanRG24, author = {Sowmya Ramaswamy Krishnan and Arijit Roy and M. Michael Gromiha}, title = {Reliable method for predicting the binding affinity of RNA-small molecule interactions using machine learning}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae002}, doi = {10.1093/BIB/BBAE002}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/KrishnanRG24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LaiH24, author = {En{-}Yu Lai and Yen{-}Tsung Huang}, title = {Identifying pleiotropic genes via the composite test amidst the complexity of polygenic traits}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae327}, doi = {10.1093/BIB/BBAE327}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LaiH24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LeeMKYC24, author = {Hwiyoung Lee and Tianzhou Ma and Hongjie Ke and Zhenyao Ye and Shuo Chen}, title = {dCCA: detecting differential covariation patterns between two types of high-throughput omics data}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae288}, doi = {10.1093/BIB/BBAE288}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LeeMKYC24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LeiHGCG24, author = {Yahui Lei and Xiao{-}Tai Huang and Xingli Guo and Kei Hang Katie Chan and Lin Gao}, title = {DeepGRNCS: deep learning-based framework for jointly inferring gene regulatory networks across cell subpopulations}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae334}, doi = {10.1093/BIB/BBAE334}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LeiHGCG24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LeiHWSWDZWG24, author = {Lixin Lei and Kaitai Han and Zijun Wang and Chaojing Shi and Zhenghui Wang and Ruoyan Dai and Zhiwei Zhang and Mengqiu Wang and Qianjin Guo}, title = {Attention-guided variational graph autoencoders reveal heterogeneity in spatial transcriptomics}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae173}, doi = {10.1093/BIB/BBAE173}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LeiHWSWDZWG24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LenhofERL24, author = {Kerstin Lenhof and Lea Eckhart and Lisa{-}Marie Rolli and Hans{-}Peter Lenhof}, title = {Trust me if you can: a survey on reliability and interpretability of machine learning approaches for drug sensitivity prediction in cancer}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae379}, doi = {10.1093/BIB/BBAE379}, timestamp = {Sat, 31 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LenhofERL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiHZYB24, author = {Fenglei Li and Qiaoyu Hu and Yongqi Zhou and Hao Yang and Fang Bai}, title = {DiffPROTACs is a deep learning-based generator for proteolysis targeting chimeras}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae358}, doi = {10.1093/BIB/BBAE358}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiHZYB24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiJLLQY24, author = {Pengyong Li and Zhengxiang Jiang and Tianxiao Liu and Xinyu Liu and Hui Qiao and Xiaojun Yao}, title = {Improving drug response prediction via integrating gene relationships with deep learning}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae153}, doi = {10.1093/BIB/BBAE153}, timestamp = {Sun, 28 Apr 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiJLLQY24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiLDGD24, author = {Yue Li and Bingyan Liu and Jinyan Deng and Yi Guo and Hongbo Du}, title = {Image-based molecular representation learning for drug development: a survey}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae294}, doi = {10.1093/BIB/BBAE294}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiLDGD24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiLSYSY24, author = {Shuo Li and Yan Liu and Long{-}Chen Shen and He Yan and Jiangning Song and Dong{-}Jun Yu}, title = {{GMFGRN:} a matrix factorization and graph neural network approach for gene regulatory network inference}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbad529}, doi = {10.1093/BIB/BBAD529}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LiLSYSY24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiLTW24, author = {Kongming Li and Jiahao Li and Yuhao Tao and Fei Wang}, title = {stDiff: a diffusion model for imputing spatial transcriptomics through single-cell transcriptomics}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae171}, doi = {10.1093/BIB/BBAE171}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiLTW24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiMWGWFLM24, author = {Yang Li and Anjun Ma and Yizhong Wang and Qi Guo and Cankun Wang and Hongjun Fu and Bingqiang Liu and Qin Ma}, title = {Enhancer-driven gene regulatory networks inference from single-cell RNA-seq and ATAC-seq data}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae369}, doi = {10.1093/BIB/BBAE369}, timestamp = {Sat, 31 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiMWGWFLM24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiSFCMW24, author = {Lei Li and Jiayi Sun and Yanbin Fu and Siriruk Changrob and Joshua J. C. McGrath and Patrick C. Wilson}, title = {A hybrid demultiplexing strategy that improves performance and robustness of cell hashing}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae254}, doi = {10.1093/BIB/BBAE254}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiSFCMW24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiWCLZ24, author = {Zeqian Li and Shilong Wang and Hai Cui and Xiaoxia Liu and Yijia Zhang}, title = {Spatiotemporal constrained RNA-protein heterogeneous network for protein complex identification}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae280}, doi = {10.1093/BIB/BBAE280}, timestamp = {Tue, 13 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiWCLZ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiWLTSHL24, author = {Bowen Li and Zhen Wang and Ziqi Liu and Yanxin Tao and Chulin Sha and Min He and Xiaolin Li}, title = {DrugMetric: quantitative drug-likeness scoring based on chemical space distance}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae321}, doi = {10.1093/BIB/BBAE321}, timestamp = {Fri, 26 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiWLTSHL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiWLZTSZPLZLXZ24, author = {Feng Li and Jingwen Wang and Mengyue Li and Xiaomeng Zhang and Yongjuan Tang and Xinyu Song and Yifang Zhang and Liying Pei and Jiaqi Liu and Chunlong Zhang and Xia Li and Yanjun Xu and Yunpeng Zhang}, title = {Identifying cell type-specific transcription factor-mediated activity immune modules reveal implications for immunotherapy and molecular classification of pan-cancer}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae368}, doi = {10.1093/BIB/BBAE368}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiWLZTSZPLZLXZ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiWW24, author = {Guangyu Li and Jiayu Wu and Xiaoyue Wang}, title = {Predicting functional {UTR} variants by integrating region-specific features}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae248}, doi = {10.1093/BIB/BBAE248}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiWW24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LinLLJ24, author = {Baohui Lin and Xiaoling Luo and Yumeng Liu and Xiaopeng Jin}, title = {A comprehensive review and comparison of existing computational methods for protein function prediction}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae289}, doi = {10.1093/BIB/BBAE289}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LinLLJ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LinPZYD24, author = {Yuefan Lin and Zixiang Pan and Yuansong Zeng and Yuedong Yang and Zhiming Dai}, title = {Detecting novel cell type in single-cell chromatin accessibility data via open-set domain adaptation}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae370}, doi = {10.1093/BIB/BBAE370}, timestamp = {Sat, 31 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LinPZYD24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuCGZYRZYHL24, author = {Huanhuan Liu and Qinwei Chen and Jintao Guo and Ying Zhou and Zhiyu You and Jun Ren and Yuanyuan Zeng and Jing Yang and Jialiang Huang and Qiyuan Li}, title = {Epigenome-augmented eQTL-hotspots reveal genome-wide transcriptional programs in 36 human tissues}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae109}, doi = {10.1093/BIB/BBAE109}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiuCGZYRZYHL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuLWZ24, author = {Zhenze Liu and Yingjian Liang and Guohua Wang and Tianjiao Zhang}, title = {scLEGA: an attention-based deep clustering method with a tendency for low expression of genes on single-cell RNA-seq data}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae371}, doi = {10.1093/BIB/BBAE371}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiuLWZ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuLZ24, author = {Jiaxuan Liu and Yonggang Lu and Li Zhu}, title = {A kinetic model for solving a combination optimization problem in \emph{ab-initio} Cryo-EM 3D reconstruction}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbad473}, doi = {10.1093/BIB/BBAD473}, timestamp = {Wed, 28 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LiuLZ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuSJATYZ24, author = {Xinze Liu and Jingxuan Shi and Yuanyuan Jiao and Jiaqi An and Jingwei Tian and Yue Yang and Li Zhuo}, title = {Integrated multi-omics with machine learning to uncover the intricacies of kidney disease}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae364}, doi = {10.1093/BIB/BBAE364}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiuSJATYZ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuSZ24, author = {Liang Liu and Peiqing Sun and Wei Zhang}, title = {A pan-cancer interrogation of intronic polyadenylation and its association with cancer characteristics}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae376}, doi = {10.1093/BIB/BBAE376}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiuSZ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuZ24, author = {Haoquan Liu and Yunjie Zhao}, title = {Integrated modeling of protein and {RNA}}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae139}, doi = {10.1093/BIB/BBAE139}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiuZ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LlopPeiroPG24, author = {Ariadna Llop{-}Peir{\'{o}} and Gerard Pujadas and Santiago Garcia{-}Vallv{\'{e}}}, title = {Challenges in distinguishing functional proteins from polyproteins in databases: implications for drug discovery}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae012}, doi = {10.1093/BIB/BBAE012}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LlopPeiroPG24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LuTLLSLZCF24, author = {Weining Lu and Yin Tang and Yu Liu and Shiyi Lin and Qifan Shuai and Bin Liang and Rongqing Zhang and Yu Cheng and Dong Fang}, title = {CatLearning: highly accurate gene expression prediction from histone mark}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae373}, doi = {10.1093/BIB/BBAE373}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LuTLLSLZCF24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LuXZWX24, author = {Zeyu Lu and Xue Xiao and Qiang Zheng and Xinlei Wang and Lin Xu}, title = {Assessing next-generation sequencing-based computational methods for predicting transcriptional regulators with query gene sets}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae366}, doi = {10.1093/BIB/BBAE366}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LuXZWX24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LuoWSLCZ24, author = {Zeyu Luo and Rui Wang and Yawen Sun and Junhao Liu and Herman Z. Q. Chen and Yu{-}Juan Zhang}, title = {Interpretable feature extraction and dimensionality reduction in {ESM2} for protein localization prediction}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbad534}, doi = {10.1093/BIB/BBAD534}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LuoWSLCZ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LyuCL24, author = {Chengshang Lyu and Lingxi Chen and Xiaoping Liu}, title = {Detecting tipping points of complex diseases by network information entropy}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae311}, doi = {10.1093/BIB/BBAE311}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LyuCL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/MaKY24, author = {Guoxuan Ma and Jian Kang and Tianwei Yu}, title = {Bayesian functional analysis for untargeted metabolomics data with matching uncertainty and small sample sizes}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae141}, doi = {10.1093/BIB/BBAE141}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/MaKY24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/MaWCXJDWMCLSBSXRJD24, author = {Wenyuan Ma and Hui Wu and Yiran Chen and Hongxia Xu and Junjie Jiang and Bang Du and Mingyu Wan and Xiaolu Ma and Xiaoyu Chen and Lili Lin and Xinhui Su and Xuanwen Bao and Yifei Shen and Nong Xu and Jian Ruan and Haiping Jiang and Yongfeng Ding}, title = {New techniques to identify the tissue of origin for cancer of unknown primary in the era of precision medicine: progress and challenges}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae028}, doi = {10.1093/BIB/BBAE028}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/MaWCXJDWMCLSBSXRJD24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/MaestriFMTUPLBNP24, author = {Simone Maestri and Mattia Furlan and Logan Mulroney and Lucia Coscujuela Tarrero and Camilla Ugolini and Fabio Dalla Pozza and Tommaso Leonardi and Ewan Birney and Francesco Nicassio and Mattia Pelizzola}, title = {Benchmarking of computational methods for m6A profiling with Nanopore direct {RNA} sequencing}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae001}, doi = {10.1093/BIB/BBAE001}, timestamp = {Fri, 22 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/MaestriFMTUPLBNP24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/MallSPGC24, author = {Raghvendra Mall and Ankita Singh and Chirag N. Patel and Gregory Guirimand and Filippo Castiglione}, title = {VISH-Pred: an ensemble of fine-tuned {ESM} models for protein toxicity prediction}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae270}, doi = {10.1093/BIB/BBAE270}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/MallSPGC24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/MallawaarachchiWXPGBPKV24, author = {Vijini Mallawaarachchi and Anuradha Wickramarachchi and Hansheng Xue and Bhavya Nalagampalli Papudeshi and Susanna R. Grigson and George Bouras and Rosa E. Prahl and Anubhav Kaphle and Andrey Verich and Berenice Talamantes{-}Becerra and Elizabeth A. Dinsdale and Robert A. Edwards}, title = {Solving genomic puzzles: computational methods for metagenomic binning}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae372}, doi = {10.1093/BIB/BBAE372}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/MallawaarachchiWXPGBPKV24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/McLeishSMNC24, author = {Emily McLeish and Nataliya Slater and Frank L. Mastaglia and Merrilee Needham and Jerome D. Coudert}, title = {Balancing Clinical Applicability and Scientific Depth in {ML} Models for {MDA5-DM} Prognosis}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae295}, doi = {10.1093/BIB/BBAE295}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/McLeishSMNC24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/MelloTBV24, author = {Fabio N. de Mello and Ana C. Tahira and Maria Gabriela Berzoti{-}Coelho and Sergio Verjovski{-}Almeida}, title = {The CUT{\&}RUN greenlist: genomic regions of consistent noise are effective normalizing factors for quantitative epigenome mapping}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbad538}, doi = {10.1093/BIB/BBAD538}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/MelloTBV24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/MengLLJM24, author = {Zhaohan Meng and Siwei Liu and Shangsong Liang and Bhautesh Jani and Zaiqiao Meng}, title = {Heterogeneous biomedical entity representation learning for gene-disease association prediction}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae380}, doi = {10.1093/BIB/BBAE380}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/MengLLJM24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/MengLSLWZPWJ24, author = {Jing Meng and Jingze Liu and Wenkai Song and Honglei Li and Jiangyuan Wang and Le Zhang and Yousong Peng and Aiping Wu and Taijiao Jiang}, title = {{PREDAC-CNN:} predicting antigenic clusters of seasonal influenza {A} viruses with convolutional neural network}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae033}, doi = {10.1093/BIB/BBAE033}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/MengLSLWZPWJ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/MengWMSLHLZ24, author = {Qiuchen Meng and Lei Wei and Kun Ma and Ming Shi and Xinyi Lin and Joshua W. K. Ho and Yinqing Li and Xuegong Zhang}, title = {scDecouple: decoupling cellular response from infected proportion bias in scCRISPR-seq}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae011}, doi = {10.1093/BIB/BBAE011}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/MengWMSLHLZ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/MiaoSLGMLW24, author = {Yan Miao and Zhenyuan Sun and Chen Lin and Haoran Gu and Chenjing Ma and Yingjian Liang and Guohua Wang}, title = {DeePhafier: a phage lifestyle classifier using a multilayer self-attention neural network combining protein information}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae377}, doi = {10.1093/BIB/BBAE377}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/MiaoSLGMLW24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/MiaoSMLWY24, author = {Yan Miao and Zhenyuan Sun and Chenjing Ma and Chen Lin and Guohua Wang and Chunxue Yang}, title = {VirGrapher: a graph-based viral identifier for long sequences from metagenomes}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae036}, doi = {10.1093/BIB/BBAE036}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/MiaoSMLWY24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/MuLZZIWWFC24, author = {Junxi Mu and Zhengxin Li and Bo Zhang and Qi Zhang and Jamshed Iqbal and Abdul Wadood and Ting Wei and Yan Feng and Hai{-}Feng Chen}, title = {Graphormer supervised \emph{de novo} protein design method and function validation}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae135}, doi = {10.1093/BIB/BBAE135}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/MuLZZIWWFC24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/NaleczCharkiewiczCN24, author = {Katarzyna Nalecz{-}Charkiewicz and Kamil Charkiewicz and Robert M. Nowak}, title = {Quantum computing in bioinformatics: a systematic review mapping}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae391}, doi = {10.1093/BIB/BBAE391}, timestamp = {Sat, 31 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/NaleczCharkiewiczCN24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/NiuWCZX24, author = {Mengting Niu and Chunyu Wang and Yaojia Chen and Quan Zou and Lei Xu}, title = {Identification, characterization and expression analysis of circRNA encoded by SARS-CoV-1 and SARS-CoV-2}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbad537}, doi = {10.1093/BIB/BBAD537}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/NiuWCZX24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/NourbakhshDSTP24, author = {Mona Nourbakhsh and Kristine Degn and Astrid Saksager and Matteo Tiberti and Elena Papaleo}, title = {Prediction of cancer driver genes and mutations: the potential of integrative computational frameworks}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbad519}, doi = {10.1093/BIB/BBAD519}, timestamp = {Wed, 28 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/NourbakhshDSTP24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/NovoloacaBBYB24, author = {Alexei Novoloaca and Camilo Broc and Laurent Beloeil and Wen{-}Han Yu and J{\'{e}}r{\'{e}}mie Becker}, title = {Comparative analysis of integrative classification methods for multi-omics data}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae331}, doi = {10.1093/BIB/BBAE331}, timestamp = {Thu, 22 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/NovoloacaBBYB24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/OlaverriMendizabalVBRP24, author = {Danel Olaverri{-}Mendizabal and Luis Vitores Valcarcel and Naroa Barrena and Carlos J. Rodr{\'{\i}}guez and Francisco J. Planes}, title = {Review and meta-analysis of the genetic Minimal Cut Set approach for gene essentiality prediction in cancer metabolism}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae115}, doi = {10.1093/BIB/BBAE115}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/OlaverriMendizabalVBRP24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ParkMH24, author = {Youngjune Park and Nils P. Muttray and Anne{-}Christin Hauschild}, title = {Species-agnostic transfer learning for cross-species transcriptomics data integration without gene orthology}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae004}, doi = {10.1093/BIB/BBAE004}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ParkMH24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/PathakK24, author = {Rajesh Kumar Pathak and Jun{-}Mo Kim}, title = {Veterinary systems biology for bridging the phenotype-genotype gap via computational modeling for disease epidemiology and animal welfare}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae025}, doi = {10.1093/BIB/BBAE025}, timestamp = {Wed, 01 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/PathakK24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/PengCTSJ24, author = {Chen Peng and Qiong Chen and Shangjin Tan and Xiaotao Shen and Chao Jiang}, title = {Generalized reporter score-based enrichment analysis for omics data}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae116}, doi = {10.1093/BIB/BBAE116}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/PengCTSJ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/PengLJW24, author = {Zhao Peng and Jiaqiang Li and Xingpeng Jiang and Cuihong Wan}, title = {sOCP: a framework predicting smORF coding potential based on {TIS} and in-frame features and effectively applied in the human genome}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae147}, doi = {10.1093/BIB/BBAE147}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/PengLJW24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/PertsevaFSR24, author = {Margarita Pertseva and Oceane Follonier and Daniele Scarcella and Sai T. Reddy}, title = {{TCR} clustering by contrastive learning on antigen specificity}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae375}, doi = {10.1093/BIB/BBAE375}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/PertsevaFSR24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/QiuNDDWLZXTWQ24, author = {Jingxuan Qiu and Wanchun Nie and Hao Ding and Jia Dai and Yiwen Wei and Dezhi Li and Yuxi Zhang and Junting Xie and Xinxin Tian and Nannan Wu and Tianyi Qiu}, title = {{PB-LKS:} a python package for predicting phage-bacteria interaction through local K-mer strategy}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae010}, doi = {10.1093/BIB/BBAE010}, timestamp = {Wed, 20 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/QiuNDDWLZXTWQ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/RafatiJVWA24, author = {Ali H. Rafati and S{\^{a}}mia Joca and Regina T. Vontell and Gregers Wegener and Maryam Ardalan}, title = {Approaches to embryonic neurodevelopment: from neural cell to neural tube formation through mathematical models}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae265}, doi = {10.1093/BIB/BBAE265}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/RafatiJVWA24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/RashidS24, author = {Md. Mamunur Rashid and Kumar Selvarajoo}, title = {Advancing drug-response prediction using multi-modal and -omics machine learning integration {(MOMLIN):} a case study on breast cancer clinical data}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae300}, doi = {10.1093/BIB/BBAE300}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/RashidS24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/RenMW24, author = {Lixin Ren and Wanbiao Ma and Yong Wang}, title = {Predicting {RNA} polymerase {II} transcriptional elongation pausing and associated histone code}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae246}, doi = {10.1093/BIB/BBAE246}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/RenMW24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/RenYTMBTY24, author = {Ruohan Ren and Hongyu Yu and Jiahao Teng and Sihui Mao and Zixuan Bian and Yangtianze Tao and Stephen S.{-}T. Yau}, title = {{CAPE:} a deep learning framework with Chaos-Attention net for Promoter Evolution}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae398}, doi = {10.1093/BIB/BBAE398}, timestamp = {Sat, 31 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/RenYTMBTY24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/RoyBRHRP24, author = {Suronjit Kumar Roy and Mohammad Shahangir Biswas and Md Foyzur Raman and Rubait Hasan and Zahidur Rahmann and Md Moyen Uddin Pk}, title = {A computational approach to developing a multi-epitope vaccine for combating \emph{Pseudomonas aeruginosa}-induced pneumonia and sepsis}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae401}, doi = {10.1093/BIB/BBAE401}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/RoyBRHRP24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/RuanCYWCYLY24, author = {Xinjia Ruan and Yu Cheng and Yuqing Ye and Yuhang Wang and Xinyi Chen and Yuqing Yang and Tiantian Liu and Fangrong Yan}, title = {{PIPET:} predicting relevant subpopulations in single-cell data using phenotypic information from bulk data}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae260}, doi = {10.1093/BIB/BBAE260}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/RuanCYWCYLY24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/RujanoBOCCDEFCCNMHABHFS24, author = {Maria A Rujano and Jan{-}Willem Boiten and Christian Ohmann and Steve Canham and Sergio Contrino and Romain David and Jonathan Ewbank and Claudia Filippone and Claire Connellan and Ilse Custers and Rick van Nuland and Michaela Theresia Mayrhofer and Petr Holub and Eva Garc{\'{\i}}a {\'{A}}lvarez and Emmanuel Bacry and Nigel Hughes and Mallory Ann Freeberg and Birgit Schaffhauser and Harald Wagener and Alex S{\'{a}}nchez{-}Pla and Guido Bertolini and Maria Panagiotopoulou}, title = {Sharing sensitive data in life sciences: an overview of centralized and federated approaches}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae262}, doi = {10.1093/BIB/BBAE262}, timestamp = {Mon, 12 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/RujanoBOCCDEFCCNMHABHFS24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/SeamanCDYG24, author = {Ryan P. Seaman and Ross Campbell and Valena Doe and Zelaikha Yosufzai and Joel H. Graber}, title = {A cloud-based training module for efficient \emph{de novo} transcriptome assembly using Nextflow and Google cloud}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae313}, doi = {10.1093/BIB/BBAE313}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/SeamanCDYG24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ShenYMDW24, author = {Ao Shen and Mingzhi Yuan and Yingfan Ma and Jie Du and Manning Wang}, title = {Complementary multi-modality molecular self-supervised learning via non-overlapping masking for property prediction}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae256}, doi = {10.1093/BIB/BBAE256}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ShenYMDW24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/SiLSZKLZF24, author = {Zhihao Si and Hanshuang Li and Wenjing Shang and Yanan Zhao and Lingjiao Kong and Chunshen Long and Yongchun Zuo and Zhenxing Feng}, title = {SpaNCMG: improving spatial domains identification of spatial transcriptomics using neighborhood-complementary mixed-view graph convolutional network}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae259}, doi = {10.1093/BIB/BBAE259}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/SiLSZKLZF24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/SilSKMS24, author = {Priyotosh Sil and Ajay Subbaroyan and Saumitra Kulkarni and Olivier C. Martin and Areejit Samal}, title = {Biologically meaningful regulatory logic enhances the convergence rate in Boolean networks and bushiness of their state transition graph}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae150}, doi = {10.1093/BIB/BBAE150}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/SilSKMS24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/SinghSHEALMPPSSL24, author = {Sandeep Singh and Xinrui Shi and Samuel Haddox and Justin Elfman and Syed Basil Ahmad and Sarah Lynch and Tommy Manley and Claire Piczak and Christopher Phung and Yunan Sun and Aadi Sharma and Hui Li}, title = {RTCpredictor: identification of read-through chimeric RNAs from {RNA} sequencing data}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae251}, doi = {10.1093/BIB/BBAE251}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/SinghSHEALMPPSSL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/SuljicZZVKKPPAK24, author = {Alen Suljic and Tomaz Mark Zorec and Samo Zakotnik and Doroteja Vlaj and Rok Kogoj and Natasa Knap and Miroslav Petrovec and Mario Poljak and Tatjana Avsic{-}Zupanc and Misa Korva}, title = {Efficient SARS-CoV-2 variant detection and monitoring with Spike Screen next-generation sequencing}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae263}, doi = {10.1093/BIB/BBAE263}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/SuljicZZVKKPPAK24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/SunCZZLZZG24, author = {Min Sun and Jing Chen and Chang Zhao and Lihua Zhang and Maili Liu and Yukui Zhang and Qun Zhao and Zhou Gong}, title = {Enhancing protein dynamics analysis with hydrophilic polyethylene glycol cross-linkers}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae026}, doi = {10.1093/BIB/BBAE026}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/SunCZZLZZG24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TamLLZSLW24, author = {Benjamin Tam and Philip Naderev P. Lagniton and Mariano Da Luz and Bojin Zhao and Siddharth Sinha and Chon Lok Lei and San Ming Wang}, title = {Comprehensive classification of \emph{TP53} somatic missense variants based on their impact on p53 structural stability}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae400}, doi = {10.1093/BIB/BBAE400}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/TamLLZSLW24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TanXCWZZL24, author = {Qingxiong Tan and Jin Xiao and Jiayang Chen and Yixuan Wang and Zeliang Zhang and Tiancheng Zhao and Yu Li}, title = {ifDEEPre: large protein language-based deep learning enables interpretable and fast predictions of enzyme commission numbers}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae225}, doi = {10.1093/BIB/BBAE225}, timestamp = {Tue, 13 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/TanXCWZZL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TangDKWLLG24, author = {Xiangru Tang and Howard Dai and Elizabeth Knight and Fang Wu and Yunyang Li and Tianxiao Li and Mark Gerstein}, title = {A survey of generative {AI} for \emph{de novo} drug design: new frontiers in molecule and protein generation}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae338}, doi = {10.1093/BIB/BBAE338}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/TangDKWLLG24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TangRSJFCDKBLLL24, author = {Qiaosi Tang and Ranjala Ratnayake and Gustavo de M. Seabra and Zhe Jiang and Ruogu Fang and Lina Cui and Yousong Ding and Tamer Kahveci and Jiang Bian and Chenglong Li and Hendrik Luesch and Yanjun Li}, title = {Morphological profiling for drug discovery in the era of deep learning}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae284}, doi = {10.1093/BIB/BBAE284}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/TangRSJFCDKBLLL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TaoXHLLH24, author = {Quyuan Tao and Yiheng Xu and Youzhe He and Ting Luo and Xiaoming Li and Lei Han}, title = {Benchmarking mapping algorithms for cell-type annotating in mouse brain by integrating single-nucleus RNA-seq and Stereo-seq data}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae250}, doi = {10.1093/BIB/BBAE250}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/TaoXHLLH24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TengZZZWTWSNZ24, author = {Jun Teng and Tingting Zhai and Xinyi Zhang and Changheng Zhao and Wenwen Wang and Hui Tang and Dan Wang and Yingli Shang and Chao Ning and Qin Zhang}, title = {Improving multi-population genomic prediction accuracy using multi-trait {GBLUP} models which incorporate global or local genetic correlation information}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae276}, doi = {10.1093/BIB/BBAE276}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/TengZZZWTWSNZ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TianHXTS24, author = {Zhen Tian and Chenguang Han and Lewen Xu and Zhixia Teng and Wei Song}, title = {{MGCNSS:} miRNA-disease association prediction with multi-layer graph convolution and distance-based negative sample selection strategy}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae168}, doi = {10.1093/BIB/BBAE168}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/TianHXTS24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TianSMZLT24, author = {Meihui Tian and Weifang Sun and Yinhui Mao and Yanan Zhang and Huan Liu and Yong Tang}, title = {Mechanistic study of acupuncture on the pterygopalatine ganglion to improve allergic rhinitis: analysis of multi-target effects based on bioinformatics/network topology strategie}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae287}, doi = {10.1093/BIB/BBAE287}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/TianSMZLT24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TianZI24, author = {Renmao Tian and Jizhong Zhou and Behzad Imanian}, title = {PlasmidHunter: accurate and fast prediction of plasmid sequences using gene content profile and machine learning}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae322}, doi = {10.1093/BIB/BBAE322}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/TianZI24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TongHM24, author = {Gregory Tong and Nasun Hah and Thomas F. Martinez}, title = {Comparison of software packages for detecting unannotated translated small open reading frames by Ribo-seq}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae268}, doi = {10.1093/BIB/BBAE268}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/TongHM24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TutsoyS24, author = {Onder Tutsoy and Hilmi Erdem Sumbul}, title = {A novel deep machine learning algorithm with dimensionality and size reduction approaches for feature elimination: thyroid cancer diagnoses with randomly missing data}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae344}, doi = {10.1093/BIB/BBAE344}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/TutsoyS24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/VasighizakerHZR24, author = {Akram Vasighizaker and Sheena Hora and Raymond Zeng and Luis Rueda}, title = {{SEGCECO:} Subgraph Embedding of Gene expression matrix for prediction of CEll-cell COmmunication}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae160}, doi = {10.1093/BIB/BBAE160}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/VasighizakerHZR24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/VisonaBDS24, author = {Giovanni Vison{\`{a}} and Emmanuelle Bouzigon and Florence Demenais and Gabriele Beate Schweikert}, title = {Network propagation for {GWAS} analysis: a practical guide to leveraging molecular networks for disease gene discovery}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae014}, doi = {10.1093/BIB/BBAE014}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/VisonaBDS24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/VuralOzdenizCAYODK24, author = {Merve Vural{-}Ozdeniz and Kubra Calisir and Rana Acar and Aysenur Yavuz and Mustafa M. Ozgur and Ertugrul Dalgic and Ozlen Konu}, title = {CAP-RNAseq: an integrated pipeline for functional annotation and prioritization of co-expression clusters}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbad536}, doi = {10.1093/BIB/BBAD536}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/VuralOzdenizCAYODK24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
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@article{DBLP:journals/bib/WangCZZ24, author = {Jing{-}Tian Wang and Xiao{-}Yu Chang and Qiong Zhao and Yuan{-}Ming Zhang}, title = {FastBiCmrMLM: a fast and powerful compressed variance component mixed logistic model for big genomic case-control genome-wide association study}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae290}, doi = {10.1093/BIB/BBAE290}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangCZZ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangHXZSC24, author = {Lequn Wang and Yaofeng Hu and Kai Xiao and Chuanchao Zhang and Qianqian Shi and Luonan Chen}, title = {Multi-modal domain adaptation for revealing spatial functional landscape from spatially resolved transcriptomics}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae257}, doi = {10.1093/BIB/BBAE257}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangHXZSC24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangL24, author = {Seunghyun Wang and Doheon Lee}, title = {Community cohesion looseness in gene networks reveals individualized drug targets and resistance}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae175}, doi = {10.1093/BIB/BBAE175}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangLLZYECLT24, author = {Lijuan Wang and Ying Lu and Doudou Li and Yajing Zhou and Lili Yu and Ines Mesa Eguiagaray and Harry Campbell and Xue Li and Evropi Theodoratou}, title = {The landscape of the methodology in drug repurposing using human genomic data: a systematic review}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbad527}, doi = {10.1093/BIB/BBAD527}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangLLZYECLT24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangLWLL24, author = {Meng Wang and Chuqi Lei and Jianxin Wang and Yaohang Li and Min Li}, title = {TripHLApan: predicting {HLA} molecules binding peptides based on triple coding matrix and transfer learning}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae154}, doi = {10.1093/BIB/BBAE154}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangLWLL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangLYG24, author = {Han Wang and Chang Li and Xinyu Yu and Jingyang Gao}, title = {Deletion variants calling in third-generation sequencing data based on a dual-attention mechanism}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae269}, doi = {10.1093/BIB/BBAE269}, timestamp = {Fri, 26 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangLYG24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangLZWZ24, author = {Hui Wang and Dong Liu and Kailong Zhao and Yajun Wang and Guijun Zhang}, title = {SPDesign: protein sequence designer based on structural sequence profile using ultrafast shape recognition}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae146}, doi = {10.1093/BIB/BBAE146}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangLZWZ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangOCR24, author = {Conghao Wang and Hiok Hian Ong and Shunsuke Chiba and Jagath C. Rajapakse}, title = {{GLDM:} hit molecule generation with constrained graph latent diffusion model}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae142}, doi = {10.1093/BIB/BBAE142}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangOCR24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangSHWCPS24, author = {Tao Wang and Han Shu and Jialu Hu and Yongtian Wang and Jin Chen and Jiajie Peng and Xuequn Shang}, title = {Accurately deciphering spatial domains for spatially resolved transcriptomics with stCluster}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae329}, doi = {10.1093/BIB/BBAE329}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangSHWCPS24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangSYJTTOTT24, author = {Yinyin Wang and Yihang Sui and Jiaqi Yao and Hong Jiang and Qimeng Tian and Yun Tang and Yongyu Ou and Jing Tang and Ninghua Tan}, title = {Herb-CMap: a multimodal fusion framework for deciphering the mechanisms of action in traditional Chinese medicine using Suhuang antitussive capsule as a case study}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae362}, doi = {10.1093/BIB/BBAE362}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangSYJTTOTT24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangWLGWMZL24, author = {Zechen Wang and Sheng Wang and Yangyang Li and Jingjing Guo and Yanjie Wei and Yuguang Mu and Liangzhen Zheng and Weifeng Li}, title = {A new paradigm for applying deep learning to protein-ligand interaction prediction}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae145}, doi = {10.1093/BIB/BBAE145}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangWLGWMZL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangXZLZYWYZZWZ24, author = {Xinglong Wang and Kangjie Xu and Xuan Zeng and Kai Linghu and Beichen Zhao and Shangyang Yu and Kun Wang and Shuyao Yu and Xinyi Zhao and Weizhu Zeng and Kai Wang and Jingwen Zhou}, title = {Machine learning-assisted substrate binding pocket engineering based on structural information}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae381}, doi = {10.1093/BIB/BBAE381}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangXZLZYWYZZWZ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangYCYWBDWJ24, author = {Jingjing Wang and Zhijiang Yang and Chang Chen and Ge Yao and Xiukun Wan and Shaoheng Bao and Junjie Ding and Liangliang Wang and Hui Jiang}, title = {{MPEK:} a multitask deep learning framework based on pretrained language models for enzymatic reaction kinetic parameters prediction}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae387}, doi = {10.1093/BIB/BBAE387}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangYCYWBDWJ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangYG24, author = {Weibing Wang and Yusen Ye and Lin Gao}, title = {Statistical modeling and significance estimation of multi-way chromatin contacts with HyperloopFinder}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae341}, doi = {10.1093/BIB/BBAE341}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangYG24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangYJGWXSXZZ24, author = {Xinyan Wang and Kuo Yang and Ting Jia and Fanghui Gu and Chongyu Wang and Kuan Xu and Zixin Shu and Jianan Xia and Qiang Zhu and Xuezhong Zhou}, title = {KDGene: knowledge graph completion for disease gene prediction using interactional tensor decomposition}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae161}, doi = {10.1093/BIB/BBAE161}, timestamp = {Tue, 27 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangYJGWXSXZZ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangZWLZCWSW24, author = {Shenjie Wang and Xiaoyan Zhu and Xuwen Wang and Yuqian Liu and Minchao Zhao and Zhili Chang and Xiaonan Wang and Yang Shao and Jiayin Wang}, title = {TMBstable: a variant caller controls performance variation across heterogeneous sequencing samples}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae159}, doi = {10.1093/BIB/BBAE159}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangZWLZCWSW24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangZXHTZGLJ24, author = {Yuxing Wang and Junhan Zhao and Hongye Xu and Cheng Han and Zhiqiang Tao and Dawei Zhou and Tong Geng and Dongfang Liu and Zhicheng Ji}, title = {A systematic evaluation of computational methods for cell segmentation}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae407}, doi = {10.1093/BIB/BBAE407}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangZXHTZGLJ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WeiGGDCSZ24, author = {Pi{-}Jing Wei and Ziqiang Guo and Zhen Gao and Zheng Ding and Rui{-}Fen Cao and Yansen Su and Chun{-}Hou Zheng}, title = {Inference of gene regulatory networks based on directed graph convolutional networks}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae309}, doi = {10.1093/BIB/BBAE309}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WeiGGDCSZ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WeiIZX24, author = {Qingyue Wei and Md Tauhidul Islam and Yuyin Zhou and Lei Xing}, title = {Self-supervised deep learning of gene-gene interactions for improved gene expression recovery}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae031}, doi = {10.1093/BIB/BBAE031}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WeiIZX24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WeiZZXXWXYF24, author = {Zhenyu Wei and Chengkui Zhao and Min Zhang and Jiayu Xu and Nan Xu and Shiwei Wu and Xiaohui Xin and Lei Yu and Weixing Feng}, title = {Meta-DHGNN: method for CRS-related cytokines analysis in {CAR-T} therapy based on meta-learning directed heterogeneous graph neural network}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae104}, doi = {10.1093/BIB/BBAE104}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WeiZZXXWXYF24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WrightWMCRSPJGRYSM24, author = {Adam Wright and Mark D. Wilkinson and Christopher J. Mungall and Scott Cain and Stephen Richards and Paul W. Sternberg and Ellen Provin and Jonathan L. Jacobs and Scott Geib and Daniela Raciti and Karen Yook and Lincoln Stein and David C. Molik}, title = {{FAIR} Header Reference genome: a TRUSTworthy standard}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae122}, doi = {10.1093/BIB/BBAE122}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WrightWMCRSPJGRYSM24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WuG24, author = {Siwen Wu and Jun{-}tao Guo}, title = {Improved prediction of {DNA} and {RNA} binding proteins with deep learning models}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae285}, doi = {10.1093/BIB/BBAE285}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WuG24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WuZCLLQ24, author = {Shengbo Wu and Haonan Zhou and Danlei Chen and Yutong Lu and Yanni Li and Jianjun Qiao}, title = {Multi-omic analysis tools for microbial metabolites prediction}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae264}, doi = {10.1093/BIB/BBAE264}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WuZCLLQ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WuZH24, author = {Yida Wu and Da Zhou and Jie Hu}, title = {Reconstruction of gene regulatory networks for \emph{Caenorhabditis elegans} using tree-shaped gene expression data}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae396}, doi = {10.1093/BIB/BBAE396}, timestamp = {Sat, 31 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WuZH24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WuZHPLJLHH24, author = {Jiashuo Wu and Xilong Zhao and Yalan He and Bingyue Pan and Jiyin Lai and Miao Ji and Siyuan Li and Junling Huang and Junwei Han}, title = {{IDMIR:} identification of dysregulated miRNAs associated with disease based on a miRNA-miRNA interaction network constructed through gene expression data}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae258}, doi = {10.1093/BIB/BBAE258}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WuZHPLJLHH24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/X24, title = {Correction to: Introducing {\(\pi\)}-HelixNovo for practical large-scale de novo peptide sequencing}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae134}, doi = {10.1093/BIB/BBAE134}, timestamp = {Sun, 28 Apr 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/X24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/X24a, title = {Correction to: Adjustment of scRNA-seq data to improve cell-type decomposition of spatial transcriptomics}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae155}, doi = {10.1093/BIB/BBAE155}, timestamp = {Sun, 28 Apr 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/X24a.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/X24b, title = {Correction to: Inflated false discovery rate due to volcano plots: problem and solutions}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae149}, doi = {10.1093/BIB/BBAE149}, timestamp = {Sun, 28 Apr 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/X24b.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/X24c, title = {Correction to: DeepFormer: a hybrid network based on convolutional neural network and flow-attention mechanism for identifying the function of {DNA} sequences}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae181}, doi = {10.1093/BIB/BBAE181}, timestamp = {Sun, 28 Apr 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/X24c.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/X24d, title = {Correction to: Diagnostic Prediction of portal vein thrombosis in chronic cirrhosis patients using data-driven precision medicine model}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae252}, doi = {10.1093/BIB/BBAE252}, timestamp = {Fri, 26 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/X24d.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/X24e, title = {Correction to: Prediction of protein-ligand binding affinity via deep learning models}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae310}, doi = {10.1093/BIB/BBAE310}, timestamp = {Fri, 26 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/X24e.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/X24f, title = {Correction to: Accurate prediction of antibody function and structure using bio-inspired antibody language model}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae402}, doi = {10.1093/BIB/BBAE402}, timestamp = {Sat, 31 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/X24f.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/X24g, title = {Correction to: Revolutionizing GPCR-ligand predictions: DeepGPCR with experimental validation for high-precision drug discovery}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae427}, doi = {10.1093/BIB/BBAE427}, timestamp = {Sat, 31 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/X24g.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/XiZDLSZTJZCZZH24, author = {Yue Xi and Kun Zheng and Fulan Deng and Yujun Liu and Hourong Sun and Yingxia Zheng and Henry H. Y. Tong and Yuan Ji and Yingchun Zhang and Wantao Chen and Yiming Zhang and Xin Zou and Jie Hao}, title = {Themis: advancing precision oncology through comprehensive molecular subtyping and optimization}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae261}, doi = {10.1093/BIB/BBAE261}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/XiZDLSZTJZCZZH24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/XiaLDLZLL24, author = {Simin Xia and Dianke Li and Xinru Deng and Zhongyang Liu and Huaqing Zhu and Yuan Liu and Dong Li}, title = {Integration of protein sequence and protein-protein interaction data by hypergraph learning to identify novel protein complexes}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae274}, doi = {10.1093/BIB/BBAE274}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/XiaLDLZLL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/XiangZNZLSW24, author = {Wenkai Xiang and Feisheng Zhong and Lin Ni and Mingyue Zheng and Xutong Li and Qian Shi and Dingyan Wang}, title = {Gram matrix: an efficient representation of molecular conformation and learning objective for molecular pretraining}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae340}, doi = {10.1093/BIB/BBAE340}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/XiangZNZLSW24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/XuCH24, author = {Sheng{-}Yong Xu and Shanshan Cai and Zhi{-}Qiang Han}, title = {Evaluating the efficacy of {MEANGS} for mitochondrial genome assembly of cartilaginous and ray-finned fish species}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae041}, doi = {10.1093/BIB/BBAE041}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/XuCH24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/XuLHCLL24, author = {Zhanyu Xu and Haibo Liao and Liuliu Huang and Qingfeng Chen and Wei Lan and Shikang Li}, title = {{IBPGNET:} lung adenocarcinoma recurrence prediction based on neural network interpretability}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae080}, doi = {10.1093/BIB/BBAE080}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/XuLHCLL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/XuZCZYYWLGZYXX24, author = {Yang Xu and Yuxiang Zhang and Yanru Cui and Kai Zhou and Guangning Yu and Wenyan Yang and Xin Wang and Furong Li and Xiusheng Guan and Xuecai Zhang and Zefeng Yang and Shizhong Xu and Chenwu Xu}, title = {{GA-GBLUP:} leveraging the genetic algorithm to improve the predictability of genomic selection}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae385}, doi = {10.1093/BIB/BBAE385}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/XuZCZYYWLGZYXX24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/XuZGJZP24, author = {Wang Xu and Houfang Zhang and Wenhan Guo and Lijun Jiang and Yunjie Zhao and Yunhui Peng}, title = {Deciphering principles of nucleosome interactions and impact of cancer-associated mutations from comprehensive interaction network analysis}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbad532}, doi = {10.1093/BIB/BBAD532}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/XuZGJZP24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/XueZZLZJW24, author = {Zhengfa Xue and Aifen Zhou and Xiaoyan Zhu and Linxuan Li and Huanhuan Zhu and Xin Jin and Jiayin Wang}, title = {{NIPT-PG:} empowering non-invasive prenatal testing to learn from population genomics through an incremental pan-genomic approach}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae266}, doi = {10.1093/BIB/BBAE266}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/XueZZLZJW24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YangLSLXHXHLHWC24, author = {Tingpeng Yang and Tianze Ling and Boyan Sun and Zhendong Liang and Fan Xu and Xiansong Huang and Linhai Xie and Yonghong He and Leyuan Li and Fuchu He and Yu Wang and Cheng Chang}, title = {Introducing {\(\pi\)}-HelixNovo for practical large-scale de novo peptide sequencing}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae021}, doi = {10.1093/BIB/BBAE021}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YangLSLXHXHLHWC24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YangWLJWZZD24, author = {Xiaodi Yang and Stefan Wuchty and Zeyin Liang and Li Ji and Bingjie Wang and Jialin Zhu and Ziding Zhang and Yujun Dong}, title = {Multi-modal features-based human-herpesvirus protein-protein interaction prediction by using LightGBM}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae005}, doi = {10.1093/BIB/BBAE005}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/YangWLJWZZD24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YangXDLWDZYJZLGW24, author = {Qiang Yang and Long Xu and Weihe Dong and Xiaokun Li and Kuanquan Wang and Suyu Dong and Xianyu Zhang and Tiansong Yang and Feng Jiang and Bin Zhang and Gongning Luo and Xin Gao and Guohua Wang}, title = {HLAIImaster: a deep learning method with adaptive domain knowledge predicts {HLA} {II} neoepitope immunogenic responses}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae302}, doi = {10.1093/BIB/BBAE302}, timestamp = {Mon, 05 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YangXDLWDZYJZLGW24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YiLWMM24, author = {Xinhao Yi and Siwei Liu and Yu Wu and Douglas McCloskey and Zaiqiao Meng}, title = {{BPP:} a platform for automatic biochemical pathway prediction}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae355}, doi = {10.1093/BIB/BBAE355}, timestamp = {Sat, 31 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YiLWMM24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YinWZ24, author = {Wang Yin and You Wan and Yuan Zhou}, title = {SpatialcoGCN: deconvolution and spatial information-aware simulation of spatial transcriptomics data via deep graph co-embedding}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae130}, doi = {10.1093/BIB/BBAE130}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YinWZ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YuHLS24, author = {Runzhou Yu and Ziyi Huang and Theo Y. C. Lam and Yanni Sun}, title = {Utilizing profile hidden Markov model databases for discovering viruses from metagenomic data: a comprehensive review}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae292}, doi = {10.1093/BIB/BBAE292}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YuHLS24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YuZCZLLLZMS24, author = {Chunjiang Yu and Hui Zong and Yalan Chen and Yibin Zhou and Xingyun Liu and Yuxin Lin and Jiakun Li and Xiaonan Zheng and Hua Min and Bairong Shen}, title = {{PCAO2:} an ontology for integration of prostate cancer associated genotypic, phenotypic and lifestyle data}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae136}, doi = {10.1093/BIB/BBAE136}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YuZCZLLLZMS24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YuanWWGD24, author = {Musu Yuan and Hui Wan and Zihao Wang and Qirui Guo and Minghua Deng}, title = {{SPANN:} annotating single-cell resolution spatial transcriptome data with scRNA-seq data}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbad533}, doi = {10.1093/BIB/BBAD533}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YuanWWGD24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZangRYWWLTS24, author = {Yue Zang and Xia Ran and Jie Yuan and Hao Wu and Youya Wang and He Li and Huajing Teng and Zhongsheng Sun}, title = {Genomic hallmarks and therapeutic targets of ribosome biogenesis in cancer}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae023}, doi = {10.1093/BIB/BBAE023}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZangRYWWLTS24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZawiszaAlvarezPVRGH24, author = {Michal Zawisza{-}{\'{A}}lvarez and Jes{\'{u}}s Pe{\~{n}}uela{-}Melero and Esteban Vegas and Ferran Reverter and Jordi Garcia{-}Fern{\`{a}}ndez and Carlos Herrera{-}{\'{U}}beda}, title = {Exploring functional conservation \emph{in silico}: a new machine learning approach to RNA-editing}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae332}, doi = {10.1093/BIB/BBAE332}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZawiszaAlvarezPVRGH24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZengGGYSP24, author = {Junxiang Zeng and Xiupan Gao and Limei Gao and Youyou Yu and Lisong Shen and Xiujun Pan}, title = {Recognition of rare antinuclear antibody patterns based on a novel attention-based enhancement framework}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbad531}, doi = {10.1093/BIB/BBAD531}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZengGGYSP24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhaiCD24, author = {Yuyao Zhai and Liang Chen and Minghua Deng}, title = {scEVOLVE: cell-type incremental annotation without forgetting for single-cell RNA-seq data}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae039}, doi = {10.1093/BIB/BBAE039}, timestamp = {Fri, 22 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhaiCD24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangCLLPN24, author = {Weihang Zhang and Yang Cui and Bowen Liu and Martin Loza and Sung{-}Joon Park and Kenta Nakai}, title = {HyGAnno: hybrid graph neural network-based cell type annotation for single-cell {ATAC} sequencing data}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae152}, doi = {10.1093/BIB/BBAE152}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangCLLPN24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangFWHSXKLZLC24, author = {Haiping Zhang and Hongjie Fan and Jixia Wang and Tao Hou and Konda Mani Saravanan and Wei Xia and Hei Wun Kan and Junxin Li and John Z. H. Zhang and Xinmiao Liang and Yang Chen}, title = {Revolutionizing GPCR-ligand predictions: DeepGPCR with experimental validation for high-precision drug discovery}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae281}, doi = {10.1093/BIB/BBAE281}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangFWHSXKLZLC24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangGLG24, author = {Dezhen Zhang and Shuhua Gao and Zhi{-}Ping Liu and Rui Gao}, title = {LogicGep: Boolean networks inference using symbolic regression from time-series transcriptomic profiling data}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae286}, doi = {10.1093/BIB/BBAE286}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangGLG24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangJZWGH24, author = {Tinghe Zhang and Sumin Jo and Michelle Zhang and Kai Wang and Shou{-}Jiang Gao and Yufei Huang}, title = {Understanding YTHDF2-mediated mRNA degradation by m6A-BERT-Deg}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae170}, doi = {10.1093/BIB/BBAE170}, timestamp = {Mon, 03 Jun 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangJZWGH24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangLD24, author = {Yibo Zhang and Wenyu Liu and Junbo Duan}, title = {On the core segmentation algorithms of copy number variation detection tools}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae022}, doi = {10.1093/BIB/BBAE022}, timestamp = {Fri, 05 Apr 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangLD24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangLW24, author = {Lei Zhang and Shu Liang and Lin Wan}, title = {A multi-view graph contrastive learning framework for deciphering spatially resolved transcriptomics data}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae255}, doi = {10.1093/BIB/BBAE255}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangLW24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangLWDZLP24, author = {Ru Zhang and Yanmei Lin and Yijia Wu and Lei Deng and Hao Zhang and Mingzhi Liao and Yuzhong Peng}, title = {MvMRL: a multi-view molecular representation learning method for molecular property prediction}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae298}, doi = {10.1093/BIB/BBAE298}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangLWDZLP24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangLWZHCFLSC24, author = {Shunjie Zhang and Pan Li and Shenghan Wang and Jijun Zhu and Zhongting Huang and Fuqiang Cai and Sebastian Freidel and Fei Ling and Emanuel Schwarz and Junfang Chen}, title = {\emph{BioM2}: biologically informed multi-stage machine learning for phenotype prediction using omics data}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae384}, doi = {10.1093/BIB/BBAE384}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangLWZHCFLSC24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangMYGD24, author = {Jin Zhang and Zikang Ma and Yan Yang and Lei Guo and Lei Du}, title = {Modeling genotype-protein interaction and correlation for Alzheimer's disease: a multi-omics imaging genetics study}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae038}, doi = {10.1093/BIB/BBAE038}, timestamp = {Wed, 28 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhangMYGD24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangSZLCC24, author = {Le Zhang and Wenkai Song and Tinghao Zhu and Yang Liu and Wei Chen and Yang Cao}, title = {ConvNeXt-MHC: improving MHC-peptide affinity prediction by structure-derived degenerate coding and the ConvNeXt model}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae133}, doi = {10.1093/BIB/BBAE133}, timestamp = {Fri, 09 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangSZLCC24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangWZZGYYJ24, author = {Guoqing Zhang and Hui Wang and Zhiguo Zhang and Lu Zhang and Guibing Guo and Jian Yang and Fajie Yuan and Feng Ju}, title = {Highly accurate classification and discovery of microbial protein-coding gene functions using FunGeneTyper: an extensible deep learning framework}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae319}, doi = {10.1093/BIB/BBAE319}, timestamp = {Thu, 08 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangWZZGYYJ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangZYYLLNX24, author = {Shi Zhang and Rui Zhang and Kai Yuan and Lu Yang and Chang Liu and Yuting Liu and Xumin Ni and Shuhua Xu}, title = {Reconstructing complex admixture history using a hierarchical model}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbad540}, doi = {10.1093/BIB/BBAD540}, timestamp = {Fri, 22 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhangZYYLLNX24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangZZ24, author = {Chengcheng Zhang and Tianyi Zang and Tianyi Zhao}, title = {{KGE-UNIT:} toward the unification of molecular interactions prediction based on knowledge graph and multi-task learning on drug discovery}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae043}, doi = {10.1093/BIB/BBAE043}, timestamp = {Wed, 28 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhangZZ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhaoB24, author = {Hangjia Zhao and Michael Baudis}, title = {labelSeg: segment annotation for tumor copy number alteration profiles}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbad541}, doi = {10.1093/BIB/BBAD541}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhaoB24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhaoZQLMHML24, author = {Hongyuan Zhao and Suyi Zhang and Hui Qin and Xiaogang Liu and Dongna Ma and Xiao Han and Jian Mao and Shuangping Liu}, title = {DSNetax: a deep learning species annotation method based on a deep-shallow parallel framework}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae157}, doi = {10.1093/BIB/BBAE157}, timestamp = {Sat, 04 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhaoZQLMHML24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhengSLF24, author = {Mengxin Zheng and Guicong Sun and Xueping Li and Yongxian Fan}, title = {{EGPDI:} identifying protein-DNA binding sites based on multi-view graph embedding fusion}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae330}, doi = {10.1093/BIB/BBAE330}, timestamp = {Fri, 02 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhengSLF24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhengSSLLZZPFZLLXZ24, author = {Lingyan Zheng and Shuiyang Shi and Xiuna Sun and Mingkun Lu and Yang Liao and Sisi Zhu and Hongning Zhang and Ziqi Pan and Pan Fang and Zhenyu Zeng and Honglin Li and Zhaorong Li and Weiwei Xue and Feng Zhu}, title = {MoDAFold: a strategy for predicting the structure of missense mutant protein based on AlphaFold2 and molecular dynamics}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae006}, doi = {10.1093/BIB/BBAE006}, timestamp = {Tue, 16 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhengSSLLZZPFZLLXZ24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhouLWL24, author = {Songqi Zhou and Yang Li and Wenyuan Wu and Li Li}, title = {scMMT: a multi-use deep learning approach for cell annotation, protein prediction and embedding in single-cell RNA-seq data}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbad523}, doi = {10.1093/BIB/BBAD523}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhouLWL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhouQHLCS24, author = {Guoqiang Zhou and Yuke Qin and Qiansen Hong and Haoran Li and Huaming Chen and Jun Shen}, title = {{GEMF:} a novel geometry-enhanced mid-fusion network for {PLA} prediction}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae333}, doi = {10.1093/BIB/BBAE333}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhouQHLCS24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhuHWGLLT24, author = {Keyun Zhu and Mengting Huang and Yimeng Wang and Yaxin Gu and Weihua Li and Guixia Liu and Yun Tang}, title = {MetaPredictor: \emph{in silico} prediction of drug metabolites based on deep language models with prompt engineering}, journal = {Briefings Bioinform.}, volume = {25}, number = {5}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae374}, doi = {10.1093/BIB/BBAE374}, timestamp = {Sun, 08 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhuHWGLLT24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhuLLJY24, author = {Yi{-}Heng Zhu and Zi Liu and Yan Liu and Zhiwei Ji and Dong{-}Jun Yu}, title = {{ULDNA:} integrating unsupervised multi-source language models with LSTM-attention network for high-accuracy protein-DNA binding site prediction}, journal = {Briefings Bioinform.}, volume = {25}, number = {2}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae040}, doi = {10.1093/BIB/BBAE040}, timestamp = {Sat, 16 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhuLLJY24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhuZSZZCXSSSLD24, author = {Cheng Zhu and Chengyun Zhang and Tianfeng Shang and Chenhao Zhang and Silong Zhai and Lujing Cao and Zhenyu Xu and Zhihao Su and Ying Song and An Su and Chengxi Li and Hongliang Duan}, title = {{GAPS:} a geometric attention-based network for peptide binding site identification by the transfer learning approach}, journal = {Briefings Bioinform.}, volume = {25}, number = {4}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae297}, doi = {10.1093/BIB/BBAE297}, timestamp = {Mon, 05 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhuZSZZCXSSSLD24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AbdellahGGFCCAZKHMMS23, author = {Marwan Abdellah and Juan Jose Garcia{-}Cantero and Nadir Rom{\'{a}}n Guerrero and Alessandro Foni and Jay S. Coggan and Corrado Cal{\`{\i}} and Marco Agus and Eleftherios Zisis and Daniel Keller and Markus Hadwiger and Pierre J. Magistretti and Henry Markram and Felix Sch{\"{u}}rmann}, title = {Ultraliser: a framework for creating multiscale, high-fidelity and geometrically realistic 3D models for \emph{in silico} neuroscience}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac491}, doi = {10.1093/BIB/BBAC491}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/AbdellahGGFCCAZKHMMS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AbeS23, author = {Ko Abe and Teppei Shimamura}, title = {{UNMF:} a unified nonnegative matrix factorization for multi-dimensional omics data}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad253}, doi = {10.1093/BIB/BBAD253}, timestamp = {Sat, 28 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/AbeS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AdamsKGBYO23, author = {Alison K. Adams and Brandon D. Kristy and Myranda Gorman and Peter Balint{-}Kurti and G. Craig Yencho and Bode A. Olukolu}, title = {Qmatey: an automated pipeline for fast exact matching-based alignment and strain-level taxonomic binning and profiling of metagenomes}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad351}, doi = {10.1093/BIB/BBAD351}, timestamp = {Sat, 28 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/AdamsKGBYO23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AhmedCLYZ23, author = {Khandakar Tanvir Ahmed and Sze Cheng and Qian Li and Jeongsik Yong and Wei Zhang}, title = {Incomplete time-series gene expression in integrative study for islet autoimmunity prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac537}, doi = {10.1093/BIB/BBAC537}, timestamp = {Wed, 15 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/AhmedCLYZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AhmedRRR23, author = {Shehab Sarar Ahmed and Zaara Tasnim Rifat and M. Saifur Rahman and M. Sohel Rahman}, title = {Succinylated lysine residue prediction revisited}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac510}, doi = {10.1093/BIB/BBAC510}, timestamp = {Sun, 12 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/AhmedRRR23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AkhtyamovSRSM23, author = {Pavel Akhtyamov and Layal Shaheen and Mikhail Raevskiy and Alexey Stupnikov and Yulia A. Medvedeva}, title = {scATAC-seq preprocessing and imputation evaluation system for visualization, clustering and digital footprinting}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad447}, doi = {10.1093/BIB/BBAD447}, timestamp = {Sat, 13 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/AkhtyamovSRSM23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AlamSAYLJJC23, author = {Mohammad Rizwan Alam and Kyung Jin Seo and Jamshid Abdul{-}Ghafar and Kwangil Yim and Sung Hak Lee and Hyun{-}Jong Jang and Chan Kwon Jung and Yosep Chong}, title = {Recent application of artificial intelligence on histopathologic image-based prediction of gene mutation in solid cancers}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad151}, doi = {10.1093/BIB/BBAD151}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/AlamSAYLJJC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AlcorizaBalaguerGBJL23, author = {Mar{\'{\i}}a Isabel Alcoriza{-}Balaguer and Juan Carlos Garc{\'{\i}}a{-}Ca{\~{n}}averas and Marta Benet and Oscar Juan{-}Vidal and Agust{\'{\i}}n Lahoz}, title = {FAMetA: a mass isotopologue-based tool for the comprehensive analysis of fatty acid metabolism}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad064}, doi = {10.1093/BIB/BBAD064}, timestamp = {Sat, 13 May 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/AlcorizaBalaguerGBJL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AsimIFDA23, author = {Muhammad Nabeel Asim and Muhammad Ali Ibrahim and Ahtisham Fazeel and Andreas Dengel and Sheraz Ahmed}, title = {{DNA-MP:} a generalized {DNA} modifications predictor for multiple species based on powerful sequence encoding method}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac546}, doi = {10.1093/BIB/BBAC546}, timestamp = {Sun, 12 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/AsimIFDA23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AthayaRLH23, author = {Tasbiraha Athaya and Rony Chowdhury Ripan and Xiaoman Li and Haiyan Hu}, title = {Multimodal deep learning approaches for single-cell multi-omics data integration}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad313}, doi = {10.1093/BIB/BBAD313}, timestamp = {Wed, 01 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/AthayaRLH23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BaiYL23, author = {Tao Bai and Ke Yan and Bin Liu}, title = {DAmiRLocGNet: miRNA subcellular localization prediction by combining miRNA-disease associations and graph convolutional networks}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad212}, doi = {10.1093/BIB/BBAD212}, timestamp = {Thu, 28 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BaiYL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BajiyaDAR23, author = {Nisha Bajiya and Anjali Dhall and Suchet Aggarwal and Gajendra P. S. Raghava}, title = {Advances in the field of phage-based therapy with special emphasis on computational resources}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac574}, doi = {10.1093/BIB/BBAC574}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BajiyaDAR23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BangLPPNGPK23, author = {Ina Bang and Sang{-}Mok Lee and Seojoung Park and Joon Young Park and Linh Khanh Nong and Ye Gao and Bernhard O. Palsson and Donghyuk Kim}, title = {Deep-learning optimized {DEOCSU} suite provides an iterable pipeline for accurate ChIP-exo peak calling}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad024}, doi = {10.1093/BIB/BBAD024}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BangLPPNGPK23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BaoCZSSL23, author = {Jingxuan Bao and Changgee Chang and Qiyiwen Zhang and Andrew J. Saykin and Li Shen and Qi Long}, title = {Integrative analysis of multi-omics and imaging data with incorporation of biological information via structural Bayesian factor analysis}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad073}, doi = {10.1093/BIB/BBAD073}, timestamp = {Mon, 01 May 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BaoCZSSL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BeltranBFZLMC23, author = {Jorge Beltr{\'{a}}n and Lisandra Herrera Bel{\'{e}}n and Jorge G. Farias and Mauricio Zamorano and Nicol{\'{a}}s Lefin and Javiera Miranda and Fernanda Parraguez Contreras}, title = {VirusHound-I: prediction of viral proteins involved in the evasion of host adaptive immune response using the random forest algorithm and generative adversarial network for data augmentation}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad434}, doi = {10.1093/BIB/BBAD434}, timestamp = {Fri, 26 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/BeltranBFZLMC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BeslicTRWM23, author = {Denis Beslic and Georg Tscheuschner and Bernhard Y. Renard and Michael G. Weller and Thilo Muth}, title = {Comprehensive evaluation of peptide \emph{de novo} sequencing tools for monoclonal antibody assembly}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac542}, doi = {10.1093/BIB/BBAC542}, timestamp = {Tue, 28 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/BeslicTRWM23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BhartiNJSB23, author = {Vandana Bharti and Shabari S. Nair and Akshat Jain and Kaushal Kumar Shukla and Bhaskar Biswas}, title = {Concept drift detection in toxicology datasets using discriminative subgraph-based drift detector}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac506}, doi = {10.1093/BIB/BBAC506}, timestamp = {Fri, 10 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/BhartiNJSB23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BianZZXW23, author = {Jilong Bian and Xi Zhang and Xiying Zhang and Dali Xu and Guohua Wang}, title = {MCANet: shared-weight-based MultiheadCrossAttention network for drug-target interaction prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad082}, doi = {10.1093/BIB/BBAD082}, timestamp = {Wed, 19 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BianZZXW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/Bishop23, author = {Martin Bishop}, title = {Editorial}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad176}, doi = {10.1093/BIB/BBAD176}, timestamp = {Thu, 22 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/Bishop23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BistTC23, author = {Prem Singh Bist and Hilal Tayara and Kil To Chong}, title = {Sars-escape network for escape prediction of {SARS-COV-2}}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad140}, doi = {10.1093/BIB/BBAD140}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BistTC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BlampeyBDPRAC23, author = {Quentin Blampey and Nad{\`{e}}ge Bercovici and Charles{-}Antoine Dutertre and Isabelle Pic and Joana Mourato Ribeiro and Fabrice Andr{\'{e}} and Paul{-}Henry Courn{\`{e}}de}, title = {A biology-driven deep generative model for cell-type annotation in cytometry}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad260}, doi = {10.1093/BIB/BBAD260}, timestamp = {Thu, 09 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/BlampeyBDPRAC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BuratinBG23, author = {Alessia Buratin and Stefania Bortoluzzi and Enrico Gaffo}, title = {Systematic benchmarking of statistical methods to assess differential expression of circular RNAs}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac612}, doi = {10.1093/BIB/BBAC612}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/BuratinBG23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/CaiZZG23, author = {Guoxing Cai and Wenyi Zhao and Zhan Zhou and Xun Gu}, title = {{MATTE:} a pipeline of transcriptome module alignment for anti-noise phenotype-gene-related analysis}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad207}, doi = {10.1093/BIB/BBAD207}, timestamp = {Sun, 24 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/CaiZZG23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/CaoGWHZMWJMCJYWWCY23, author = {Qiushi Cao and Cheng Ge and Xuejie Wang and Peta J. Harvey and Zixuan Zhang and Yuan Ma and Xianghong Wang and Xinying Jia and Mehdi Mobli and David J. Craik and Tao Jiang and Jinbo Yang and Zhiqiang Wei and Yan Wang and Shan Chang and Rilei Yu}, title = {Designing antimicrobial peptides using deep learning and molecular dynamic simulations}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad058}, doi = {10.1093/BIB/BBAD058}, timestamp = {Tue, 30 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/CaoGWHZMWJMCJYWWCY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/CaoGYY23, author = {Yue Cao and Shila Ghazanfar and Pengyi Yang and Jean Y. H. Yang}, title = {Benchmarking of analytical combinations for {COVID-19} outcome prediction using single-cell {RNA} sequencing data}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad159}, doi = {10.1093/BIB/BBAD159}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/CaoGYY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/CarterCA23, author = {Elena Lucy Carter and Chrystala Constantinidou and Mohammad Tauqeer Alam}, title = {Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad439}, doi = {10.1093/BIB/BBAD439}, timestamp = {Mon, 01 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/CarterCA23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChangCLLKWT23, author = {Kai{-}Li Chang and Jia{-}Hong Chen and Tzu{-}Chieh Lin and Jun{-}Yi Leu and Cheng{-}Fu Kao and Jin Yung Wong and Huai{-}Kuang Tsai}, title = {Short human eccDNAs are predictable from sequences}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad147}, doi = {10.1093/BIB/BBAD147}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChangCLLKWT23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenBL23, author = {Feng Chen and Yubo Bai and Chunhe Li}, title = {Estimation of non-equilibrium transition rate from gene expression data}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad113}, doi = {10.1093/BIB/BBAD113}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenBL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenC23, author = {Lei Chen and Yuwei Chen}, title = {RMTLysPTM: recognizing multiple types of lysine {PTM} sites by deep analysis on sequences}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad450}, doi = {10.1093/BIB/BBAD450}, timestamp = {Sat, 13 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ChenC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenCJSWW23, author = {Hongwei Chen and Yunpeng Cai and Chaojie Ji and Gurudeeban Selvaraj and Dongqing Wei and Hongyan Wu}, title = {AdaPPI: identification of novel protein functional modules via adaptive graph convolution networks in a protein-protein interaction network}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac523}, doi = {10.1093/BIB/BBAC523}, timestamp = {Tue, 21 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ChenCJSWW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenCLYZT23, author = {Juntao Chen and Jiannan Chao and Huan Liu and Fenglong Yang and Quan Zou and Furong Tang}, title = {{WMSA} 2: a multiple {DNA/RNA} sequence alignment tool implemented with accurate progressive mode and a fast win-win mode combining the center star and progressive strategies}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad190}, doi = {10.1093/BIB/BBAD190}, timestamp = {Fri, 22 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenCLYZT23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenCWLLT23, author = {Yu{-}Hsin Chen and Kuan{-}Hao Chao and Jin Yung Wong and Chien{-}Fu Liu and Jun{-}Yi Leu and Huai{-}Kuang Tsai}, title = {A feature extraction free approach for protein interactome inference from co-elution data}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad229}, doi = {10.1093/BIB/BBAD229}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenCWLLT23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenGCXSXCWD23, author = {Sikang Chen and Jian Gao and Jiexuan Chen and Yufeng Xie and Zheyuan Shen and Lei Xu and Jinxin Che and Jian Wu and Xiaowu Dong}, title = {ClusterX: a novel representation learning-based deep clustering framework for accurate visual inspection in virtual screening}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad126}, doi = {10.1093/BIB/BBAD126}, timestamp = {Thu, 22 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenGCXSXCWD23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenH23, author = {Xing Chen and Li Huang}, title = {Computational model for disease research}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac615}, doi = {10.1093/BIB/BBAC615}, timestamp = {Fri, 10 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ChenH23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenHLHTCLL23, author = {Hsin{-}Hua Chen and Chun{-}Wei Hsueh and Chia{-}Hwa Lee and Ting{-}Yi Hao and Tzu{-}Ying Tu and Lan{-}Yun Chang and Jih{-}Chin Lee and Chun{-}Yu Lin}, title = {{SWEET:} a single-sample network inference method for deciphering individual features in disease}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad032}, doi = {10.1093/BIB/BBAD032}, timestamp = {Sat, 13 May 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenHLHTCLL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenLGBLPCS23, author = {Ruyi Chen and Fuyi Li and Xudong Guo and Yue Bi and Chen Li and Shirui Pan and Lachlan J. M. Coin and Jiangning Song}, title = {{ATTIC} is an integrated approach for predicting A-to-I {RNA} editing sites in three species}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad170}, doi = {10.1093/BIB/BBAD170}, timestamp = {Mon, 05 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ChenLGBLPCS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenLLCQCWHH23, author = {Yi{-}Gang Chen and Yang{-}Chi{-}Dung Lin and Yijun Luo and Xiao{-}Xuan Cai and Peng Qiu and Shi{-}Dong Cui and Zhe Wang and Hsi{-}Yuan Huang and Hsien{-}Da Huang}, title = {Quantitative model for genome-wide cyclic {AMP} receptor protein binding site identification and characteristic analysis}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad138}, doi = {10.1093/BIB/BBAD138}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenLLCQCWHH23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenSGLM23, author = {Jiung{-}Wen Chen and Lisa Shrestha and George Green and Andr{\'{e}} Leier and Tatiana T. Marquez{-}Lago}, title = {The hitchhikers' guide to {RNA} sequencing and functional analysis}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac529}, doi = {10.1093/BIB/BBAC529}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenSGLM23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenWL23, author = {Wenlan Chen and Hong Wang and Cheng Liang}, title = {Deep multi-view contrastive learning for cancer subtype identification}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad282}, doi = {10.1093/BIB/BBAD282}, timestamp = {Thu, 26 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenWL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenXQYXT23, author = {Bo Chen and Ziwei Xie and Jiezhong Qiu and Zhaofeng Ye and Jinbo Xu and Jie Tang}, title = {Improved the heterodimer protein complex prediction with protein language models}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad221}, doi = {10.1093/BIB/BBAD221}, timestamp = {Wed, 06 Dec 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ChenXQYXT23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenYZL23, author = {Siqi Chen and Xuhua Yan and Ruiqing Zheng and Min Li}, title = {Bubble: a fast single-cell RNA-seq imputation using an autoencoder constrained by bulk RNA-seq data}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac580}, doi = {10.1093/BIB/BBAC580}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ChenYZL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenZLZC23, author = {Hongjun Chen and Yekai Zhou and Yongjing Liu and Peijing Zhang and Ming Chen}, title = {Network integration and protein structural binding analysis of neurodegeneration-related interactome}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad237}, doi = {10.1093/BIB/BBAD237}, timestamp = {Sun, 24 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenZLZC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenZLZQ23, author = {Yamao Chen and Shengyu Zhou and Ming Li and Fangqing Zhao and Ji Qi}, title = {{STEEL} enables high-resolution delineation of spatiotemporal transcriptomic data}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad068}, doi = {10.1093/BIB/BBAD068}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenZLZQ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenZS23, author = {Yuanyuan Chen and Hao Zhang and Xiao Sun}, title = {Improving the performance of single-cell RNA-seq data mining based on relative expression orderings}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac556}, doi = {10.1093/BIB/BBAC556}, timestamp = {Tue, 28 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ChenZS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenZWZHGL23, author = {Kai Chen and Xiaodong Zhu and Jiahao Wang and Ziqi Zhao and Lei Hao and Xinsheng Guo and Yuanning Liu}, title = {MFPred: prediction of ncRNA families based on multi-feature fusion}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad303}, doi = {10.1093/BIB/BBAD303}, timestamp = {Mon, 23 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenZWZHGL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChengHL23, author = {Andrew Cheng and Guanyu Hu and Wei Vivian Li}, title = {Benchmarking cell-type clustering methods for spatially resolved transcriptomics data}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac475}, doi = {10.1093/BIB/BBAC475}, timestamp = {Fri, 10 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ChengHL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChengLZRGWZL23, author = {Zhiwei Cheng and Leijie Li and Yuening Zhang and Yongyong Ren and Jianlei Gu and Xinbo Wang and Hongyu Zhao and Hui Lu}, title = {HBV-infected hepatocellular carcinoma can be robustly classified into three clinically relevant subgroups by a novel analytical protocol}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac601}, doi = {10.1093/BIB/BBAC601}, timestamp = {Mon, 05 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ChengLZRGWZL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChoQLTLLRARLDW23, author = {Hunyong Cho and Yixiang Qu and Chuwen Liu and Boyang Tang and Ruiqi Lyu and Bridget M. Lin and Jeffrey Roach and M. Andrea Azcarate{-}Peril and Apoena Aguiar Ribeiro and Michael I. Love and Kimon Divaris and Di Wu}, title = {Comprehensive evaluation of methods for differential expression analysis of metatranscriptomics data}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad279}, doi = {10.1093/BIB/BBAD279}, timestamp = {Sat, 28 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChoQLTLLRARLDW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChristensenLTHMNDBPRS23, author = {Erik Christensen and Ping Luo and Andrei L. Turinsky and Mia Husic and Alaina Mahalanabis and Alaine Naidas and Juan Javier D{\'{\i}}az{-}Mej{\'{\i}}a and Michael Brudno and Trevor J. Pugh and Arun K. Ramani and Parisa Shooshtari}, title = {Evaluation of single-cell RNAseq labelling algorithms using cancer datasets}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac561}, doi = {10.1093/BIB/BBAC561}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ChristensenLTHMNDBPRS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/CiaPR23, author = {Gabriel Cia and Fabrizio Pucci and Marianne Rooman}, title = {Critical review of conformational B-cell epitope prediction methods}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac567}, doi = {10.1093/BIB/BBAC567}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/CiaPR23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ConevRDFKFCZAK23, author = {Anja Conev and Maur{\'{\i}}cio Menegatti Rigo and Didier Devaurs and Andr{\'{e}} Faustino Fonseca and Hussain Kalavadwala and Martiela Vaz de Freitas and Cecilia Clementi and Geancarlo Zanatta and Dinler Amaral Antunes and Lydia E. Kavraki}, title = {EnGens: a computational framework for generation and analysis of representative protein conformational ensembles}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad242}, doi = {10.1093/BIB/BBAD242}, timestamp = {Sun, 24 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ConevRDFKFCZAK23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/CuiLBWL23, author = {Lingyu Cui and Hongfei Li and Jilong Bian and Guohua Wang and Yingjian Liang}, title = {Unsupervised construction of gene regulatory network based on single-cell multi-omics data of colorectal cancer}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad011}, doi = {10.1093/BIB/BBAD011}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/CuiLBWL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/CuiW23, author = {Tao Cui and Tingting Wang}, title = {A comprehensive assessment of hurdle and zero-inflated models for single cell RNA-sequencing analysis}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad272}, doi = {10.1093/BIB/BBAD272}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/CuiW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DarmawanLAR23, author = {Jeremie Theddy Darmawan and Jenq{-}Shiou Leu and Cries Avian and Nanda Rizqia Pradana Ratnasari}, title = {MITNet: a fusion transformer and convolutional neural network architecture approach for T-cell epitope prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad202}, doi = {10.1093/BIB/BBAD202}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DarmawanLAR23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DavydovBPC23, author = {Alexey N. Davydov and Dmitry Bolotin and Stanislav V. Poslavsky and Dmitry M. Chudakov}, title = {Comment on 'rigorous benchmarking of {T} cell receptor repertoire profiling methods for cancer {RNA} sequencing'}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad354}, doi = {10.1093/BIB/BBAD354}, timestamp = {Sun, 12 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/DavydovBPC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DefoAR23, author = {Joel Defo and Denis Awany and Raj Ramesar}, title = {From {SNP} to pathway-based {GWAS} meta-analysis: do current meta-analysis approaches resolve power and replication in genetic association studies?}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac600}, doi = {10.1093/BIB/BBAC600}, timestamp = {Sun, 12 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/DefoAR23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DengCZXFWS23, author = {Tao Deng and Siyu Chen and Ying Zhang and Yuanbin Xu and Da Feng and Hao Wu and Xiaobo Sun}, title = {A cofunctional grouping-based approach for non-redundant feature gene selection in unannotated single-cell RNA-seq analysis}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad042}, doi = {10.1093/BIB/BBAD042}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DengCZXFWS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DengLWJYLVKWZ23, author = {Wenxuan Deng and Bolun Li and Jiawei Wang and Wei Jiang and Xiting Yan and Ningshan Li and Milica Vukmirovic and Naftali Kaminski and Jing Wang and Hongyu Zhao}, title = {A novel Bayesian framework for harmonizing information across tissues and studies to increase cell type deconvolution accuracy}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac616}, doi = {10.1093/BIB/BBAC616}, timestamp = {Wed, 14 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DengLWJYLVKWZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DengZZCLT23, author = {Juntao Deng and Xiao Zhou and Pengyan Zhang and Weibin Cheng and Min Liu and Junzhang Tian}, title = {{IEPAPI:} a method for immune epitope prediction by incorporating antigen presentation and immunogenicity}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad171}, doi = {10.1093/BIB/BBAD171}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DengZZCLT23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DingKHZ23, author = {Wubin Ding and Diljeet Kaur and Steve Horvath and Wanding Zhou}, title = {Comparative epigenome analysis using Infinium {DNA} methylation BeadChips}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac617}, doi = {10.1093/BIB/BBAC617}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DingKHZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DingWZGLY23, author = {Pengju Ding and Yifei Wang and Xinyu Zhang and Xin Gao and Guozhu Liu and Bin Yu}, title = {DeepSTF: predicting transcription factor binding sites by interpretable deep neural networks combining sequence and shape}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad231}, doi = {10.1093/BIB/BBAD231}, timestamp = {Sun, 24 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DingWZGLY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DingZQGCMGYWL23, author = {Ruofan Ding and Xudong Zou and Yangmei Qin and Lihai Gong and Hui Chen and Xuelian Ma and Shouhong Guang and Chen Yu and Gao Wang and Lei Li}, title = {xQTLbiolinks: a comprehensive and scalable tool for integrative analysis of molecular QTLs}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad440}, doi = {10.1093/BIB/BBAD440}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DingZQGCMGYWL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DongWXO23, author = {Jie Dong and Zheng Wu and Huanle Xu and Defang Ouyang}, title = {FormulationAI: a novel web-based platform for drug formulation design driven by artificial intelligence}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad419}, doi = {10.1093/BIB/BBAD419}, timestamp = {Fri, 08 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/DongWXO23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DongYWXLLG23, author = {Weihe Dong and Qiang Yang and Jian Wang and Long Xu and Xiaokun Li and Gongning Luo and Xin Gao}, title = {Multi-modality attribute learning-based method for drug-protein interaction prediction based on deep neural network}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad161}, doi = {10.1093/BIB/BBAD161}, timestamp = {Tue, 06 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DongYWXLLG23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DorneyDRHS23, author = {Ryley Dorney and Bijay P. Dhungel and John E. J. Rasko and Lionel Hebbard and Ulf Schmitz}, title = {Recent advances in cancer fusion transcript detection}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac519}, doi = {10.1093/BIB/BBAC519}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DorneyDRHS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DouDCDGT23, author = {Mingliang Dou and Jiaqi Ding and Genlang Chen and Junwen Duan and Fei Guo and Jijun Tang}, title = {{IK-DDI:} a novel framework based on instance position embedding and key external text for {DDI} extraction}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad099}, doi = {10.1093/BIB/BBAD099}, timestamp = {Thu, 22 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DouDCDGT23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DuDXL23, author = {Zhenjiao Du and Xingjian Ding and Yixiang Xu and Yonghui Li}, title = {UniDL4BioPep: a universal deep learning architecture for binary classification in peptide bioactivity}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad135}, doi = {10.1093/BIB/BBAD135}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DuDXL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DuGZHTCZ23, author = {Lianming Du and Chaoyue Geng and Qiang{-}Lin Zeng and Ting Huang and Jie Tang and Yiwen Chu and Kelei Zhao}, title = {Dockey: a modern integrated tool for large-scale molecular docking and virtual screening}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad047}, doi = {10.1093/BIB/BBAD047}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DuGZHTCZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DuYWMZBHJCW23, author = {Wenjie Du and Xiaoting Yang and Di Wu and Fenfen Ma and Baicheng Zhang and Chaochao Bao and Yaoyuan Huo and Jun Jiang and Xin Chen and Yang Wang}, title = {Fusing 2D and 3D molecular graphs as unambiguous molecular descriptors for conformational and chiral stereoisomers}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac560}, doi = {10.1093/BIB/BBAC560}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DuYWMZBHJCW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DuanTWGF23, author = {Daoyu Duan and Wen Tang and Runshu Wang and Zhenxing Guo and Hao Feng}, title = {Evaluation of epitranscriptome-wide N6-methyladenosine differential analysis methods}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad139}, doi = {10.1093/BIB/BBAD139}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DuanTWGF23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DuanWZLZLZHZZ23, author = {Meiyu Duan and Yueying Wang and Dong Zhao and Hongmei Liu and Gongyou Zhang and Kewei Li and Haotian Zhang and Lan Huang and Ruochi Zhang and Fengfeng Zhou}, title = {Orchestrating information across tissues via a novel multitask {GAT} framework to improve quantitative gene regulation relation modeling for survival analysis}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad238}, doi = {10.1093/BIB/BBAD238}, timestamp = {Sun, 24 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DuanWZLZLZHZZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DurouxS23, author = {Diane Duroux and Kristel Van Steen}, title = {netANOVA: novel graph clustering technique with significance assessment via hierarchical {ANOVA}}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad029}, doi = {10.1093/BIB/BBAD029}, timestamp = {Sat, 13 May 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DurouxS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ElimelechZoharO23, author = {Karin Elimelech{-}Zohar and Yaron Orenstein}, title = {An overview on nucleic-acid G-quadruplex prediction: from rule-based methods to deep neural networks}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad252}, doi = {10.1093/BIB/BBAD252}, timestamp = {Sun, 24 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ElimelechZoharO23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FalgaroneVROK23, author = {Th{\'{e}}o Falgarone and Etienne Villain and Fran{\c{c}}ois D. Richard and Zarifa Osmanli and Andrey V. Kajava}, title = {Census of exposed aggregation-prone regions in proteomes}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad183}, doi = {10.1093/BIB/BBAD183}, timestamp = {Mon, 25 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/FalgaroneVROK23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FanCZLF23, author = {Yetian Fan and April S. Chan and Jun Zhu and Suet Yi Leung and Xiaodan Fan}, title = {A Bayesian model for identifying cancer subtypes from paired methylation profiles}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac568}, doi = {10.1093/BIB/BBAC568}, timestamp = {Tue, 28 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/FanCZLF23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FanJLCC23, author = {Rui Fan and Xiangwen Ji and Jianwei Li and Qinghua Cui and Chunmei Cui}, title = {Defining the single base importance of human mRNAs and lncRNAs}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad321}, doi = {10.1093/BIB/BBAD321}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/FanJLCC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FanPTCS23, author = {Xiao Fan and Hongbing Pan and Alan Tian and Wendy K. Chung and Yufeng Shen}, title = {{SHINE:} protein language model-based pathogenicity prediction for short inframe insertion and deletion variants}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac584}, doi = {10.1093/BIB/BBAC584}, timestamp = {Fri, 10 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/FanPTCS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FangLW23, author = {Kechi Fang and Chuan Li and Jing Wang}, title = {An automatic immunofluorescence pattern classification framework for HEp-2 image based on supervised learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad144}, doi = {10.1093/BIB/BBAD144}, timestamp = {Thu, 22 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/FangLW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FangXWJCWW23, author = {Yitian Fang and Fan Xu and Lesong Wei and Yi Jiang and Jie Chen and Leyi Wei and Dong{-}Qing Wei}, title = {{AFP-MFL:} accurate identification of antifungal peptides using multi-view feature learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac606}, doi = {10.1093/BIB/BBAC606}, timestamp = {Mon, 01 May 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/FangXWJCWW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FarhadiAMAA23, author = {Fatemeh Farhadi and Mohammad Allahbakhsh and Ali Maghsoudi and Nadieh Armin and Haleh Amintoosi}, title = {DiMo: discovery of microRNA motifs using deep learning and motif embedding}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad182}, doi = {10.1093/BIB/BBAD182}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/FarhadiAMAA23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FengJLLZL23, author = {Hailin Feng and Dongdong Jin and Jian Li and Yane Li and Quan Zou and Tongcun Liu}, title = {Matrix reconstruction with reliable neighbors for predicting potential MiRNA-disease associations}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac571}, doi = {10.1093/BIB/BBAC571}, timestamp = {Wed, 14 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/FengJLLZL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FengWMLHCY23, author = {Ze{-}Ying Feng and Xue{-}Hong Wu and Jun{-}Long Ma and Min Li and Ge{-}Fei He and Dong{-}Sheng Cao and Guo{-}Ping Yang}, title = {{DKADE:} a novel framework based on deep learning and knowledge graph for identifying adverse drug events and related medications}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad228}, doi = {10.1093/BIB/BBAD228}, timestamp = {Sun, 24 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/FengWMLHCY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FengZFZSS23, author = {Yue{-}Hua Feng and Shao{-}Wu Zhang and Yi{-}Yang Feng and Qing{-}Qing Zhang and Ming{-}Hui Shi and Jian{-}Yu Shi}, title = {A social theory-enhanced graph representation learning framework for multitask prediction of drug-drug interactions}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac602}, doi = {10.1093/BIB/BBAC602}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/FengZFZSS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FiannacaRPGU23, author = {Antonino Fiannaca and Massimo La Rosa and Laura La Paglia and Salvatore Gaglio and Alfonso Urso}, title = {{GOWDL:} gene ontology-driven wide and deep learning model for cell typing of scRNA-seq data}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad332}, doi = {10.1093/BIB/BBAD332}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/FiannacaRPGU23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FuWZQWP23, author = {Ping Fu and Yifan Wu and Zhiyuan Zhang and Ye Qiu and Yirong Wang and Yousong Peng}, title = {{VIGA:} a one-stop tool for eukaryotic virus identification and genome assembly from next-generation-sequencing data}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad444}, doi = {10.1093/BIB/BBAD444}, timestamp = {Sat, 13 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/FuWZQWP23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FuYLZTZZXZ23, author = {Jianbo Fu and Qingxia Yang and Yongchao Luo and Song Zhang and Jing Tang and Ying Zhang and Hongning Zhang and Hanxiang Xu and Feng Zhu}, title = {Label-free proteome quantification and evaluation}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac477}, doi = {10.1093/BIB/BBAC477}, timestamp = {Sat, 06 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/FuYLZTZZXZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GanCXGZ23, author = {Yanglan Gan and Yuhan Chen and Guangwei Xu and Wenjing Guo and Guobing Zou}, title = {Deep enhanced constraint clustering based on contrastive learning for scRNA-seq data}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad222}, doi = {10.1093/BIB/BBAD222}, timestamp = {Fri, 22 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GanCXGZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GaoSWLLZS23, author = {Hongyan Gao and Jianqiang Sun and Yukun Wang and Yuer Lu and Liyu Liu and Qi Zhao and Jianwei Shuai}, title = {Predicting metabolite-disease associations based on auto-encoder and non-negative matrix factorization}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad259}, doi = {10.1093/BIB/BBAD259}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GaoSWLLZS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GaoSXLLCBGSWZHHCD23, author = {Jian Gao and Zheyuan Shen and Yufeng Xie and Jialiang Lu and Yang Lu and Sikang Chen and Qingyu Bian and Yue Guo and Liteng Shen and Jian Wu and Binbin Zhou and Tingjun Hou and Qiaojun He and Jinxin Che and Xiaowu Dong}, title = {TransFoxMol: predicting molecular property with focused attention}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad306}, doi = {10.1093/BIB/BBAD306}, timestamp = {Tue, 30 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GaoSXLLCBGSWZHHCD23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GaoZCLZDXZS23, author = {Siqi Gao and Hanwen Zhu and Kangwen Cai and Leiqin Liu and Zhiqiang Zhang and Yi Ding and Yaochen Xu and Xiaoqi Zheng and Jiantao Shi}, title = {TRAmHap: accurate prediction of transcriptional activity from {DNA} methylation haplotypes in bisulfite-sequencing data}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad214}, doi = {10.1093/BIB/BBAD214}, timestamp = {Sun, 24 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GaoZCLZDXZS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GaoZLLFLKLFW23, author = {Pengfei Gao and Haonan Zhao and Zheng Luo and Yifan Lin and Wanjie Feng and Yaling Li and Fanjiang Kong and Xia Li and Chao Fang and Xutong Wang}, title = {SoyDNGP: a web-accessible deep learning framework for genomic prediction in soybean breeding}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad349}, doi = {10.1093/BIB/BBAD349}, timestamp = {Mon, 23 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GaoZLLFLKLFW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GaoZLLGY23, author = {Hongli Gao and Bin Zhang and Long Liu and Shan Li and Xin Gao and Bin Yu}, title = {A universal framework for single-cell multi-omics data integration with graph convolutional networks}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad081}, doi = {10.1093/BIB/BBAD081}, timestamp = {Tue, 12 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GaoZLLGY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GautamBBZLHP23, author = {Anupam Gautam and Debaleena Bhowmik and Sayantani Basu and Wenhuan Zeng and Abhishake Lahiri and Daniel H. Huson and Sandip Paul}, title = {Microbiome Metabolome Integration Platform {(MMIP):} a web-based platform for microbiome and metabolome data integration and feature identification}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad325}, doi = {10.1093/BIB/BBAD325}, timestamp = {Sun, 12 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/GautamBBZLHP23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GeLCMW23, author = {Shu{-}Guang Ge and Jian Liu and Yuhu Cheng and Xiaojing Meng and Xuesong Wang}, title = {Multi-view spectral clustering with latent representation learning for applications on multi-omics cancer subtyping}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac500}, doi = {10.1093/BIB/BBAC500}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GeLCMW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GeLIALTYWXSY23, author = {Fang Ge and Chen Li and Shahid Iqbal and Muhammad Arif and Fuyi Li and Maha A. Thafar and Zihao Yan and Apilak Worachartcheewan and Xiaofeng Xu and Jiangning Song and Dong{-}Jun Yu}, title = {VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac535}, doi = {10.1093/BIB/BBAC535}, timestamp = {Mon, 05 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/GeLIALTYWXSY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GePCXZ23, author = {Fengqi Ge and Chunxiang Peng and Xinyue Cui and Yuhao Xia and Guijun Zhang}, title = {Inter-domain distance prediction based on deep learning for domain assembly}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad100}, doi = {10.1093/BIB/BBAD100}, timestamp = {Fri, 07 Jul 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GePCXZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GimenoRR23, author = {Marian Gimeno and Katyna Sada del Real and Angel Rubio}, title = {Precision oncology: a review to assess interpretability in several explainable methods}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad200}, doi = {10.1093/BIB/BBAD200}, timestamp = {Sun, 24 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GimenoRR23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GinerIHP23, author = {G{\"{o}}knur Giner and Saima Ikram and Marco J. Herold and Anthony T. Papenfuss}, title = {A systematic review of computational methods for designing efficient guides for {CRISPR} {DNA} base editor systems}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad205}, doi = {10.1093/BIB/BBAD205}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GinerIHP23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GongWLFGFZ23, author = {Haoran Gong and Jianguo Wen and Ruihan Luo and Yuzhou Feng and Jingjing Guo and Hongguang Fu and Xiaobo Zhou}, title = {Integrated mRNA sequence optimization using deep learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad001}, doi = {10.1093/BIB/BBAD001}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GongWLFGFZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GossiPCMJR23, author = {Federico Gossi and Pushpak Pati and Panagiotis Chouvardas and Adriano Luca Martinelli and Marianna Kruithof{-}de Julio and Maria Anna Rapsomaniki}, title = {Matching single cells across modalities with contrastive learning and optimal transport}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad130}, doi = {10.1093/BIB/BBAD130}, timestamp = {Mon, 05 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/GossiPCMJR23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GuBYLKK23, author = {Jeonghyeon Gu and Dongmin Bang and Jungseob Yi and Sangseon Lee and Dong Kyu Kim and Sun Kim}, title = {A model-agnostic framework to enhance knowledge graph-based drug combination prediction with drug-drug interaction data and supervised contrastive learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad285}, doi = {10.1093/BIB/BBAD285}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GuBYLKK23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GuSYZLLSXWHK23, author = {Shukai Gu and Chao Shen and Jiahui Yu and Hong Zhao and Huanxiang Liu and Liwei Liu and Rong Sheng and Lei Xu and Zhe Wang and Tingjun Hou and Yu Kang}, title = {Can molecular dynamics simulations improve predictions of protein-ligand binding affinity with machine learning?}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad008}, doi = {10.1093/BIB/BBAD008}, timestamp = {Tue, 16 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GuSYZLLSXWHK23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GuanJ23, author = {Zengrui Guan and Zhenran Jiang}, title = {Transformer-based anti-noise models for CRISPR-Cas9 off-target activities prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad127}, doi = {10.1093/BIB/BBAD127}, timestamp = {Thu, 22 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GuanJ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GuoZJLGZZYW23, author = {Binjie Guo and Hanyu Zheng and Haohan Jiang and Xiaodan Li and Naiyu Guan and Yanming Zuo and Yicheng Zhang and Hengfu Yang and Xuhua Wang}, title = {Enhanced compound-protein binding affinity prediction by representing protein multimodal information via a coevolutionary strategy}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac628}, doi = {10.1093/BIB/BBAC628}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GuoZJLGZZYW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GuptaS23, author = {Sagar Gupta and Ravi Shankar}, title = {miWords: transformer-based composite deep learning for highly accurate discovery of pre-miRNA regions across plant genomes}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad088}, doi = {10.1093/BIB/BBAD088}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GuptaS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HamamotoTSMKAKK23, author = {Ryuji Hamamoto and Ken Takasawa and Norio Shinkai and Hidenori Machino and Nobuji Kouno and Ken Asada and Masaaki Komatsu and Syuzo Kaneko}, title = {Analysis of super-enhancer using machine learning and its application to medical biology}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad107}, doi = {10.1093/BIB/BBAD107}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HamamotoTSMKAKK23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HanFWZSHZLZ23, author = {Shen Han and Haitao Fu and Yuyang Wu and Ganglan Zhao and Zhenyu Song and Feng Huang and Zhongfei Zhang and Shichao Liu and Wen Zhang}, title = {HimGNN: a novel hierarchical molecular graph representation learning framework for property prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad305}, doi = {10.1093/BIB/BBAD305}, timestamp = {Fri, 01 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HanFWZSHZLZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HanPKLLLOK23, author = {So{-}Ra Han and Mingyu Park and Sai Kosaraju and Jeungmin Lee and Hyun Lee and Jun Hyuck Lee and Tae{-}Jin Oh and Mingon Kang}, title = {Evidential deep learning for trustworthy prediction of enzyme commission number}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad401}, doi = {10.1093/BIB/BBAD401}, timestamp = {Sat, 08 Jun 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HanPKLLLOK23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HanWCACYWL23, author = {Yanqiang Han and Zhilong Wang and An Chen and Imran Ali and Junfei Cai and Simin Ye and Zhiyun Wei and Jin{-}Jin Li}, title = {A deep transfer learning-based protocol accelerates full quantum mechanics calculation of protein}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac532}, doi = {10.1093/BIB/BBAC532}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HanWCACYWL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HanWHC23, author = {Chen{-}Di Han and Chun{-}Chun Wang and Li Huang and Xing Chen}, title = {{MCFF-MTDDI:} multi-channel feature fusion for multi-typed drug-drug interaction prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad215}, doi = {10.1093/BIB/BBAD215}, timestamp = {Sun, 24 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HanWHC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HanWWZYXZXDW23, author = {Ke Han and Jianchun Wang and Yu Wang and Lei Zhang and Mengyao Yu and Fang Xie and Dequan Zheng and Yaoqun Xu and Yijie Ding and Jie Wan}, title = {A review of methods for predicting {DNA} N6-methyladenine sites}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac514}, doi = {10.1093/BIB/BBAC514}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HanWWZYXZXDW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HaoZZCWCSYWSZWCZ23, author = {Jie Hao and Jiawei Zou and Jiaqiang Zhang and Ke Chen and Duojiao Wu and Wei Cao and Guoguo Shang and Jean Yee Hwa Yang and KongFatt Wong{-}Lin and Hourong Sun and Zhen Zhang and Xiangdong Wang and Wantao Chen and Xin Zou}, title = {scSTAR reveals hidden heterogeneity with a real-virtual cell pair structure across conditions in single-cell {RNA} sequencing data}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad062}, doi = {10.1093/BIB/BBAD062}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HaoZZCWCSYWSZWCZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HeGSS23, author = {Shujun He and Baizhen Gao and Rushant Sabnis and Qing Sun}, title = {RNAdegformer: accurate prediction of mRNA degradation at nucleotide resolution with deep learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac581}, doi = {10.1093/BIB/BBAC581}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HeGSS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HeLLZ23, author = {Guang{-}Xing He and Jun Liu and Dong Liu and Guijun Zhang}, title = {GraphGPSM: a global scoring model for protein structure using graph neural networks}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad219}, doi = {10.1093/BIB/BBAD219}, timestamp = {Sun, 24 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HeLLZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HeQFB23, author = {Qiang He and Wei Qiao and Hui Fang and Yang Bao}, title = {Improving the identification of miRNA-disease associations with multi-task learning on gene-disease networks}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad203}, doi = {10.1093/BIB/BBAD203}, timestamp = {Mon, 05 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HeQFB23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HeXCWW23, author = {Wenchuang He and Kunli Xiang and Caijin Chen and Jie Wang and Zhiqiang Wu}, title = {Master graph: an essential integrated assembly model for the plant mitogenome based on a graph-based framework}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac522}, doi = {10.1093/BIB/BBAC522}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HeXCWW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HeYSZXH23, author = {Yi{-}Zhou He and Yue Yang and Xiao{-}Rui Su and Bo{-}Wei Zhao and Shengwu Xiong and Lun Hu}, title = {Incorporating higher order network structures to improve miRNA-disease association prediction based on functional modularity}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac562}, doi = {10.1093/BIB/BBAC562}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HeYSZXH23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HeYYHSZCFWWY23, author = {Chun He and Xinhai Ye and Yi Yang and Liya Hu and Yuxuan Si and Xianxin Zhao and Longfei Chen and Qi Fang and Ying Wei and Fei Wu and Gongyin Ye}, title = {DeepAlgPro: an interpretable deep neural network model for predicting allergenic proteins}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad246}, doi = {10.1093/BIB/BBAD246}, timestamp = {Tue, 16 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HeYYHSZCFWWY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HenaoLAGTLOS23, author = {Juan D. Henao and Michael Lauber and Manuel Azevedo and Anastasiia Grekova and Fabian J. Theis and Markus List and Christoph Ogris and Benjamin Schubert}, title = {Multi-omics regulatory network inference in the presence of missing data}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad309}, doi = {10.1093/BIB/BBAD309}, timestamp = {Mon, 05 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HenaoLAGTLOS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HongLLSDLTH23, author = {Danni Hong and Hongli Lin and Lifang Liu and Muya Shu and Jianwu Dai and Falong Lu and Mengsha Tong and Jialiang Huang}, title = {Complexity of enhancer networks predicts cell identity and disease genes revealed by single-cell multi-omics analysis}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac508}, doi = {10.1093/BIB/BBAC508}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HongLLSDLTH23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HorlacherCHSGLMM23, author = {Marc Horlacher and Giulia Cantini and Julian Hesse and Patrick Schinke and Nicolas Goedert and Shubhankar Londhe and Lambert Moyon and Annalisa Marsico}, title = {A systematic benchmark of machine learning methods for protein-RNA interaction prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad307}, doi = {10.1093/BIB/BBAD307}, timestamp = {Sat, 28 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HorlacherCHSGLMM23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
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@article{DBLP:journals/bib/HuFCCQS23, author = {Ruyun Hu and Lihao Fu and Yongcan Chen and Junyu Chen and Yu Qiao and Tong Si}, title = {Protein engineering via Bayesian optimization-guided evolutionary algorithm and robotic experiments}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac570}, doi = {10.1093/BIB/BBAC570}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HuFCCQS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuFLZZXCCMSZS23, author = {Huan Hu and Zhen Feng and Hai Lin and Junjie Zhao and Yaru Zhang and Fei Xu and Lingling Chen and Feng Chen and Yunlong Ma and Jianzhong Su and Qi Zhao and Jianwei Shuai}, title = {Modeling and analyzing single-cell multimodal data with deep parametric inference}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad005}, doi = {10.1093/BIB/BBAD005}, timestamp = {Tue, 21 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HuFLZZXCCMSZS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuLZHZYXLKH23, author = {Zhiqiang Hu and Wenfeng Liu and Chenbin Zhang and Jiawen Huang and Shaoting Zhang and Huiqun Yu and Yi Xiong and Hao Liu and Song Ke and Liang Hong}, title = {{SAM-DTA:} a sequence-agnostic model for drug-target binding affinity prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac533}, doi = {10.1093/BIB/BBAC533}, timestamp = {Mon, 02 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HuLZHZYXLKH23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuLZTLL23, author = {Dayu Hu and Ke Liang and Sihang Zhou and Wenxuan Tu and Meng Liu and Xinwang Liu}, title = {scDFC: {A} deep fusion clustering method for single-cell RNA-seq data}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad216}, doi = {10.1093/BIB/BBAD216}, timestamp = {Fri, 01 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HuLZTLL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuS23, author = {Jianchang Hu and Silke Szymczak}, title = {A review on longitudinal data analysis with random forest}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad002}, doi = {10.1093/BIB/BBAD002}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HuS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuangSCLHS23, author = {Yuan{-}Qin Huang and Ping Sun and Yi Chen and Huanxiang Liu and Ge{-}Fei Hao and Bao{-}An Song}, title = {Bioinformatics toolbox for exploring target mutation-induced drug resistance}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad033}, doi = {10.1093/BIB/BBAD033}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HuangSCLHS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuangVPAM23, author = {Yu{-}Ning Huang and Mohammad Vahed and Kerui Peng and Houda Alachkar and Serghei Mangul}, title = {Response to 'comment on rigorous benchmarking of {T} cell receptor repertoire profiling methods for cancer {RNA} sequencing' by Davydov A.N.; Bolotin D.A.; Poslavsky S. V. and Chudakov {D.M}}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad355}, doi = {10.1093/BIB/BBAD355}, timestamp = {Sun, 12 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HuangVPAM23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuangWLZY23, author = {Zimo Huang and Jun Wang and Xudong Lu and Azlan Mohd Zain and Guoxian Yu}, title = {scGGAN: single-cell RNA-seq imputation by graph-based generative adversarial network}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad040}, doi = {10.1093/BIB/BBAD040}, timestamp = {Sun, 12 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HuangWLZY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuangWZZ23, author = {Yan Huang and Stefan Wuchty and Yuan Zhou and Ziding Zhang}, title = {{SGPPI:} structure-aware prediction of protein-protein interactions in rigorous conditions with graph convolutional network}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad020}, doi = {10.1093/BIB/BBAD020}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HuangWZZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuangZCYLZXYXHZ23, author = {Weibin Huang and Yuhui Zhang and Songyao Chen and Haofan Yin and Guangyao Liu and Huaqi Zhang and Jiannan Xu and Jishang Yu and Yujian Xia and Yulong He and Changhua Zhang}, title = {Personalized immune subtypes based on machine learning predict response to checkpoint blockade in gastric cancer}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac554}, doi = {10.1093/BIB/BBAC554}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HuangZCYLZXYXHZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuangZLZYHCCWJ23, author = {Yu'e Huang and Shunheng Zhou and Haizhou Liu and Xu Zhou and Mengqin Yuan and Fei Hou and Sina Chen and Jiahao Chen and Lihong Wang and Wei Jiang}, title = {DRdriver: identifying drug resistance driver genes using individual-specific gene regulatory network}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad066}, doi = {10.1093/BIB/BBAD066}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HuangZLZYHCCWJ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuangZYZXCX23, author = {Xiaoqiang Huang and Jun Zhou and Dongshan Yang and Jifeng Zhang and Xiaofeng Xia and Yuqing Eugene Chen and Jie Xu}, title = {Decoding CRISPR-Cas {PAM} recognition with UniDesign}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad133}, doi = {10.1093/BIB/BBAD133}, timestamp = {Thu, 22 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HuangZYZXCX23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/IbeneLPAT23, author = {Mandy Ib{\'{e}}n{\'{e}} and Audrey Legendre and Guillaume Postic and Eric Angel and Fariza Tahi}, title = {C-RCPred: a multi-objective algorithm for interactive secondary structure prediction of {RNA} complexes integrating user knowledge and {SHAPE} data}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad225}, doi = {10.1093/BIB/BBAD225}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/IbeneLPAT23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JiLLDHC23, author = {Kai{-}Yue Ji and Chong Liu and Zhao{-}Qian Liu and Yafeng Deng and Tingjun Hou and Dong{-}Sheng Cao}, title = {Comprehensive assessment of nine target prediction web services: which should we choose for target fishing?}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad014}, doi = {10.1093/BIB/BBAD014}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JiLLDHC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JiWC23, author = {Xiangwen Ji and Edwin Wang and Qinghua Cui}, title = {Deciphering gene contributions and etiologies of somatic mutational signatures of cancer}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad017}, doi = {10.1093/BIB/BBAD017}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JiWC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JiaHZ23, author = {Peilin Jia and Ruifeng Hu and Zhongming Zhao}, title = {Benchmark of embedding-based methods for accurate and transferable prediction of drug response}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad098}, doi = {10.1093/BIB/BBAD098}, timestamp = {Fri, 07 Jul 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JiaHZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JiaLBST23, author = {Shangru Jia and Artem Lysenko and Keith A. Boroevich and Alok Sharma and Tatsuhiko Tsunoda}, title = {scDeepInsight: a supervised cell-type identification method for scRNA-seq data with deep learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad266}, doi = {10.1093/BIB/BBAD266}, timestamp = {Wed, 01 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/JiaLBST23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JiaWDCCZ23, author = {Long{-}Hao Jia and Yingjian Wu and Yanqi Dong and Jingchao Chen and Wei{-}Hua Chen and Xing{-}Ming Zhao}, title = {A survey on computational strategies for genome-resolved gut metagenomics}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad162}, doi = {10.1093/BIB/BBAD162}, timestamp = {Thu, 22 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JiaWDCCZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JiaZLQRLMZADCS23, author = {Xiaoti Jia and Pei Zhao and Fuyi Li and Zhaohui Qin and Haoran Ren and Junzhou Li and Chunbo Miao and Quanzhi Zhao and Tatsuya Akutsu and Gensheng Dou and Zhen Chen and Jiangning Song}, title = {ResNetKhib: a novel cell type-specific tool for predicting lysine 2-hydroxyisobutylation sites via transfer learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad063}, doi = {10.1093/BIB/BBAD063}, timestamp = {Fri, 19 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JiaZLQRLMZADCS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JiangCLG23, author = {Peiran Jiang and Ruoxi Cai and Jose Lugo{-}Martinez and Yaping Guo}, title = {A hybrid positive unlabeled learning framework for uncovering scaffolds across human proteome by measuring the propensity to drive phase separation}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad009}, doi = {10.1093/BIB/BBAD009}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JiangCLG23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JiangHL23, author = {Yuepeng Jiang and Miaozhe Huo and Shuai Cheng Li}, title = {TEINet: a deep learning framework for prediction of TCR-epitope binding specificity}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad086}, doi = {10.1093/BIB/BBAD086}, timestamp = {Thu, 08 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JiangHL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JiangL23, author = {Yuepeng Jiang and Shuai Cheng Li}, title = {Deep autoregressive generative models capture the intrinsics embedded in T-cell receptor repertoires}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad038}, doi = {10.1093/BIB/BBAD038}, timestamp = {Thu, 08 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JiangL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JiangXLSGZZ23, author = {Jing Jiang and Junlin Xu and Yuansheng Liu and Bosheng Song and Xiulan Guo and Xiangxiang Zeng and Quan Zou}, title = {Dimensionality reduction and visualization of single-cell RNA-seq data with an improved deep variational autoencoder}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad152}, doi = {10.1093/BIB/BBAD152}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JiangXLSGZZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JiangYSSYLZJSY23, author = {Jing{-}Zhe Jiang and Wen{-}Guang Yuan and Jiayu Shang and Ying{-}Hui Shi and Li{-}Ling Yang and Min Liu and Peng Zhu and Tao Jin and Yanni Sun and Li{-}Hong Yuan}, title = {Virus classification for viral genomic fragments using PhaGCN2}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac505}, doi = {10.1093/BIB/BBAC505}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/JiangYSSYLZJSY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JiangZYZM23, author = {Minghao Jiang and Shiyan Zhang and Hongxin Yin and Zhiyi Zhuo and Guoyu Meng}, title = {A comprehensive benchmarking of differential splicing tools for RNA-seq analysis at the event level}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad121}, doi = {10.1093/BIB/BBAD121}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JiangZYZM23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JiangZZYLWCZWXSX23, author = {Gaofei Jiang and Jiaxuan Zhang and Yaozhong Zhang and Xinrun Yang and Tingting Li and Ningqi Wang and Xingjian Chen and Fang{-}Jie Zhao and Zhong Wei and Yangchun Xu and Qirong Shen and Wei Xue}, title = {DCiPatho: deep cross-fusion networks for genome scale identification of pathogens}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad194}, doi = {10.1093/BIB/BBAD194}, timestamp = {Sat, 08 Jun 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JiangZZYLWCZWXSX23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JingXYYNHDCLTZ23, author = {Kai Jing and Yewen Xu and Yang Yang and Pengfei Yin and Duo Ning and Guangyu Huang and Yuqing Deng and Gengzhan Chen and Guoliang Li and Simon Zhongyuan Tian and Meizhen Zheng}, title = {ScSmOP: a universal computational pipeline for single-cell single-molecule multiomics data analysis}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad343}, doi = {10.1093/BIB/BBAD343}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JingXYYNHDCLTZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JustynaAS23, author = {Marek Justyna and Maciej Antczak and Marta Szachniuk}, title = {Machine learning for {RNA} 2D structure prediction benchmarked on experimental data}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad153}, doi = {10.1093/BIB/BBAD153}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JustynaAS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/KangXWPYRC23, author = {Yan Kang and Yulong Xu and Xinchao Wang and Bin Pu and Xuekun Yang and Yulong Rao and Jianguo Chen}, title = {{HN-PPISP:} a hybrid network based on MLP-Mixer for protein-protein interaction site prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac480}, doi = {10.1093/BIB/BBAC480}, timestamp = {Mon, 01 Apr 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/KangXWPYRC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/KarimISBLCRD23, author = {Md. Rezaul Karim and Tanhim Islam and Md Shajalal and Oya Beyan and Christoph Lange and Michael Cochez and Dietrich Rebholz{-}Schuhmann and Stefan Decker}, title = {Explainable {AI} for Bioinformatics: Methods, Tools and Applications}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad236}, doi = {10.1093/BIB/BBAD236}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/KarimISBLCRD23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/KattanAW23, author = {Rebecca Elizabeth Kattan and Deena Ayesh and Wenqi Wang}, title = {Analysis of affinity purification-related proteomic data for studying protein-protein interaction networks in cells}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad010}, doi = {10.1093/BIB/BBAD010}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/KattanAW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/KawaguchiTFRTKG23, author = {Risa Karakida Kawaguchi and Ziqi Tang and Stephan Fischer and Chandana Rajesh and Rohit Tripathy and Peter K. Koo and Jesse A. Gillis}, title = {Learning single-cell chromatin accessibility profiles using meta-analytic marker genes}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac541}, doi = {10.1093/BIB/BBAC541}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/KawaguchiTFRTKG23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/KhandujaKM23, author = {Akshay Khanduja and Manish Kumar and Debasisa Mohanty}, title = {ProsmORF-pred: a machine learning-based method for the identification of small ORFs in prokaryotic genomes}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad101}, doi = {10.1093/BIB/BBAD101}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/KhandujaKM23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/KimHLLKK23, author = {Donghyo Kim and Doyeon Ha and Kwanghwan Lee and Heetak Lee and Inhae Kim and Sanguk Kim}, title = {An evolution-based machine learning to identify cancer type-specific driver mutations}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac593}, doi = {10.1093/BIB/BBAC593}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/KimHLLKK23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/KimKYLLZ23, author = {Pora Kim and Himansu Kumar and Chengyuan Yang and Ruihan Luo and Jiajia Liu and Xiaobo Zhou}, title = {Systematic investigation of the homology sequences around the human fusion gene breakpoints in pan-cancer - bioinformatics study for a potential link to {MMEJ}}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad314}, doi = {10.1093/BIB/BBAD314}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/KimKYLLZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/KnightKPGOW23, author = {Connor H. Knight and Faraz Khan and Ankit Patel and Upkar S. Gill and Jessica Okosun and Jun Wang}, title = {{IBRAP:} integrated benchmarking single-cell RNA-sequencing analytical pipeline}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad061}, doi = {10.1093/BIB/BBAD061}, timestamp = {Sat, 13 May 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/KnightKPGOW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/KobetsUGDMGSRK23, author = {Victoria A Kobets and Sergey V. Ulianov and Aleksandra A. Galitsyna and Semen A. Doronin and Elena A. Mikhaleva and Mikhail S. Gelfand and Yuri Y. Shevelyov and Sergey V. Razin and Ekaterina E. Khrameeva}, title = {HiConfidence: a novel approach uncovering the biological signal in Hi-C data affected by technical biases}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad044}, doi = {10.1093/BIB/BBAD044}, timestamp = {Mon, 05 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/KobetsUGDMGSRK23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/KongWHLWWG23, author = {Weijia Kong and Bertrand Jern Han Wong and Harvard Wai Hann Hui and Kai Peng Lim and Yulan Wang and Limsoon Wong and Wilson Wen Bin Goh}, title = {ProJect: a powerful mixed-model missing value imputation method}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad233}, doi = {10.1093/BIB/BBAD233}, timestamp = {Sun, 24 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/KongWHLWWG23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/KoudijsBG23, author = {Karel K. M. Koudijs and Stefan B{\"{o}}hringer and Henk{-}Jan Guchelaar}, title = {Validation of transcriptome signature reversion for drug repurposing in oncology}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac490}, doi = {10.1093/BIB/BBAC490}, timestamp = {Tue, 28 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/KoudijsBG23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/KumarPCTDR23, author = {Nishant Kumar and Sumeet Patiyal and Shubham Choudhury and Ritu Tomer and Anjali Dhall and Gajendra P. S. Raghava}, title = {DMPPred: a tool for identification of antigenic regions responsible for inducing type 1 diabetes mellitus}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac525}, doi = {10.1093/BIB/BBAC525}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/KumarPCTDR23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LaiG23, author = {Fei{-}Liao Lai and Feng Gao}, title = {Auto-Kla: a novel web server to discriminate lysine lactylation sites using automated machine learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad070}, doi = {10.1093/BIB/BBAD070}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LaiG23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LainscsekT23, author = {Xenia Lainscsek and Leila Taher}, title = {Predicting chromosomal compartments directly from the nucleotide sequence with {DNA-DDA}}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad198}, doi = {10.1093/BIB/BBAD198}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LainscsekT23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LanDZLCLWC23, author = {Wei Lan and Yi Dong and Hongyu Zhang and Chunling Li and Qingfeng Chen and Jin Liu and Jianxin Wang and Yi{-}Ping Phoebe Chen}, title = {Benchmarking of computational methods for predicting circRNA-disease associations}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac613}, doi = {10.1093/BIB/BBAC613}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LanDZLCLWC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LeLC23, author = {Nguyen{-}Quoc{-}Khanh Le and Wanru Li and Yanshuang Cao}, title = {Sequence-based prediction model of protein crystallization propensity using machine learning and two-level feature selection}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad319}, doi = {10.1093/BIB/BBAD319}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LeLC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LeeCJCJSJL23, author = {Kanggeun Lee and Dongbin Cho and Jinho Jang and Kang Choi and Hyoung{-}oh Jeong and Jiwon Seo and Won{-}Ki Jeong and Semin Lee}, title = {{RAMP:} response-aware multi-task learning with contrastive regularization for cancer drug response prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac504}, doi = {10.1093/BIB/BBAC504}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LeeCJCJSJL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LeeHHLMHBDTLP23, author = {Sanghun Lee and Georg Hahn and Julian Hecker and Sharon Marie Lutz and Kristina Mullin and Winston Hide and Lars Bertram and Dawn L. Demeo and Rudolph E. Tanzi and Christoph Lange and Dmitry Prokopenko}, title = {A comparison between similarity matrices for principal component analysis to assess population stratification in sequenced genetic data sets}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac611}, doi = {10.1093/BIB/BBAC611}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LeeHHLMHBDTLP23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LeeKKYY23, author = {Joongho Lee and Minsoo Kim and Keunsoo Kang and Chul{-}Su Yang and Seokhyun Yoon}, title = {Hierarchical cell-type identifier accurately distinguishes immune-cell subtypes enabling precise profiling of tissue microenvironment with single-cell RNA-sequencing}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad006}, doi = {10.1093/BIB/BBAD006}, timestamp = {Mon, 28 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LeeKKYY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LeeYLZZYCMRLH23, author = {Lindsay Lee and Miao Yu and Xiaoqi Li and Chenxu Zhu and Yanxiao Zhang and Hongyu Yu and Ziyin Chen and Shreya Mishra and Bing Ren and Yun Li and Ming Hu}, title = {SnapHiC-D: a computational pipeline to identify differential chromatin contacts from single-cell Hi-C data}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad315}, doi = {10.1093/BIB/BBAD315}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LeeYLZZYCMRLH23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LeiCZC23, author = {Tianyuan Lei and Ruoyu Chen and Shaoqiang Zhang and Yong Chen}, title = {Self-supervised deep clustering of single-cell RNA-seq data to hierarchically detect rare cell populations}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad335}, doi = {10.1093/BIB/BBAD335}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LeiCZC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LeventhalDL23, author = {Emily L. Leventhal and Andrea R. Daamen and Peter E. Lipsky}, title = {Letter to the editor: testing the effectiveness of MyPROSLE in classifying patients with lupus nephritis}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad322}, doi = {10.1093/BIB/BBAD322}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LeventhalDL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiARLHTCLHZL23, author = {Ruoxing Li and Mehmet Altan and Alexandre Reuben and Ruitao Lin and John V. Heymach and Hai Tran and Runzhe Chen and Latasha Little and Shawna Hubert and Jianjun Zhang and Ziyi Li}, title = {A novel statistical method for decontaminating T-cell receptor sequencing data}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad230}, doi = {10.1093/BIB/BBAD230}, timestamp = {Fri, 22 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiARLHTCLHZL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiCW23, author = {Xiayang Li and Moxuan Chen and Huaming Wu}, title = {Multiple errors correction for position-limited {DNA} sequences with {GC} balance and no homopolymer for DNA-based data storage}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac484}, doi = {10.1093/BIB/BBAC484}, timestamp = {Fri, 10 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LiCW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiCXJ23, author = {Mei Li and Xiangrui Cai and Sihan Xu and Hua Ji}, title = {Metapath-aggregated heterogeneous graph neural network for drug-target interaction prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac578}, doi = {10.1093/BIB/BBAC578}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LiCXJ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiGWGW23, author = {Yang Li and Zihou Guo and Keqi Wang and Xin Gao and Guohua Wang}, title = {End-to-end interpretable disease-gene association prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad118}, doi = {10.1093/BIB/BBAD118}, timestamp = {Wed, 12 Jul 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiGWGW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiHCGWSNR23, author = {Xue Li and Peifu Han and Wenqi Chen and Changnan Gao and Shuang Wang and Tao Song and Muyuan Niu and Alfonso Rodr{\'{\i}}guez{-}Pat{\'{o}}n}, title = {{MARPPI:} boosting prediction of protein-protein interactions with multi-scale architecture residual network}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac524}, doi = {10.1093/BIB/BBAC524}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LiHCGWSNR23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiHKZZZ23, author = {Han Li and Xuan He and Lawrence Kurowski and Ruotian Zhang and Dan Zhao and Jianyang Zeng}, title = {Improving comparative analyses of Hi-C data via contrastive self-supervised learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad193}, doi = {10.1093/BIB/BBAD193}, timestamp = {Wed, 14 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiHKZZZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiLSLL23, author = {Pingjing Li and Hong Liu and Jialiang Sun and Jianguo Lu and Jian Liu}, title = {HiBrowser: an interactive and dynamic browser for synchronous Hi-C data visualization}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad283}, doi = {10.1093/BIB/BBAD283}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiLSLL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiMHGGZW23, author = {Haochen Li and Tianxing Ma and Minsheng Hao and Wenbo Guo and Jin Gu and Xuegong Zhang and Lei Wei}, title = {Decoding functional cell-cell communication events by multi-view graph learning on spatial transcriptomics}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad359}, doi = {10.1093/BIB/BBAD359}, timestamp = {Thu, 02 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LiMHGGZW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiNAA23, author = {Yijia Li and Jonathan Nguyen and David C. Anastasiu and Edgar A. Arriaga}, title = {CosTaL: an accurate and scalable graph-based clustering algorithm for high-dimensional single-cell data analysis}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad157}, doi = {10.1093/BIB/BBAD157}, timestamp = {Thu, 22 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiNAA23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiRC23, author = {Baiqing Li and Ting Ran and Hongming Chen}, title = {3D based generative {PROTAC} linker design with reinforcement learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad323}, doi = {10.1093/BIB/BBAD323}, timestamp = {Wed, 27 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LiRC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiSWSYLLCWWWL23, author = {Huiyu Li and Chen Shen and Gongji Wang and Qinru Sun and Kai Yu and Zefeng Li and Xinggong Liang and Run Chen and Hao Wu and Fan Wang and Zhenyuan Wang and Chunfeng Lian}, title = {BloodNet: An attention-based deep network for accurate, efficient, and costless bloodstain time since deposition inference}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac557}, doi = {10.1093/BIB/BBAC557}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LiSWSYLLCWWWL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiWQW23, author = {Bing Li and Tian Wang and Min Qian and Shuang Wang}, title = {{MKMR:} a multi-kernel machine regression model to predict health outcomes using human microbiome data}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad158}, doi = {10.1093/BIB/BBAD158}, timestamp = {Thu, 22 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiWQW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiWZ23, author = {Peilong Li and Junfeng Wei and Ying Zhu}, title = {CellGO: a novel deep learning-based framework and webserver for cell-type-specific gene function interpretation}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad417}, doi = {10.1093/BIB/BBAD417}, timestamp = {Sat, 13 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LiWZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiWZC23, author = {Tian{-}Hao Li and Chun{-}Chun Wang and Li Zhang and Xing Chen}, title = {{SNRMPACDC:} computational model focused on Siamese network and random matrix projection for anticancer synergistic drug combination prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac503}, doi = {10.1093/BIB/BBAC503}, timestamp = {Sun, 12 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LiWZC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiXCZTC23, author = {Lin Li and Rui Xia and Wei Chen and Qi Zhao and Peng Tao and Luonan Chen}, title = {Single-cell causal network inferred by cross-mapping entropy}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad281}, doi = {10.1093/BIB/BBAD281}, timestamp = {Sun, 12 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LiXCZTC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiXTWZLLZSXZBZS23, author = {Lun Li and Bo Xu and Dongmei Tian and Anke Wang and Junwei Zhu and Cuiping Li and Na Li and Wei Zhao and Leisheng Shi and Yongbiao Xue and Zhang Zhang and Yiming Bao and Wenming Zhao and Shuhui Song}, title = {McAN: a novel computational algorithm and platform for constructing and visualizing haplotype networks}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad174}, doi = {10.1093/BIB/BBAD174}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiXTWZLLZSXZBZS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiZMZZ23, author = {Juntao Li and Hongmei Zhang and Bingyu Mu and Hongliang Zuo and Kanglei Zhou}, title = {Identifying phenotype-associated subpopulations through LP{\_}SGL}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad424}, doi = {10.1093/BIB/BBAD424}, timestamp = {Sat, 13 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LiZMZZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiZSZWL23, author = {Zimeng Li and Shichao Zhu and Bin Shao and Xiangxiang Zeng and Tong Wang and Tie{-}Yan Liu}, title = {{DSN-DDI:} an accurate and generalized framework for drug-drug interaction prediction by dual-view representation learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac597}, doi = {10.1093/BIB/BBAC597}, timestamp = {Tue, 04 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiZSZWL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiZWSSXWL23, author = {Kai Li and Ping Zhang and Zilin Wang and Wei Shen and Weicheng Sun and Jinsheng Xu and Zi Wen and Li Li}, title = {iEnhance: a multi-scale spatial projection encoding network for enhancing chromatin interaction data resolution}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad245}, doi = {10.1093/BIB/BBAD245}, timestamp = {Mon, 02 Sep 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiZWSSXWL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiZXZ23, author = {Yan Li and Shao{-}Wu Zhang and Ming{-}Yu Xie and Tong Zhang}, title = {PhenoDriver: interpretable framework for studying personalized phenotype-associated driver genes in breast cancer}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad291}, doi = {10.1093/BIB/BBAD291}, timestamp = {Wed, 01 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LiZXZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiZYLGZ23, author = {Min Li and Baoying Zhao and Rui Yin and Chengqian Lu and Fei Guo and Min Zeng}, title = {GraphLncLoc: long non-coding {RNA} subcellular localization prediction using graph convolutional networks based on sequence to graph transformation}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac565}, doi = {10.1093/BIB/BBAC565}, timestamp = {Wed, 17 May 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiZYLGZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiangCDDLADXZGLGG23, author = {Mang Liang and Sheng Cao and Tianyu Deng and Lili Du and Keanning Li and Bingxing An and Yueying Du and Lingyang Xu and Lupei Zhang and Xue Gao and Junya Li and Peng Guo and Huijiang Gao}, title = {{MAK:} a machine learning framework improved genomic prediction via multi-target ensemble regressor chains and automatic selection of assistant traits}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad043}, doi = {10.1093/BIB/BBAD043}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiangCDDLADXZGLGG23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiangZWL23, author = {Qi Liang and Wenxiang Zhang and Hao Wu and Bin Liu}, title = {LncRNA-disease association identification using graph auto-encoder and learning to rank}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac539}, doi = {10.1093/BIB/BBAC539}, timestamp = {Fri, 30 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiangZWL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiaoXZW23, author = {Ying Liao and Yisha Xiang and Mingjie Zheng and Jun Wang}, title = {DeepMiceTL: a deep transfer learning based prediction of mice cardiac conduction diseases using early electrocardiograms}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad109}, doi = {10.1093/BIB/BBAD109}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiaoXZW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiaoZQZ23, author = {Shaofeng Liao and Yujun Zhang and Yifei Qi and Zhuqing Zhang}, title = {Evaluation of sequence-based predictors for phase-separating protein}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad213}, doi = {10.1093/BIB/BBAD213}, timestamp = {Sun, 24 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiaoZQZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LimFL23, author = {Hendrick Gao{-}Min Lim and Yang C. Fann and Yuan{-}Chii Gladys Lee}, title = {{COWID:} an efficient cloud-based genomics workflow for scalable identification of {SARS-COV-2}}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad280}, doi = {10.1093/BIB/BBAD280}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LimFL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LinDZYZSCZCSYZ23, author = {Xuan Lin and Lichang Dai and Yafang Zhou and Zu{-}Guo Yu and Wen Zhang and Jian{-}Yu Shi and Dong{-}Sheng Cao and Li Zeng and Haowen Chen and Bosheng Song and Philip S. Yu and Xiangxiang Zeng}, title = {Comprehensive evaluation of deep and graph learning on drug-drug interactions prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad235}, doi = {10.1093/BIB/BBAD235}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LinDZYZSCZCSYZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LinJWKY23, author = {Jiadong Lin and Peng Jia and Songbo Wang and Walter A. Kosters and Kai Ye}, title = {Comparison and benchmark of structural variants detected from long read and long-read assembly}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad188}, doi = {10.1093/BIB/BBAD188}, timestamp = {Mon, 05 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LinJWKY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LinO23, author = {Zerun Lin and Le Ou{-}Yang}, title = {Inferring gene regulatory networks from single-cell gene expression data via deep multi-view contrastive learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac586}, doi = {10.1093/BIB/BBAC586}, timestamp = {Tue, 21 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LinO23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LinQCSZACWLLJ23, author = {Zhe Lin and Yangmei Qin and Hao Chen and Dan Shi and Mindong Zhong and Te An and Linshan Chen and Yiquan Wang and Fan Lin and Guang Li and Zhi{-}Liang Ji}, title = {TransIntegrator: capture nearly full protein-coding transcript variants via integrating Illumina and PacBio transcriptomes}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad334}, doi = {10.1093/BIB/BBAD334}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LinQCSZACWLLJ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LinWZLXXQL23, author = {Jiacheng Lin and Lijun Wu and Jinhua Zhu and Xiaobo Liang and Yingce Xia and Shufang Xie and Tao Qin and Tie{-}Yan Liu}, title = {{R2-DDI:} relation-aware feature refinement for drug-drug interaction prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac576}, doi = {10.1093/BIB/BBAC576}, timestamp = {Mon, 26 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LinWZLXXQL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LinYH23, author = {Peicong Lin and Yumeng Yan and Sheng{-}You Huang}, title = {DeepHomo2.0: improved protein-protein contact prediction of homodimers by transformer-enhanced deep learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac499}, doi = {10.1093/BIB/BBAC499}, timestamp = {Fri, 10 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LinYH23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuFLX23, author = {Xiang Liu and Huitao Feng and Zhi L{\"{u}} and Kelin Xia}, title = {Persistent Tor-algebra for protein-protein interaction analysis}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad046}, doi = {10.1093/BIB/BBAD046}, timestamp = {Wed, 19 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiuFLX23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuFLZCY23, author = {Teng Liu and Zhao{-}Yu Fang and Xin Li and Li{-}Ning Zhang and Dong{-}Sheng Cao and Ming{-}Zhu Yin}, title = {Graph deep learning enabled spatial domains identification for spatial transcriptomics}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad146}, doi = {10.1093/BIB/BBAD146}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiuFLZCY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuHHF23, author = {Ran Liu and Ye{-}Fan Hu and Jian{-}Dong Huang and Xiaodan Fan}, title = {A Bayesian approach to estimate MHC-peptide binding threshold}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad208}, doi = {10.1093/BIB/BBAD208}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiuHHF23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuHSHGXZL23, author = {Li Liu and Kaiyuan Han and Huimin Sun and Lu Han and Dong Gao and Qilemuge Xi and Lirong Zhang and Hao Lin}, title = {A comprehensive review of bioinformatics tools for chromatin loop calling}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad072}, doi = {10.1093/BIB/BBAD072}, timestamp = {Wed, 04 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiuHSHGXZL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuHXMLZG23, author = {Chun{-}Jie Liu and Fei{-}Fei Hu and Gui{-}Yan Xie and Ya{-}Ru Miao and Xin{-}Wen Li and Yan Zeng and An{-}Yuan Guo}, title = {{GSCA:} an integrated platform for gene set cancer analysis at genomic, pharmacogenomic and immunogenomic levels}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac558}, doi = {10.1093/BIB/BBAC558}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LiuHXMLZG23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuJD23, author = {Hui Liu and Ye Jin and Hanjing Ding}, title = {MDBuilder: a PyMOL plugin for the preparation of molecular dynamics simulations}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad057}, doi = {10.1093/BIB/BBAD057}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiuJD23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuKL23, author = {Jiayi Liu and Anat Kreimer and Wei Vivian Li}, title = {Differential variability analysis of single-cell gene expression data}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad294}, doi = {10.1093/BIB/BBAD294}, timestamp = {Wed, 01 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LiuKL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuLSG23, author = {Jian Liu and Pingjing Li and Jialiang Sun and Jun Guo}, title = {{LPAD:} using network construction and label propagation to detect topologically associating domains from Hi-C data}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad165}, doi = {10.1093/BIB/BBAD165}, timestamp = {Thu, 22 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiuLSG23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuLSHPGLSL23, author = {Hongjia Liu and Huamei Li and Amit Sharma and Wenjuan Huang and Duo Pan and Yu Gu and Lu Lin and Xiao Sun and Hongde Liu}, title = {scAnno: a deconvolution strategy-based automatic cell type annotation tool for single-cell RNA-sequencing data sets}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad179}, doi = {10.1093/BIB/BBAD179}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiuLSHPGLSL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuLZLHLGL23, author = {Jiashu Liu and Cui{-}Xiang Lin and Xiaoqi Zhang and Zongxuan Li and Wenkui Huang and Jin Liu and Yuanfang Guan and Hong{-}Dong Li}, title = {Computational approaches for detecting disease-associated alternative splicing events}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad106}, doi = {10.1093/BIB/BBAD106}, timestamp = {Fri, 07 Jul 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiuLZLHLGL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuS23, author = {Qingchun Liu and Kai Song}, title = {ProgCAE: a deep learning-based method that integrates multi-omics data to predict cancer subtypes}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad196}, doi = {10.1093/BIB/BBAD196}, timestamp = {Fri, 22 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiuS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuSGLSZ23, author = {Yuansheng Liu and Xiangzhen Shen and Yongshun Gong and Yiping Liu and Bosheng Song and Xiangxiang Zeng}, title = {Sequence Alignment/Map format: a comprehensive review of approaches and applications}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad320}, doi = {10.1093/BIB/BBAD320}, timestamp = {Sat, 28 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiuSGLSZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuTG23, author = {Jing Liu and Xinghua Tang and Xiao Guan}, title = {Grain protein function prediction based on self-attention mechanism and bidirectional {LSTM}}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac493}, doi = {10.1093/BIB/BBAC493}, timestamp = {Fri, 10 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LiuTG23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuTLFYP23, author = {Wei Liu and Ting Tang and Xu Lu and Xiangzheng Fu and Yu Yang and Li Peng}, title = {{MPCLCDA:} predicting circRNA-disease associations by using automatically selected meta-path and contrastive learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad227}, doi = {10.1093/BIB/BBAD227}, timestamp = {Sun, 12 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LiuTLFYP23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuW23, author = {Tong Liu and Zheng Wang}, title = {HiC4D: forecasting spatiotemporal Hi-C data with residual ConvLSTM}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad263}, doi = {10.1093/BIB/BBAD263}, timestamp = {Mon, 23 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiuW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuWLSGSCY23, author = {Yan Liu and Guo Wei and Chen Li and Long{-}Chen Shen and Robin B. Gasser and Jiangning Song and Dijun Chen and Dong{-}Jun Yu}, title = {TripletCell: a deep metric learning framework for accurate annotation of cell types at the single-cell level}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad132}, doi = {10.1093/BIB/BBAD132}, timestamp = {Tue, 23 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiuWLSGSCY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuWST23, author = {Bin Liu and Jin Wang and Kaiwei Sun and Grigorios Tsoumakas}, title = {Fine-grained selective similarity integration for drug-target interaction prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad085}, doi = {10.1093/BIB/BBAD085}, timestamp = {Mon, 01 May 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiuWST23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuWYZZ23, author = {Yuhang Liu and Zixuan Wang and Hao Yuan and Guiquan Zhu and Yongqing Zhang}, title = {{HEAP:} a task adaptive-based explainable deep learning framework for enhancer activity prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad286}, doi = {10.1093/BIB/BBAD286}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiuWYZZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuYLFSYP23, author = {Wei Liu and Yu Yang and Xu Lu and Xiangzheng Fu and Ruiqing Sun and Li Yang and Li Peng}, title = {{NSRGRN:} a network structure refinement method for gene regulatory network inference}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad129}, doi = {10.1093/BIB/BBAD129}, timestamp = {Sun, 12 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LiuYLFSYP23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuZHHDCTLRHLCW23, author = {Tianyuan Liu and Bohao Zou and Manman He and Yongfei Hu and Yiying Dou and Tianyu Cui and Puwen Tan and Shaobin Li and Shuan Rao and Yan Huang and Sixi Liu and Kaican Cai and Dong Wang}, title = {LncReader: identification of dual functional long noncoding RNAs using a multi-head self-attention mechanism}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac579}, doi = {10.1093/BIB/BBAC579}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LiuZHHDCTLRHLCW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuZLLSZ23, author = {Dong Liu and Biao Zhang and Jun Liu and Hui Li and Le Song and Guijun Zhang}, title = {Assessing protein model quality based on deep graph coupled networks using protein language model}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad420}, doi = {10.1093/BIB/BBAD420}, timestamp = {Sat, 13 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LiuZLLSZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuZXLLLGLTYZ23, author = {Mingzhu Liu and Jian Zhou and Qilemuge Xi and Yuchao Liang and Haicheng Li and Pengfei Liang and Yuting Guo and Ming Liu and Temuqile Temuqile and Lei Yang and Yongchun Zuo}, title = {A computational framework of routine test data for the cost-effective chronic disease prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad054}, doi = {10.1093/BIB/BBAD054}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiuZXLLLGLTYZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuZZ23, author = {Jun Liu and Kai{-}Long Zhao and Guijun Zhang}, title = {Improved model quality assessment using sequence and structural information by enhanced deep neural networks}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac507}, doi = {10.1093/BIB/BBAC507}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LiuZZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuZZWCJZZ23, author = {Qiao Liu and Wanwen Zeng and Wei Zhang and Sicheng Wang and Hongyang Chen and Rui Jiang and Mu Zhou and Shaoting Zhang}, title = {Deep generative modeling and clustering of single cell Hi-C data}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac494}, doi = {10.1093/BIB/BBAC494}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiuZZWCJZZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LuPX23, author = {Yao Lu and Zhiqiang Pang and Jianguo Xia}, title = {Comprehensive investigation of pathway enrichment methods for functional interpretation of {LC-MS} global metabolomics data}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac553}, doi = {10.1093/BIB/BBAC553}, timestamp = {Sun, 12 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LuPX23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LuQALBLLT23, author = {Na Lu and Yi Qiao and Pengfei An and Jiajian Luo and Changwei Bi and Musheng Li and Zuhong Lu and Jing Tu}, title = {Exploration of whole genome amplification generated chimeric sequences in long-read sequencing data}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad275}, doi = {10.1093/BIB/BBAD275}, timestamp = {Sun, 12 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LuQALBLLT23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LuWLLTPLGXY23, author = {Ruiqiang Lu and Jun Wang and Pengyong Li and Yuquan Li and Shuoyan Tan and Yiting Pan and Huanxiang Liu and Peng Gao and Guotong Xie and Xiaojun Yao}, title = {Improving drug-target affinity prediction via feature fusion and knowledge distillation}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad145}, doi = {10.1093/BIB/BBAD145}, timestamp = {Mon, 22 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LuWLLTPLGXY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LuZJZ23, author = {Haojie Lu and Shuo Zhang and Zhou Jiang and Ping Zeng}, title = {Leveraging trans-ethnic genetic risk scores to improve association power for complex traits in underrepresented populations}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad232}, doi = {10.1093/BIB/BBAD232}, timestamp = {Sun, 24 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LuZJZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LuZZLDW23, author = {Chengqian Lu and Lishen Zhang and Min Zeng and Wei Lan and Guihua Duan and Jianxin Wang}, title = {Inferring disease-associated circRNAs by multi-source aggregation based on heterogeneous graph neural network}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac549}, doi = {10.1093/BIB/BBAC549}, timestamp = {Sun, 12 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LuZZLDW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LuZZNXL23, author = {Qi Lu and Ruihan Zhang and Hongyuan Zhou and Dongxuan Ni and Weilie Xiao and Jin Li}, title = {MetaHMEI: meta-learning for prediction of few-shot histone modifying enzyme inhibitors}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad115}, doi = {10.1093/BIB/BBAD115}, timestamp = {Thu, 22 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LuZZNXL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LuoGCYZYL23, author = {Junwei Luo and Ting Guan and Guolin Chen and Zhonghua Yu and Haixia Zhai and Chaokun Yan and Huimin Luo}, title = {{SLHSD:} hybrid scaffolding method based on short and long reads}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad169}, doi = {10.1093/BIB/BBAD169}, timestamp = {Thu, 22 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LuoGCYZYL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LuoLPYMHHL23, author = {Mengqi Luo and Shangfu Li and Yuxuan Pang and Lantian Yao and Renfei Ma and Hsi{-}Yuan Huang and Hsien{-}Da Huang and Tzong{-}Yi Lee}, title = {Extraction of microRNA-target interaction sentences from biomedical literature by deep learning approach}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac497}, doi = {10.1093/BIB/BBAC497}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LuoLPYMHHL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LuoWMZHTZ23, author = {Yongchao Luo and Panpan Wang and Minjie Mou and Hanqi Zheng and Jiajun Hong and Lin Tao and Feng Zhu}, title = {A novel strategy for designing the magic shotguns for distantly related target pairs}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac621}, doi = {10.1093/BIB/BBAC621}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LuoWMZHTZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LuoWZCLZL23, author = {Jiaqi Luo and Xueying Wang and Yiping Zou and Lingxi Chen and Wei Liu and Wei Zhang and Shuai Cheng Li}, title = {Quantitative annotations of T-Cell repertoire specificity}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad175}, doi = {10.1093/BIB/BBAD175}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LuoWZCLZL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/Ma23, author = {Shuangge Ma}, title = {Editorial}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad258}, doi = {10.1093/BIB/BBAD258}, timestamp = {Sun, 24 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/Ma23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/MaLPLHL23, author = {Renfei Ma and Shangfu Li and Luca Parisi and Wenshuo Li and Hsien{-}Da Huang and Tzong{-}Yi Lee}, title = {Holistic similarity-based prediction of phosphorylation sites for understudied kinases}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac624}, doi = {10.1093/BIB/BBAC624}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/MaLPLHL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/MaSL23, author = {Wentai Ma and Leisheng Shi and Mingkun Li}, title = {A fast and accurate method for SARS-CoV-2 genomic tracing}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad339}, doi = {10.1093/BIB/BBAD339}, timestamp = {Sun, 12 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/MaSL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/MaZ23, author = {Yingjun Ma and Junjiang Zhong}, title = {Logistic tensor decomposition with sparse subspace learning for prediction of multiple disease types of human-virus protein-protein interactions}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac604}, doi = {10.1093/BIB/BBAC604}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/MaZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/MakrodimitrisPAR23, author = {Stavros Makrodimitris and Bram Pronk and Tamim Abdelaal and Marcel J. T. Reinders}, title = {An in-depth comparison of linear and non-linear joint embedding methods for bulk and single-cell multi-omics}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad416}, doi = {10.1093/BIB/BBAD416}, timestamp = {Sat, 13 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/MakrodimitrisPAR23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/MallickCMB23, author = {Koushik Mallick and Sikim Chakraborty and Saurav Mallik and Sanghamitra Bandyopadhyay}, title = {A scalable unsupervised learning of scRNAseq data detects rare cells through integration of structure-preserving embedding, clustering and outlier detection}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad125}, doi = {10.1093/BIB/BBAD125}, timestamp = {Thu, 22 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/MallickCMB23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/MartinezEnguitaDJG23, author = {David Mart{\'{\i}}nez{-}Enguita and Sanjiv K. Dwivedi and Rebecka J{\"{o}}rnsten and Mika Gustafsson}, title = {{NCAE:} data-driven representations using a deep network-coherent {DNA} methylation autoencoder identify robust disease and risk factor signatures}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad293}, doi = {10.1093/BIB/BBAD293}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/MartinezEnguitaDJG23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
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@article{DBLP:journals/bib/McGibbonSDGHXYSB23, author = {Miles McGibbon and Steven R. Shave and Jie Dong and Yumiao Gao and Douglas R. Houston and Jiancong Xie and Yuedong Yang and Philippe Schwaller and Vincent Blay}, title = {From intuition to {AI:} evolution of small molecule representations in drug discovery}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad422}, doi = {10.1093/BIB/BBAD422}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/McGibbonSDGHXYSB23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/MengGT23, author = {Qiaozhen Meng and Fei Guo and Jijun Tang}, title = {Improved structure-related prediction for insufficient homologous proteins using {MSA} enhancement and pre-trained language model}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad217}, doi = {10.1093/BIB/BBAD217}, timestamp = {Fri, 22 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/MengGT23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/MengTHLF23, author = {Guanqun Meng and Wen Tang and Emina Huang and Ziyi Li and Hao Feng}, title = {A comprehensive assessment of cell type-specific differential expression methods in bulk data}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac516}, doi = {10.1093/BIB/BBAC516}, timestamp = {Sat, 13 May 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/MengTHLF23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/MengWXLTPZTY23, author = {Yajie Meng and Yi Wang and Junlin Xu and Changcheng Lu and Xianfang Tang and Tao Peng and Ben{-}gong Zhang and Geng Tian and Jialiang Yang}, title = {Drug repositioning based on weighted local information augmented graph neural network}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad431}, doi = {10.1093/BIB/BBAD431}, timestamp = {Wed, 14 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/MengWXLTPZTY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/MilanoC23, author = {Marianna Milano and Mario Cannataro}, title = {Network models in bioinformatics: modeling and analysis for complex diseases}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad016}, doi = {10.1093/BIB/BBAD016}, timestamp = {Wed, 19 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/MilanoC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/MinadakisTDS23, author = {George Minadakis and Marios Tomazou and Nikolas Dietis and George M. Spyrou}, title = {Vir2Drug: a drug repurposing framework based on protein similarities between pathogens}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac536}, doi = {10.1093/BIB/BBAC536}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/MinadakisTDS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/MingWYZTTL23, author = {Yongfan Ming and Wenkang Wang and Rui Yin and Min Zeng and Li Tang and Shizhe Tang and Min Li}, title = {A review of enzyme design in catalytic stability by artificial intelligence}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad065}, doi = {10.1093/BIB/BBAD065}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/MingWYZTTL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
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@article{DBLP:journals/bib/NguyenVM23, author = {An{-}phi Nguyen and Stefania Vasilaki and Mar{\'{\i}}a Rodr{\'{\i}}guez Mart{\'{\i}}nez}, title = {{FLAN:} feature-wise latent additive neural models for biological applications}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad056}, doi = {10.1093/BIB/BBAD056}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/NguyenVM23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/NingZGCLLY23, author = {Qiao Ning and Yaomiao Zhao and Jun Gao and Chen Chen and Xiang Li and Tingting Li and Minghao Yin}, title = {{AMHMDA:} attention aware multi-view similarity networks and hypergraph learning for miRNA-disease associations identification}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad094}, doi = {10.1093/BIB/BBAD094}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/NingZGCLLY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/NiuLTLZZTWLLWZ23, author = {Qikai Niu and Hongtao Li and Lin Tong and Sihong Liu and Wenjing Zong and Siqi Zhang and Siwei Tian and Jingai Wang and Jun Liu and Bing Li and Zhong Wang and Huamin Zhang}, title = {{TCMFP:} a novel herbal formula prediction method based on network target's score integrated with semi-supervised learning genetic algorithms}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad102}, doi = {10.1093/BIB/BBAD102}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/NiuLTLZZTWLLWZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/NoorAAQQ23, author = {Fatima Noor and Muhammad Asif and Usman Ali Ashfaq and Muhammad Qasim and Muhammad Tahir Ul Qamar}, title = {Machine learning for synergistic network pharmacology: a comprehensive overview}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad120}, doi = {10.1093/BIB/BBAD120}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/NoorAAQQ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/NourbakhshSTCCOTP23, author = {Mona Nourbakhsh and Astrid Saksager and Nikola Tom and Xi Steven Chen and Antonio Colaprico and Catharina Olsen and Matteo Tiberti and Elena Papaleo}, title = {A workflow to study mechanistic indicators for driver gene prediction with Moonlight}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad274}, doi = {10.1093/BIB/BBAD274}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/NourbakhshSTCCOTP23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/OellerKBASV23, author = {Marc Oeller and Ryan Kang and Rosie Bell and Hannes Ausserw{\"{o}}ger and Pietro Sormanni and Michele Vendruscolo}, title = {Sequence-based prediction of pH-dependent protein solubility using CamSol}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad004}, doi = {10.1093/BIB/BBAD004}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/OellerKBASV23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/OrozcoAriasLCAJPTIG23, author = {Simon Orozco{-}Arias and Luis Humberto L{\'{o}}pez{-}Murillo and Mariana S. Candamil{-}Cortes and Maradey Arias and Paula A. Jaimes and Alexandre Rossi Paschoal and Reinel Tabares{-}Soto and Gustavo A. Isaza and Romain Guyot}, title = {Inpactor2: a software based on deep learning to identify and classify LTR-retrotransposons in plant genomes}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac511}, doi = {10.1093/BIB/BBAC511}, timestamp = {Tue, 21 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/OrozcoAriasLCAJPTIG23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
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@article{DBLP:journals/bib/PaisSCBABGMC23, author = {Giulia Pais and Giulio Spinozzi and Daniela Cesana and Fabrizio Benedicenti and Alessandra Albertini and Maria Ester Bernardo and Bernhard Gentner and Eugenio Montini and Andrea Calabria}, title = {ISAnalytics enables longitudinal and high-throughput clonal tracking studies in hematopoietic stem cell gene therapy applications}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac551}, doi = {10.1093/BIB/BBAC551}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/PaisSCBABGMC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
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@article{DBLP:journals/bib/PanAGJSWHSY23, author = {Xingxin Pan and Zeynep H. Coban Akdemir and Ruixuan Gao and Xiaoqian Jiang and Gloria M. Sheynkman and Erxi Wu and Jason H. Huang and Nidhi Sahni and S. Stephen Yi}, title = {AD-Syn-Net: systematic identification of Alzheimer's disease-associated mutation and co-mutation vulnerabilities via deep learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad030}, doi = {10.1093/BIB/BBAD030}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/PanAGJSWHSY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
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@article{DBLP:journals/bib/PanRHR23, author = {Chenxu Pan and Ren{\'{e}} Rahn and David Heller and Knut Reinert}, title = {Linear: a framework to enable existing software to resolve structural variants in long reads with flexible and efficient alignment-free statistical models}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad071}, doi = {10.1093/BIB/BBAD071}, timestamp = {Sun, 12 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/PanRHR23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/PanYYZFZRMWWS23, author = {Jie Pan and Zhuhong You and Wencai You and Tian Zhao and Chenlu Feng and Xuexia Zhang and Fengzhi Ren and Sanxing Ma and Fan Wu and Shiwei Wang and Yanmei Sun}, title = {{PTBGRP:} predicting phage-bacteria interactions with graph representation learning on microbial heterogeneous information network}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad328}, doi = {10.1093/BIB/BBAD328}, timestamp = {Thu, 11 Apr 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/PanYYZFZRMWWS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/PangLDYCX23, author = {Jiali Pang and Bilin Liang and Ruifeng Ding and Qiujuan Yan and Ruiyao Chen and Jie Xu}, title = {A denoised multi-omics integration framework for cancer subtype classification and survival prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad304}, doi = {10.1093/BIB/BBAD304}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/PangLDYCX23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ParkBPYC23, author = {Musun Park and Su{-}Jin Baek and Sang{-}Min Park and Jin{-}Mu Yi and Seongwon Cha}, title = {Comparative study of the mechanism of natural compounds with similar structures using docking and transcriptome data for improving \emph{in silico} herbal medicine experimentations}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad344}, doi = {10.1093/BIB/BBAD344}, timestamp = {Sat, 28 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ParkBPYC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ParsaniaCSMDW23, author = {Chirag Parsania and Ruiwen Chen and Pooja Sethiya and Zhengqiang Miao and Liguo Dong and Koon Ho Wong}, title = {FungiExpresZ: an intuitive package for fungal gene expression data analysis, visualization and discovery}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad051}, doi = {10.1093/BIB/BBAD051}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ParsaniaCSMDW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/PatiyalDBSR23, author = {Sumeet Patiyal and Anjali Dhall and Khushboo Bajaj and Harshita Sahu and Gajendra P. S. Raghava}, title = {Prediction of RNA-interacting residues in a protein using {CNN} and evolutionary profile}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac538}, doi = {10.1093/BIB/BBAC538}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/PatiyalDBSR23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/PengLMZK23, author = {Zhenling Peng and Zixia Li and Qiaozhen Meng and Bi Zhao and Lukasz A. Kurgan}, title = {{CLIP:} accurate prediction of disordered linear interacting peptides from protein sequences using co-evolutionary information}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac502}, doi = {10.1093/BIB/BBAC502}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/PengLMZK23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/PengLZKS23, author = {Xiaoqing Peng and Yiming Li and Mengxi Zou and Xiangyan Kong and Yu Sheng}, title = {{CATAD:} exploring topologically associating domains from an insight of core-attachment structure}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad204}, doi = {10.1093/BIB/BBAD204}, timestamp = {Sun, 24 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/PengLZKS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/PengNCVPMNHKMBNPABARM23, author = {Kerui Peng and Theodore S. Nowicki and Katie Campbell and Mohammad Vahed and Dandan Peng and Yiting Meng and Anish Nagareddy and Yu{-}Ning Huang and Aaron Karlsberg and Zachary Miller and Jaqueline J. Brito and Brian B. Nadel and Victoria M. Pak and Malak S. Abedalthagafi and Amanda M. Burkhardt and Houda Alachkar and Antoni Ribas and Serghei Mangul}, title = {Rigorous benchmarking of T-cell receptor repertoire profiling methods for cancer {RNA} sequencing}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad220}, doi = {10.1093/BIB/BBAD220}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/PengNCVPMNHKMBNPABARM23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/PhamPSKSLJM23, author = {Nhat Truong Pham and Le Thi Phan and Jimin Seo and Yeonwoo Kim and Minkyung Song and Sukchan Lee and Young{-}Jun Jeon and Balachandran Manavalan}, title = {Advancing the accuracy of SARS-CoV-2 phosphorylation site detection via meta-learning approach}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad433}, doi = {10.1093/BIB/BBAD433}, timestamp = {Sat, 13 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/PhamPSKSLJM23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/PradhanMNPGP23, author = {Upendra Kumar Pradhan and Prabina Kumar Meher and Sanchita Naha and Soumen Pal and Ajit Gupta and Rajender Parsad}, title = {P\emph{l}DBPred: a novel computational model for discovery of {DNA} binding proteins in plants}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac483}, doi = {10.1093/BIB/BBAC483}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/PradhanMNPGP23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/PrakashB23, author = {Anil Prakash and Moinak Banerjee}, title = {An interpretable block-attention network for identifying regulatory feature interactions}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad250}, doi = {10.1093/BIB/BBAD250}, timestamp = {Sun, 24 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/PrakashB23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/PuWLCL23, author = {Juhua Pu and Bingchen Wang and Xingwu Liu and Lingxi Chen and Shuai Cheng Li}, title = {{SMURF:} embedding single-cell RNA-seq data with matrix factorization preserving self-consistency}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad026}, doi = {10.1093/BIB/BBAD026}, timestamp = {Mon, 01 May 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/PuWLCL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/QianHTX23, author = {Hao Qian and Wenjing Huang and Shikui Tu and Lei Xu}, title = {KGDiff: towards explainable target-aware molecule generation with knowledge guidance}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad435}, doi = {10.1093/BIB/BBAD435}, timestamp = {Mon, 01 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/QianHTX23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/QianSWFCTLZZYOC23, author = {Sheng Hu Qian and Meng{-}Wei Shi and Dan{-}Yang Wang and Justin M. Fear and Lu Chen and Yi{-}Xuan Tu and Hong{-}Shan Liu and Yuan Zhang and Shuai{-}Jie Zhang and Shan{-}Shan Yu and Brian Oliver and Zhen{-}Xia Chen}, title = {Integrating massive RNA-seq data to elucidate transcriptome dynamics in \emph{Drosophila melanogaster}}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad177}, doi = {10.1093/BIB/BBAD177}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/QianSWFCTLZZYOC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/QiuW23, author = {Yuchi Qiu and Guo{-}Wei Wei}, title = {Artificial intelligence-aided protein engineering: from topological data analysis to deep protein language models}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad289}, doi = {10.1093/BIB/BBAD289}, timestamp = {Sat, 28 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/QiuW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/QiuYZZ23, author = {Yushan Qiu and Chang Yan and Pu Zhao and Quan Zou}, title = {{SSNMDI:} a novel joint learning model of semi-supervised non-negative matrix factorization and data imputation for clustering of single-cell RNA-seq data}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad149}, doi = {10.1093/BIB/BBAD149}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/QiuYZZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/RaffoP23, author = {Andrea Raffo and Jonas Paulsen}, title = {The shape of chromatin: insights from computational recognition of geometric patterns in Hi-C data}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad302}, doi = {10.1093/BIB/BBAD302}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/RaffoP23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/RebolledoSSM23, author = {Camilo Rebolledo and Juan Pablo Silva and Nicol{\'{a}}s Saavedra and Vinicius Maracaja{-}Coutinho}, title = {Computational approaches for circRNAs prediction and \emph{in silico} characterization}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad154}, doi = {10.1093/BIB/BBAD154}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/RebolledoSSM23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/RhrissorrakraiULP23, author = {Kahn Rhrissorrakrai and Filippo Utro and Chaya Levovitz and Laxmi Parida}, title = {Lesion Shedding Model: unraveling site-specific contributions to ctDNA}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad059}, doi = {10.1093/BIB/BBAD059}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/RhrissorrakraiULP23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/RomagnoliNGPLBFPSMDMBMB23, author = {Dario Romagnoli and Agostina Nardone and Francesca Galardi and Marta Paoli and Francesca De Luca and Chiara Biagioni and Gian Marco Franceschini and Marta Pestrin and Giuseppina Sanna and Erica Moretti and Francesca Demichelis and Ilenia Migliaccio and Laura Biganzoli and Luca Malorni and Matteo Benelli}, title = {{MIMESIS:} minimal DNA-methylation signatures to quantify and classify tumor signals in tissue and cell-free {DNA} samples}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad015}, doi = {10.1093/BIB/BBAD015}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/RomagnoliNGPLBFPSMDMBMB23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/RoseKFKLP23, author = {Tim D. Rose and Nikolai K{\"{o}}hler and Lisa Falk and Lucie Klischat and Olga Lazareva and Josch Konstantin Pauling}, title = {Lipid network and moiety analysis for revealing enzymatic dysregulation and mechanistic alterations from lipidomics data}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac572}, doi = {10.1093/BIB/BBAC572}, timestamp = {Tue, 09 Apr 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/RoseKFKLP23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/RuWSYQM23, author = {Zhongying Ru and Yangyang Wu and Jinning Shao and Jianwei Yin and Linghui Qian and Xiaoye Miao}, title = {A dual-modal graph learning framework for identifying interaction events among chemical and biotech drugs}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad271}, doi = {10.1093/BIB/BBAD271}, timestamp = {Fri, 10 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/RuWSYQM23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/RuanJLLLHL23, author = {Xinru Ruan and Changzhi Jiang and Peixuan Lin and Yuan Lin and Juan Liu and Shaohui Huang and Xiangrong Liu}, title = {{MSGCL:} inferring miRNA-disease associations based on multi-view self-supervised graph structure contrastive learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac623}, doi = {10.1093/BIB/BBAC623}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/RuanJLLLHL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/RuizREBEAMGO23, author = {Jos{\'{e}} Luis Ruiz and Susanne Reimering and Juan David Escobar{-}Prieto and Nicolas M. B. Brancucci and Diego F. Echeverry and Abdirahman I Abdi and Matthias Marti and Elena G{\'{o}}mez{-}D{\'{\i}}az and Thomas D. Otto}, title = {From contigs towards chromosomes: automatic improvement of long read assemblies {(ILRA)}}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad248}, doi = {10.1093/BIB/BBAD248}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/RuizREBEAMGO23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/SatoH23, author = {Kengo Sato and Michiaki Hamada}, title = {Recent trends in {RNA} informatics: a review of machine learning and deep learning for {RNA} secondary structure prediction and {RNA} drug discovery}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad186}, doi = {10.1093/BIB/BBAD186}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/SatoH23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ScottBoyerDBOPPD23, author = {Marie{-}Pier Scott{-}Boyer and Pascal Dufour and Fran{\c{c}}ois Belleau and R{\'{e}}gis Ongaro{-}Carcy and Cl{\'{e}}ment Plessis and Olivier P{\'{e}}rin and Arnaud Droit}, title = {Use of Elasticsearch-based business intelligence tools for integration and visualization of biological data}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad348}, doi = {10.1093/BIB/BBAD348}, timestamp = {Sat, 28 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ScottBoyerDBOPPD23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/SebastianRK23, author = {Softya Sebastian and Swarup Roy and Jugal Kalita}, title = {A generic parallel framework for inferring large-scale gene regulatory networks from expression profiles: application to Alzheimer's disease network}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac482}, doi = {10.1093/BIB/BBAC482}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/SebastianRK23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ShangTS23, author = {Jiayu Shang and Xubo Tang and Yanni Sun}, title = {PhaTYP: predicting the lifestyle for bacteriophages using {BERT}}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac487}, doi = {10.1093/BIB/BBAC487}, timestamp = {Tue, 21 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ShangTS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ShaoYLMLYCLH23, author = {Mengjie Shao and Nanjiao Ying and Qian Liang and Nan Ma and Sebastian Leptihn and Yunsong Yu and Huan Chen and Chengzhi Liu and Xiaoting Hua}, title = {P\emph{dif}-mediated antibiotic resistance genes transfer in bacteria identified by pdifFinder}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac521}, doi = {10.1093/BIB/BBAC521}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ShaoYLMLYCLH23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/SharmaPDBS23, author = {Harsh Sharma and Trishna Pani and Ujjaini Dasgupta and Jyotsna Batra and Ravi Datta Sharma}, title = {Prediction of transcript structure and concentration using RNA-Seq data}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad022}, doi = {10.1093/BIB/BBAD022}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/SharmaPDBS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ShenDSZQS23, author = {Ke Shen and Ahmad Ud Din and Baivab Sinha and Yi Zhou and Fuliang Qian and Bairong Shen}, title = {Translational informatics for human microbiota: data resources, models and applications}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad168}, doi = {10.1093/BIB/BBAD168}, timestamp = {Thu, 22 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ShenDSZQS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ShenFLLML23, author = {Bihan Shen and Fangyoumin Feng and Kunshi Li and Ping Lin and Liangxiao Ma and Hong Li}, title = {A systematic assessment of deep learning methods for drug response prediction: from in vitro to clinical applications}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac605}, doi = {10.1093/BIB/BBAC605}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ShenFLLML23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ShengWHGCXF23, author = {Nan Sheng and Yan Wang and Lan Huang and Ling Gao and Yangkun Cao and Xuping Xie and Yuan Fu}, title = {Multi-task prediction-based graph contrastive learning for inferring the relationship among lncRNAs, miRNAs and diseases}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad276}, doi = {10.1093/BIB/BBAD276}, timestamp = {Sat, 28 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ShengWHGCXF23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ShengWLQLGCH23, author = {Yuqi Sheng and Jiashuo Wu and Xiangmei Li and Jiayue Qiu and Ji Li and Qinyu Ge and Liang Cheng and Junwei Han}, title = {iATMEcell: identification of abnormal tumor microenvironment cells to predict the clinical outcomes in cancer based on cell-cell crosstalk network}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad074}, doi = {10.1093/BIB/BBAD074}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ShengWLQLGCH23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/SherkatghanadACM23, author = {Zeinab Sherkatghanad and Moloud Abdar and J{\'{e}}r{\'{e}}my Charlier and Vladimir Makarenkov}, title = {Using traditional machine learning and deep learning methods for on- and off-target prediction in CRISPR/Cas9: a review}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad131}, doi = {10.1093/BIB/BBAD131}, timestamp = {Tue, 12 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/SherkatghanadACM23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ShiLLS23, author = {Mingguang Shi and Xuefeng Li and Mingna Li and Yichong Si}, title = {Attention-based generative adversarial networks improve prognostic outcome prediction of cancer from multimodal data}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad329}, doi = {10.1093/BIB/BBAD329}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ShiLLS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ShiZLL23, author = {Xuejing Shi and Juntong Zhu and Yahui Long and Cheng Liang}, title = {Identifying spatial domains of spatially resolved transcriptomics via multi-view graph convolutional networks}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad278}, doi = {10.1093/BIB/BBAD278}, timestamp = {Mon, 23 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ShiZLL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/SiY23, author = {Yunda Si and Chengfei Yan}, title = {Improved inter-protein contact prediction using dimensional hybrid residual networks and protein language models}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad039}, doi = {10.1093/BIB/BBAD039}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/SiY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/SilvaAP23, author = {Bruna Moreira da Silva and David B. Ascher and Douglas E. V. Pires}, title = {epitope1D: accurate taxonomy-aware B-cell linear epitope prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad114}, doi = {10.1093/BIB/BBAD114}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/SilvaAP23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/SongLJGWGCL23, author = {Bo Song and Hao Li and Mengyun Jiang and Zhongtian Gao and Suikang Wang and Lei Gao and Yunsheng Chen and Wujiao Li}, title = {slORFfinder: a tool to detect open reading frames resulting from \emph{trans}-splicing of spliced leader sequences}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac610}, doi = {10.1093/BIB/BBAC610}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/SongLJGWGCL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/SongWWHNM23, author = {Yiyou Song and Yue Wang and Xuan Wang and Daiyun Huang and Anh Nguyen and Jia Meng}, title = {Multi-task adaptive pooling enabled synergetic learning of {RNA} modification across tissue, type and species from low-resolution epitranscriptomes}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad105}, doi = {10.1093/BIB/BBAD105}, timestamp = {Mon, 27 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/SongWWHNM23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/SongYCCZY23, author = {Yidong Song and Qianmu Yuan and Sheng Chen and Ken Chen and Yaoqi Zhou and Yuedong Yang}, title = {Fast and accurate protein intrinsic disorder prediction by using a pretrained language model}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad173}, doi = {10.1093/BIB/BBAD173}, timestamp = {Wed, 21 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/SongYCCZY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/SongYZY23, author = {Yidong Song and Qianmu Yuan and Huiying Zhao and Yuedong Yang}, title = {Accurately identifying nucleic-acid-binding sites through geometric graph learning on language model predicted structures}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad360}, doi = {10.1093/BIB/BBAD360}, timestamp = {Sat, 28 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/SongYZY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/StouracBKPDPMPSSSDB23, author = {Jan Stourac and Simeon Borko and Rayyan T. Khan and Petra Pokorna and Adam Dobias and Joan Planas{-}Iglesias and Stanislav Mazurenko and Gaspar R. P. Pinto and Veronika Szotkowska and Jaroslav Sterba and Ondrej Slaby and Jir{\'{\i}} Damborsk{\'{y}} and David Bednar}, title = {PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad441}, doi = {10.1093/BIB/BBAD441}, timestamp = {Sat, 13 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/StouracBKPDPMPSSSDB23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/SuLWTZ23, author = {Yansen Su and Rongxin Lin and Jing Wang and Dayu Tan and Chun{-}Hou Zheng}, title = {Denoising adaptive deep clustering with self-attention mechanism on single-cell sequencing data}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad021}, doi = {10.1093/BIB/BBAD021}, timestamp = {Mon, 22 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/SuLWTZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/SuWLLH23, author = {Benzhe Su and Weiwei Wang and Xiaohui Lin and Shenglan Liu and Xin Huang}, title = {Identifying the potential miRNA biomarkers based on multi-view networks and reinforcement learning for diseases}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad427}, doi = {10.1093/BIB/BBAD427}, timestamp = {Fri, 19 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/SuWLLH23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/SubbaroyanSMS23, author = {Ajay Subbaroyan and Priyotosh Sil and Olivier C. Martin and Areejit Samal}, title = {Leveraging developmental landscapes for model selection in Boolean gene regulatory networks}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad160}, doi = {10.1093/BIB/BBAD160}, timestamp = {Mon, 28 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/SubbaroyanSMS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/SunKRGC23, author = {Jianfeng Sun and Arulsamy Kulandaisamy and Jinlong Ru and M. Michael Gromiha and Adam P. Cribbs}, title = {TMKit: a Python interface for computational analysis of transmembrane proteins}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad288}, doi = {10.1093/BIB/BBAD288}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/SunKRGC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/SunSCWTDZY23, author = {Haoran Sun and Zhaoqi Song and Qiuming Chen and Meiling Wang and Furong Tang and Lijun Dou and Quan Zou and Fenglong Yang}, title = {MMiKG: a knowledge graph-based platform for path mining of microbiota-mental diseases interactions}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad340}, doi = {10.1093/BIB/BBAD340}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/SunSCWTDZY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/SunWXHWHJ23, author = {Han Sun and Yue Wang and Zhen Xiao and Xiaoyun Huang and Haodong Wang and Tingting He and Xingpeng Jiang}, title = {multiMiAT: an optimal microbiome-based association test for multicategory phenotypes}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad012}, doi = {10.1093/BIB/BBAD012}, timestamp = {Thu, 28 Dec 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/SunWXHWHJ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/SunWZ23, author = {Lei Sun and Gongming Wang and Zhihua Zhang}, title = {SimCH: simulation of single-cell {RNA} sequencing data by modeling cellular heterogeneity at gene expression level}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac590}, doi = {10.1093/BIB/BBAC590}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/SunWZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/SusmeljRMGG23, author = {Anna Klimovskaia Susmelj and Yani Ren and Yann Vander Meersche and Jean{-}Christophe Gelly and Tatiana Galochkina}, title = {Poincar{\'{e}} maps for visualization of large protein families}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad103}, doi = {10.1093/BIB/BBAD103}, timestamp = {Fri, 07 Jul 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/SusmeljRMGG23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/SzulcMBS23, author = {Natalia A Szulc and Zuzanna Mackiewicz and Janusz M. Bujnicki and Filip Stefaniak}, title = {Structural interaction fingerprints and machine learning for predicting and explaining binding of small molecule ligands to {RNA}}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad187}, doi = {10.1093/BIB/BBAD187}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/SzulcMBS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TangLLZYSS23, author = {Ziyang Tang and Xiang Liu and Zuotian Li and Tonglin Zhang and Baijian Yang and Jing Su and Qianqian Song}, title = {SpaRx: elucidate single-cell spatial heterogeneity of drug responses for personalized treatment}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad338}, doi = {10.1093/BIB/BBAD338}, timestamp = {Mon, 29 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/TangLLZYSS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TangYYZFZZWLLZ23, author = {Zhenshuang Tang and Lilin Yin and Dong Yin and Haohao Zhang and Yuhua Fu and Guangliang Zhou and Yunxiang Zhao and Zhiquan Wang and Xiaolei Liu and Xinyun Li and Shuhong Zhao}, title = {Development and application of an efficient genomic mating method to maximize the production performances of three-way crossbred pigs}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac587}, doi = {10.1093/BIB/BBAC587}, timestamp = {Tue, 21 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/TangYYZFZZWLLZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TangZLPZYZ23, author = {Tao Tang and Xiaocai Zhang and Yuansheng Liu and Hui Peng and Binshuang Zheng and Yanlin Yin and Xiangxiang Zeng}, title = {Machine learning on protein-protein interaction prediction: models, challenges and trends}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad076}, doi = {10.1093/BIB/BBAD076}, timestamp = {Sun, 12 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/TangZLPZYZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TangZYSS23, author = {Ziyang Tang and Tonglin Zhang and Baijian Yang and Jing Su and Qianqian Song}, title = {spaCI: deciphering spatial cellular communications through adaptive graph model}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac563}, doi = {10.1093/BIB/BBAC563}, timestamp = {Mon, 29 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/TangZYSS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TaoWWWZNWWCDCL23, author = {Ziyu Tao and Shixiang Wang and Chenxu Wu and Tao Wu and Xiangyu Zhao and Wei Ning and Guangshuai Wang and Jinyu Wang and Jing Chen and Kaixuan Diao and Fuxiang Chen and Xue{-}Song Liu}, title = {The repertoire of copy number alteration signatures in human cancer}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad053}, doi = {10.1093/BIB/BBAD053}, timestamp = {Sat, 13 May 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/TaoWWWZNWWCDCL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TeitzSSF23, author = {Joshua Teitz and J{\"{o}}rg Sander and Hassan Sarker and Carlos Fernandez{-}Patron}, title = {Potential of dissimilarity measure-based computation of protein thermal stability data for determining protein interactions}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad143}, doi = {10.1093/BIB/BBAD143}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/TeitzSSF23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TianLXZZLXLZZ23, author = {Saisai Tian and Yanan Li and Jia Xu and Lijun Zhang and Jinbo Zhang and Jinyuan Lu and Xike Xu and Xin Luan and Jing Zhao and Weidong Zhang}, title = {{COIMMR:} a computational framework to reveal the contribution of herbal ingredients against human cancer via immune microenvironment and metabolic reprogramming}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad346}, doi = {10.1093/BIB/BBAD346}, timestamp = {Mon, 05 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/TianLXZZLXLZZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TianWYLY23, author = {Yanan Tian and Xiaorui Wang and Xiaojun Yao and Huanxiang Liu and Ying Yang}, title = {Predicting molecular properties based on the interpretable graph neural network with multistep focus mechanism}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac534}, doi = {10.1093/BIB/BBAC534}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/TianWYLY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TianXXTT23, author = {Lejin Tian and Yunxiao Xie and Zhaobin Xie and Jasmine Tian and Weidong Tian}, title = {AtacAnnoR: a reference-based annotation tool for single cell ATAC-seq data}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad268}, doi = {10.1093/BIB/BBAD268}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/TianXXTT23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TianY23, author = {Leqi Tian and Tianwei Yu}, title = {An integrated deep learning framework for the interpretation of untargeted metabolomics data}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad244}, doi = {10.1093/BIB/BBAD244}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/TianY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TianYFXG23, author = {Zhen Tian and Yue Yu and Haichuan Fang and Weixin Xie and Maozu Guo}, title = {Predicting microbe-drug associations with structure-enhanced contrastive learning and self-paced negative sampling strategy}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac634}, doi = {10.1093/BIB/BBAC634}, timestamp = {Mon, 01 May 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/TianYFXG23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TianZYWLWFFYZZZ23, author = {Saisai Tian and Jinbo Zhang and Shunling Yuan and Qun Wang and Chao Lv and Jinxing Wang and Jiansong Fang and Lu Fu and Jian Yang and Xianpeng Zu and Jing Zhao and Weidong Zhang}, title = {Exploring pharmacological active ingredients of traditional Chinese medicine by pharmacotranscriptomic map in {ITCM}}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad027}, doi = {10.1093/BIB/BBAD027}, timestamp = {Wed, 17 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/TianZYWLWFFYZZZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TiengZSMLM23, author = {Francis Yew Fu Tieng and Muhammad Redha Abdullah Zawawi and Nur Alyaa Afifah Md Shahri and Zeti{-}Azura Mohamed{-}Hussein and Learn{-}Han Lee and Nurul{-}Syakima Ab Mutalib}, title = {A Hitchhiker's guide to {RNA-RNA} structure and interaction prediction tools}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad421}, doi = {10.1093/BIB/BBAD421}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/TiengZSMLM23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TippenhauerPLS23, author = {Kevin Tippenhauer and Marwin Philips and Carlo R. Largiad{\`{e}}r and Murat Sariyar}, title = {Using the PharmCAT tool for Pharmacogenetic clinical decision support}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad452}, doi = {10.1093/BIB/BBAD452}, timestamp = {Sat, 13 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/TippenhauerPLS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TognonGP23, author = {Manuel Tognon and Rosalba Giugno and Luca Pinello}, title = {A survey on algorithms to characterize transcription factor binding sites}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad156}, doi = {10.1093/BIB/BBAD156}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/TognonGP23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TongLYSZXTLLHY23, author = {Mengsha Tong and Yuxiang Lin and Wenxian Yang and Jinsheng Song and Zheyang Zhang and Jiajing Xie and Jingyi Tian and Shijie Luo and Chenyu Liang and Jialiang Huang and Rongshan Yu}, title = {Prioritizing prognostic-associated subpopulations and individualized recurrence risk signatures from single-cell transcriptomes of colorectal cancer}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad078}, doi = {10.1093/BIB/BBAD078}, timestamp = {Sun, 06 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/TongLYSZXTLLHY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ToroDominguezMMLCBGPCA23, author = {Daniel Toro{-}Dom{\'{\i}}nguez and Jordi Martorell{-}Marugan and Manuel Mart{\'{\i}}nez{-}Bueno and Ra{\'{u}}l L{\'{o}}pez{-}Dom{\'{\i}}nguez and Elena Carnero{-}Montoro and Guillermo Barturen and Daniel Goldman and Michelle Petri and Pedro Carmona{-}Saez and Marta E. Alarc{\'{o}}n{-}Riquelme}, title = {Response to the letter 'testing the effectiveness of MyPROSLE in classifying patients with lupus nephritis'}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad454}, doi = {10.1093/BIB/BBAD454}, timestamp = {Fri, 26 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ToroDominguezMMLCBGPCA23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ToseefPWRLLW23, author = {Muhammad Toseef and Olutomilayo Olayemi Petinrin and Fuzhou Wang and Saifur Rahaman and Zhe Liu and Xiangtao Li and Ka{-}Chun Wong}, title = {Deep transfer learning for clinical decision-making based on high-throughput data: comprehensive survey with benchmark results}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad254}, doi = {10.1093/BIB/BBAD254}, timestamp = {Wed, 24 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ToseefPWRLLW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TrinidadVCECNGHM23, author = {Eva Mar{\'{\i}}a Trinidad and Enrique Vidal and Esther Coronado and Anna Esteve{-}Codina and Victoria Castel and Adela Ca{\~{n}}ete Nieto and Marta Gut and Simon Heath and Jaime Font de Mora}, title = {Liquidhope: methylome and genomic profiling from very limited quantities of plasma-derived {DNA}}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac575}, doi = {10.1093/BIB/BBAC575}, timestamp = {Sat, 11 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/TrinidadVCECNGHM23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TuJH23, author = {Yueh{-}Hua Tu and Hsueh{-}Fen Juan and Hsuan{-}Cheng Huang}, title = {Context-dependent gene regulatory network reveals regulation dynamics and cell trajectories using unspliced transcripts}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac633}, doi = {10.1093/BIB/BBAC633}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/TuJH23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/TurzoSLL23, author = {S. M. Bargeen Alam Turzo and Justin T. Seffernick and Sergey Lyskov and Steffen Lindert}, title = {Predicting ion mobility collision cross sections using projection approximation with {ROSIE-PARCS} webserver}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad308}, doi = {10.1093/BIB/BBAD308}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/TurzoSLL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ValizadehAslaniSRWZHZL23, author = {Taha ValizadehAslani and Yiwen Shi and Ping Ren and Jing Wang and Yi Zhang and Meng Hu and Liang Zhao and Hualou Liang}, title = {PharmBERT: a domain-specific {BERT} model for drug labels}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad226}, doi = {10.1093/BIB/BBAD226}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ValizadehAslaniSRWZHZL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/Wang23, author = {Kai Wang}, title = {{GPDOCK:} highly accurate docking strategy for metalloproteins based on geometric probability}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac620}, doi = {10.1093/BIB/BBAC620}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/Wang23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangC23, author = {Wengang Wang and Hailin Chen}, title = {Predicting miRNA-disease associations based on lncRNA-miRNA interactions and graph convolution networks}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac495}, doi = {10.1093/BIB/BBAC495}, timestamp = {Sun, 12 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/WangC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangC23a, author = {Yiwen Wang and Kim{-}Anh L{\^{e}} Cao}, title = {PLSDA-batch: a multivariate framework to correct for batch effects in microbiome data}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac622}, doi = {10.1093/BIB/BBAC622}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangC23a.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangCHL23, author = {Rulan Wang and Chia{-}Ru Chung and Hsien{-}Da Huang and Tzong{-}Yi Lee}, title = {Identification of species-specific {RNA} N6-methyladinosine modification sites from {RNA} sequences}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac573}, doi = {10.1093/BIB/BBAC573}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangCHL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangCWGY23, author = {Jun Wang and Xi Chen and Zhengtian Wu and Maozu Guo and Guoxian Yu}, title = {Cooperative driver pathways discovery by multiplex network embedding}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad112}, doi = {10.1093/BIB/BBAD112}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangCWGY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangDWL23, author = {Xiao Wang and Zhao{-}Yuan Ding and Rong Wang and Xi Lin}, title = {Deepro-Glu: combination of convolutional neural network and Bi-LSTM models using ProtBert and handcrafted features to identify lysine glutarylation sites}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac631}, doi = {10.1093/BIB/BBAC631}, timestamp = {Thu, 18 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangDWL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangDWWLHBP23, author = {Hong Wang and Chong Dai and Yuqi Wen and Xiaoqi Wang and Wenjuan Liu and Song He and Xiaochen Bo and Shaoliang Peng}, title = {{GADRP:} graph convolutional networks and autoencoders for cancer drug response prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac501}, doi = {10.1093/BIB/BBAC501}, timestamp = {Sun, 12 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/WangDWWLHBP23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangDZLCWWW23, author = {Zhongyu Wang and Zhaohong Deng and Wei Zhang and Qiongdan Lou and Kup{-}Sze Choi and Zhisheng Wei and Lei Wang and Jing Wu}, title = {MMSMAPlus: a multi-view multi-scale multi-attention embedding model for protein function prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad201}, doi = {10.1093/BIB/BBAD201}, timestamp = {Thu, 28 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangDZLCWWW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangFLLWSHL23, author = {Zhen Wang and Zheng Feng and Yanjun Li and Bowen Li and Yongrui Wang and Chulin Sha and Min He and Xiaolin Li}, title = {BatmanNet: bi-branch masked graph transformer autoencoder for molecular representation}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad400}, doi = {10.1093/BIB/BBAD400}, timestamp = {Sat, 20 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangFLLWSHL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangGWL23, author = {Xin Wang and Xin Gao and Guohua Wang and Dan Li}, title = {miProBERT: identification of microRNA promoters based on the pre-trained model {BERT}}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad093}, doi = {10.1093/BIB/BBAD093}, timestamp = {Wed, 24 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangGWL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangHCW23, author = {Jun Wang and Marc Horlacher and Lixin Cheng and Ole Winther}, title = {{RNA} trafficking and subcellular localization - a review of mechanisms, experimental and predictive methodologies}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad249}, doi = {10.1093/BIB/BBAD249}, timestamp = {Sat, 28 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangHCW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangHDLWTL23, author = {Yimeng Wang and Mengting Huang and Hua Deng and Weihua Li and Zengrui Wu and Yun Tang and Guixia Liu}, title = {Identification of vital chemical information via visualization of graph neural networks}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac577}, doi = {10.1093/BIB/BBAC577}, timestamp = {Tue, 27 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangHDLWTL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangHELX23, author = {Robert Wang and Ingo Helbig and Andrew C. Edmondson and Lan Lin and Yi Xing}, title = {Splicing defects in rare diseases: transcriptomics and machine learning strategies towards genetic diagnosis}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad284}, doi = {10.1093/BIB/BBAD284}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangHELX23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangHGC23, author = {Qingyong Wang and Minfan He and Long{-}Yi Guo and Hua Chai}, title = {{AFEI:} adaptive optimized vertical federated learning for heterogeneous multi-omics data integration}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad269}, doi = {10.1093/BIB/BBAD269}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangHGC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangHWC23, author = {Xiao Wang and Lijun Han and Rong Wang and Haoran Chen}, title = {DaDL-SChlo: protein subchloroplast localization prediction based on generative adversarial networks and pre-trained protein language model}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad083}, doi = {10.1093/BIB/BBAD083}, timestamp = {Thu, 23 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangHWC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangHWXW23, author = {Lei Wang and Chen Huang and Mingxia Wang and Zhidong Xue and Yan Wang}, title = {NeuroPred-PLM: an interpretable and robust model for neuropeptide prediction by protein language model}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad077}, doi = {10.1093/BIB/BBAD077}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangHWXW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangKL23, author = {Meng Wang and Lukasz A. Kurgan and Min Li}, title = {A comprehensive assessment and comparison of tools for {HLA} class {I} peptide-binding prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad150}, doi = {10.1093/BIB/BBAD150}, timestamp = {Tue, 11 Jul 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangKL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangLLMWL23, author = {Zixiao Wang and Shiyang Liang and Siwei Liu and Zhaohan Meng and Jingjie Wang and Shangsong Liang}, title = {Sequence pre-training-based graph neural network for predicting lncRNA-miRNA associations}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad317}, doi = {10.1093/BIB/BBAD317}, timestamp = {Mon, 05 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/WangLLMWL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangLLSXSL23, author = {Bo Wang and Jiawei Luo and Ying Liu and Wanwan Shi and Zehao Xiong and Cong Shen and Yahui Long}, title = {Spatial-MGCN: a novel multi-view graph convolutional network for identifying spatial domains with attention mechanism}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad262}, doi = {10.1093/BIB/BBAD262}, timestamp = {Thu, 15 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangLLSXSL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangLRWZPZ23, author = {Shudong Wang and Tiyao Liu and Chuanru Ren and Wenhao Wu and Zhiyuan Zhao and Shanchen Pang and Yuanyuan Zhang}, title = {Predicting potential small molecule-miRNA associations utilizing truncated schatten p-norm}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad234}, doi = {10.1093/BIB/BBAD234}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangLRWZPZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangLSSWSP23, author = {Yongtian Wang and Xinmeng Liu and Yewei Shen and Xuerui Song and Tao Wang and Xuequn Shang and Jiajie Peng}, title = {Collaborative deep learning improves disease-related circRNA prediction based on multi-source functional information}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad069}, doi = {10.1093/BIB/BBAD069}, timestamp = {Wed, 24 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangLSSWSP23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangLTPTL23, author = {Boshen Wang and Xue Lei and Wei Tian and Alan Perez{-}Rathke and Yan{-}Yuan Tseng and Jie Liang}, title = {Structure-based pathogenicity relationship identifier for predicting effects of single missense variants and discovery of higher-order cancer susceptibility clusters of mutations}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad206}, doi = {10.1093/BIB/BBAD206}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangLTPTL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangLZPQZW23, author = {Shudong Wang and Yunyin Li and Yuanyuan Zhang and Shanchen Pang and Sibo Qiao and Yu Zhang and Fuyu Wang}, title = {Generative Adversarial Matrix Completion Network based on Multi-Source Data Fusion for miRNA-Disease Associations Prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad270}, doi = {10.1093/BIB/BBAD270}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangLZPQZW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangPCWCCHLL23, author = {Zhuo Wang and Yuxuan Pang and Chia{-}Ru Chung and Hsin{-}Yao Wang and Haiyan Cui and Ying{-}Chih Chiang and Jorng{-}Tzong Horng and Jang{-}Jih Lu and Tzong{-}Yi Lee}, title = {A risk assessment framework for multidrug-resistant \emph{Staphylococcus aureus} using machine learning and mass spectrometry technology}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad330}, doi = {10.1093/BIB/BBAD330}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangPCWCCHLL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangQA23, author = {Yishu Wang and Juan Qi and Dongmei Ai}, title = {{DPADM:} a novel algorithm for detecting drug-pathway associations based on high-throughput transcriptional response to compounds}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac517}, doi = {10.1093/BIB/BBAC517}, timestamp = {Wed, 06 Dec 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/WangQA23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangRZLPS23, author = {Shudong Wang and Chuanru Ren and Yulin Zhang and YunYin Li and Shanchen Pang and Tao Song}, title = {Identifying potential small molecule-miRNA associations via Robust {PCA} based on \emph{{\(\gamma\)}}-norm regularization}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad312}, doi = {10.1093/BIB/BBAD312}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangRZLPS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangSLZLLDLHC23, author = {Lei Wang and Shao{-}Hua Shi and Hui Li and Xiangxiang Zeng and Su{-}You Liu and Zhao{-}Qian Liu and Yafeng Deng and Ai{-}Ping Lu and Tingjun Hou and Dong{-}Sheng Cao}, title = {Reducing false positive rate of docking-based virtual screening by active learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac626}, doi = {10.1093/BIB/BBAC626}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangSLZLLDLHC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangSWWHZ23, author = {Yu Mei Wang and Yuzhi Sun and Beiying Wang and Zhiping Wu and Xiao{-}Ying He and Yuansong Zhao}, title = {Transfer learning for clustering single-cell RNA-seq data crossing-species and batch, case on uterine fibroids}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad426}, doi = {10.1093/BIB/BBAD426}, timestamp = {Sat, 08 Jun 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangSWWHZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangVFHXLZ23, author = {Jingjing Wang and Werner Pieter Veldsman and Xiaodong Fang and Yufen Huang and Xuefeng Xie and Aiping Lyu and Lu Zhang}, title = {Benchmarking multi-platform sequencing technologies for human genome assembly}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad300}, doi = {10.1093/BIB/BBAD300}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangVFHXLZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangWNDSWWCXL23, author = {Guangshuai Wang and Tao Wu and Wei Ning and Kaixuan Diao and Xiaoqin Sun and Jinyu Wang and Chenxu Wu and Jing Chen and Dongliang Xu and Xue{-}Song Liu}, title = {TLimmuno2: predicting {MHC} class {II} antigen immunogenicity through transfer learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad116}, doi = {10.1093/BIB/BBAD116}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangWNDSWWCXL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangWSBLWYKLH23, author = {Dong Wang and Zhenxing Wu and Chao Shen and Lingjie Bao and Hao Luo and Zhe Wang and Hucheng Yao and De{-}Xin Kong and Cheng Luo and Tingjun Hou}, title = {Learning with uncertainty to accelerate the discovery of histone lysine-specific demethylase 1A {(KDM1A/LSD1)} inhibitors}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac592}, doi = {10.1093/BIB/BBAC592}, timestamp = {Tue, 16 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangWSBLWYKLH23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangWXZWG23, author = {Liugen Wang and Yan Wang and Chenxu Xuan and Bai Zhang and Hanwen Wu and Jie Gao}, title = {Predicting potential microbe-disease associations based on multi-source features and deep learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad255}, doi = {10.1093/BIB/BBAD255}, timestamp = {Sun, 24 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangWXZWG23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangWXZXSHXZLWWJCLH23, author = {Xuebin Wang and Taifu Wang and Zhihao Xie and Youjin Zhang and Shiqiang Xia and Ruixue Sun and Xinqiu He and Ruizhi Xiang and Qiwen Zheng and Zhencheng Liu and Jin'an Wang and Honglong Wu and Xiangqian Jin and Weijun Chen and Dongfang Li and Zengquan He}, title = {GPMeta: a GPU-accelerated method for ultrarapid pathogen identification from metagenomic sequences}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad092}, doi = {10.1093/BIB/BBAD092}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangWXZXSHXZLWWJCLH23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangXWHHS23, author = {Lingling Wang and Lei Xu and Zhe Wang and Tingjun Hou and Haiping Hao and Huiyong Sun}, title = {Cooperation of structural motifs controls drug selectivity in cyclin-dependent kinases: an advanced theoretical analysis}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac544}, doi = {10.1093/BIB/BBAC544}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangXWHHS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangXWSZ23, author = {Jing Wang and Junfeng Xia and Haiyun Wang and Yansen Su and Chun{-}Hou Zheng}, title = {scDCCA: deep contrastive clustering for single-cell RNA-seq data based on auto-encoder network}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac625}, doi = {10.1093/BIB/BBAC625}, timestamp = {Mon, 29 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangXWSZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangXWZDG23, author = {Yan Wang and Chenxu Xuan and Hanwen Wu and Bai Zhang and Tao Ding and Jie Gao}, title = {{P-CSN:} single-cell {RNA} sequencing data analysis by partial cell-specific network}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad180}, doi = {10.1093/BIB/BBAD180}, timestamp = {Thu, 22 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangXWZDG23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangYWCSZXPWH23, author = {Cheng Wang and Chuang Yuan and Yahui Wang and Ranran Chen and Yuying Shi and Tao Zhang and Fuzhong Xue and Gary J. Patti and Leyi Wei and Qingzhen Hou}, title = {{MPI-VGAE:} protein-metabolite enzymatic reaction link learning by variational graph autoencoders}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad189}, doi = {10.1093/BIB/BBAD189}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangYWCSZXPWH23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangYYLHRLM23, author = {Xin{-}Fei Wang and Changqing Yu and Zhu{-}Hong You and Li{-}Ping Li and Wenzhun Huang and Zhong{-}Hao Ren and Yue{-}Chao Li and Weixiao Meng}, title = {A feature extraction method based on noise reduction for circRNA-miRNA interaction prediction combining multi-structure features in the association networks}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad111}, doi = {10.1093/BIB/BBAD111}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangYYLHRLM23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangZKHLWY23, author = {Shuaiqun Wang and Kai Zheng and Wei Kong and Ruiwen Huang and Lulu Liu and Gen Wen and Yaling Yu}, title = {Multimodal data fusion based on {IGERNNC} algorithm for detecting pathogenic brain regions and genes in Alzheimer's disease}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac515}, doi = {10.1093/BIB/BBAC515}, timestamp = {Fri, 10 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/WangZKHLWY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangZKZZZ23, author = {He Wang and Yongjian Zang and Ying Kang and Jianwen Zhang and Lei Zhang and Shengli Zhang}, title = {{ETLD:} an encoder-transformation layer-decoder architecture for protein contact and mutation effects prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad290}, doi = {10.1093/BIB/BBAD290}, timestamp = {Tue, 19 Dec 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/WangZKZZZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangZLDL23, author = {Qilin Wang and Junyou Zhang and Zhaoshuo Liu and Yingying Duan and Chunyan Li}, title = {Integrative approaches based on genomic techniques in the functional studies on enhancers}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad442}, doi = {10.1093/BIB/BBAD442}, timestamp = {Sat, 13 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/WangZLDL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangZSZWZW23, author = {Ying Wang and Min Zhang and Jian Shi and Yue Zhu and Xin Wang and Shaojun Zhang and Fang Wang}, title = {Cracking the pattern of tumor evolution based on single-cell copy number alterations}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad341}, doi = {10.1093/BIB/BBAD341}, timestamp = {Sat, 28 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangZSZWZW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangZVZZ23, author = {Chonghao Wang and Jing Zhang and Werner Pieter Veldsman and Xin Zhou and Lu Zhang}, title = {A comprehensive investigation of statistical and machine learning approaches for predicting complex human diseases on genomic variants}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac552}, doi = {10.1093/BIB/BBAC552}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangZVZZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangZWL23, author = {Kaili Wang and Renyi Zhou and Yifan Wu and Min Li}, title = {RLBind: a deep learning method to predict RNA-ligand binding sites}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac486}, doi = {10.1093/BIB/BBAC486}, timestamp = {Mon, 05 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/WangZWL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangZWLWKMWL23, author = {Zechen Wang and Liangzhen Zheng and Sheng Wang and Mingzhi Lin and Zhihao Wang and Adams Wai{-}Kin Kong and Yuguang Mu and Yanjie Wei and Weifeng Li}, title = {A fully differentiable ligand pose optimization framework guided by deep learning and a traditional scoring function}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac520}, doi = {10.1093/BIB/BBAC520}, timestamp = {Thu, 06 Jun 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangZWLWKMWL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangZWYWWSZTZN23, author = {Weixu Wang and Xiaolan Zhou and Jing Wang and Jun Yao and Haimei Wen and Yi Wang and Mingwan Sun and Chao Zhang and Wei Tao and Jiahua Zou and Ting Ni}, title = {Approximate estimation of cell-type resolution transcriptome in bulk tissue through matrix completion}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad273}, doi = {10.1093/BIB/BBAD273}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangZWYWWSZTZN23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangZYZYXZ23, author = {Lihua Wang and Tao Zhang and Lihong Yu and Chun{-}Hou Zheng and Wenguang Yin and Junfeng Xia and Tiejun Zhang}, title = {Deleterious synonymous mutation identification based on selective ensemble strategy}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac598}, doi = {10.1093/BIB/BBAC598}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/WangZYZYXZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangZZS23, author = {Hai{-}Yun Wang and Jian{-}Ping Zhao and Chun{-}Hou Zheng and Yan{-}Sen Su}, title = {scGMAAE: Gaussian mixture adversarial autoencoders for diversification analysis of scRNA-seq data}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac585}, doi = {10.1093/BIB/BBAC585}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/WangZZS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WeiHLWW23, author = {Hailin Wei and Tong Han and Taiwen Li and Qiu Wu and Chenfei Wang}, title = {{SCREE:} a comprehensive pipeline for single-cell multi-modal {CRISPR} screen data processing and analysis}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad123}, doi = {10.1093/BIB/BBAD123}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WeiHLWW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WeiLZYSCC23, author = {Yifang Wei and Lingmei Li and Xin Zhao and Haitao Yang and Jian Sa and Hongyan Cao and Yuehua Cui}, title = {Cancer subtyping with heterogeneous multi-omics data via hierarchical multi-kernel learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac488}, doi = {10.1093/BIB/BBAC488}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/WeiLZYSCC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WeiZZLFY23, author = {Jinhang Wei and Linlin Zhuo and Zhecheng Zhou and Xinze Lian and Xiangzheng Fu and Xiaojun Yao}, title = {{GCFMCL:} predicting miRNA-drug sensitivity using graph collaborative filtering and multi-view contrastive learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad247}, doi = {10.1093/BIB/BBAD247}, timestamp = {Sun, 12 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/WeiZZLFY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WongKPG23, author = {Bertrand Jern Han Wong and Weijia Kong and Hui Peng and Wilson Wen Bin Goh}, title = {{PROSE:} phenotype-specific network signatures from individual proteomic samples}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad075}, doi = {10.1093/BIB/BBAD075}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WongKPG23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WuDXZCZTZW23, author = {Tao Wu and Yao Dai and Yue Xu and Jie Zheng and Shuting Chen and Yinuo Zhang and Peng Tian and Xiaoqi Zheng and Haiyun Wang}, title = {ExosomePurity: tumour purity deconvolution in serum exosomes based on miRNA signatures}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad119}, doi = {10.1093/BIB/BBAD119}, timestamp = {Tue, 12 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WuDXZCZTZW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WuH23, author = {Qilong Wu and Sheng{-}You Huang}, title = {HCovDock: an efficient docking method for modeling covalent protein-ligand interactions}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac559}, doi = {10.1093/BIB/BBAC559}, timestamp = {Mon, 27 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/WuH23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WuHZGML23, author = {Haonan Wu and Jiyun Han and Shizhuo Zhang and Xin Gao and Chaozhou Mou and Juntao Liu}, title = {Spatom: a graph neural network for structure-based protein-protein interaction site prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad345}, doi = {10.1093/BIB/BBAD345}, timestamp = {Sat, 28 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WuHZGML23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WuNDWPF23, author = {Jinyang Wu and Zhiwei Ning and Yidong Ding and Ying Wang and Qinke Peng and Laiyi Fu}, title = {{KGETCDA:} an efficient representation learning framework based on knowledge graph encoder from transformer for predicting circRNA-disease associations}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad292}, doi = {10.1093/BIB/BBAD292}, timestamp = {Mon, 05 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/WuNDWPF23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WuPKKP23, author = {Andy J. Wu and Akila Perera and Linganesan Kularatnarajah and Anna Korsakova and Jason J. Pitt}, title = {Mutational signature assignment heterogeneity is widespread and can be addressed by ensemble approaches}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad331}, doi = {10.1093/BIB/BBAD331}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WuPKKP23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WuQOZGMLS23, author = {Jun Wu and Haipeng Qing and Jian Ouyang and Jiajia Zhou and Zihao Gao and Christopher E. Mason and Zhichao Liu and Tieliu Shi}, title = {HiFun: homology independent protein function prediction by a novel protein-language self-attention model}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad311}, doi = {10.1093/BIB/BBAD311}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WuQOZGMLS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WuSFCJWYDPSW23, author = {Peike Wu and Renliang Sun and Aamir Fahira and Yongzhou Chen and Huiting Jiangzhou and Ke Wang and Qiangzhen Yang and Yang Dai and Dun Pan and Yongyong Shi and Zhuo Wang}, title = {{DROEG:} a method for cancer drug response prediction based on omics and essential genes integration}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad003}, doi = {10.1093/BIB/BBAD003}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WuSFCJWYDPSW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WuSWCJJGWLXFGY23, author = {Guiying Wu and Mengmeng Song and Ke Wang and Tianyu Cui and Zicong Jiao and Liyan Ji and Xuan Gao and Jiayin Wang and Tao Liu and Xuefeng Xia and Huan Fang and Yanfang Guan and Xin Yi}, title = {{DELFMUT:} duplex sequencing-oriented depth estimation model for stable detection of low-frequency mutations}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad277}, doi = {10.1093/BIB/BBAD277}, timestamp = {Thu, 09 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/WuSWCJJGWLXFGY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WuXYWKZH23, author = {Sijia Wu and Qiuping Xue and Mengyuan Yang and Yanfei Wang and Pora Kim and Xiaobo Zhou and Liyu Huang}, title = {Genetic control of {RNA} editing in neurodegenerative disease}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad007}, doi = {10.1093/BIB/BBAD007}, timestamp = {Fri, 15 Dec 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/WuXYWKZH23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WuZC23, author = {Kevin E. Wu and James Y. Zou and Howard Chang}, title = {Machine learning modeling of {RNA} structures: methods, challenges and future perspectives}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad210}, doi = {10.1093/BIB/BBAD210}, timestamp = {Sun, 24 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WuZC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WuZYLWYZFWX23, author = {Cuiling Wu and Yiyi Zhang and Zhiwen Ying and Ling Li and Jun Wang and Hui Yu and Mengchen Zhang and Xianzhong Feng and Xinghua Wei and Xiaogang Xu}, title = {A transformer-based genomic prediction method fused with knowledge-guided module}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad438}, doi = {10.1093/BIB/BBAD438}, timestamp = {Wed, 17 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/WuZYLWYZFWX23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/X23, title = {Correction to: siGCD: a web server to explore survival interaction of genes, cells and drugs in human cancers}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac618}, doi = {10.1093/BIB/BBAC618}, timestamp = {Fri, 10 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/X23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/X23a, title = {Correction to: VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad019}, doi = {10.1093/BIB/BBAD019}, timestamp = {Fri, 10 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/X23a.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/X23b, title = {Correction to: \emph{m}CNN-ETC: identifying electron transporters and their functional families by using multiple windows scanning techniques in convolutional neural networks with evolutionary information of protein sequences}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad089}, doi = {10.1093/BIB/BBAD089}, timestamp = {Wed, 19 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/X23b.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/X23c, title = {Correction to: kTWAS: integrating kernel machine with transcriptome-wide association studies improves statistical power and reveals novel genes}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad091}, doi = {10.1093/BIB/BBAD091}, timestamp = {Wed, 19 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/X23c.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/X23d, title = {Correction to: Prediction of transcript structure and concentration using RNA-Seq data}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad055}, doi = {10.1093/BIB/BBAD055}, timestamp = {Wed, 19 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/X23d.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/X23e, title = {Correction to: Molecular persistent spectral image (Mol-PSI) representation for machine learning models in drug design}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad128}, doi = {10.1093/BIB/BBAD128}, timestamp = {Thu, 22 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/X23e.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/X23f, title = {Correction to: Quantum computing algorithms: getting closer to critical problems in computational biology}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad134}, doi = {10.1093/BIB/BBAD134}, timestamp = {Thu, 22 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/X23f.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/X23g, title = {Correction to: DeepFormer: a hybrid network based on convolutional neural network and flow-attention mechanism for identifying the function of {DNA} sequences}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad211}, doi = {10.1093/BIB/BBAD211}, timestamp = {Fri, 22 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/X23g.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/X23h, title = {Correction: Comparison and benchmark of structural variants detected from long read and long-read assembly}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad224}, doi = {10.1093/BIB/BBAD224}, timestamp = {Fri, 22 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/X23h.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/X23i, title = {Correction to: An automatic immunofluorescence pattern classification framework for HEp-2 image based on supervised learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad350}, doi = {10.1093/BIB/BBAD350}, timestamp = {Mon, 23 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/X23i.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/X23j, title = {Correction to: Breaking the barriers of data scarcity in drug-target affinity prediction}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad477}, doi = {10.1093/BIB/BBAD477}, timestamp = {Mon, 01 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/X23j.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/XiaFXPS23, author = {Chun{-}Qiu Xia and Shi{-}Hao Feng and Ying Xia and Xiaoyong Pan and Hong{-}Bin Shen}, title = {Leveraging scaffold information to predict protein-ligand binding affinity with an empirical graph neural network}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac603}, doi = {10.1093/BIB/BBAC603}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/XiaFXPS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/XiaoWDZ23, author = {Kaixuan Xiao and Yu Wang and Kangning Dong and Shihua Zhang}, title = {SmartGate is a spatial metabolomics tool for resolving tissue structures}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad141}, doi = {10.1093/BIB/BBAD141}, timestamp = {Thu, 22 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/XiaoWDZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/XieCLGYLCLC23, author = {Guobo Xie and Rui{-}Bin Chen and Zhiyi Lin and Guosheng Gu and Jun{-}Rui Yu and Zhen{-}Guo Liu and Ji Cui and Lieqing Lin and Lang{-}Cheng Chen}, title = {Predicting lncRNA-disease associations based on combining selective similarity matrix fusion and bidirectional linear neighborhood label propagation}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac595}, doi = {10.1093/BIB/BBAC595}, timestamp = {Tue, 21 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/XieCLGYLCLC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/XieXZLWPJ23, author = {Shijie Xie and Xiaojun Xie and Xin Zhao and Fei Liu and Yiming Wang and Jihui Ping and Zhiwei Ji}, title = {{HNSPPI:} a hybrid computational model combing network and sequence information for predicting protein-protein interaction}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad261}, doi = {10.1093/BIB/BBAD261}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/XieXZLWPJ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/XieZGZ23, author = {Ailin Xie and Ziqiao Zhang and Jihong Guan and Shuigeng Zhou}, title = {Self-supervised learning with chemistry-aware fragmentation for effective molecular property prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad296}, doi = {10.1093/BIB/BBAD296}, timestamp = {Sat, 28 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/XieZGZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/XingZLHD23, author = {Wenxuan Xing and Jie Zhang and Chen Li and Yujia Huo and Gaifang Dong}, title = {iAMP-Attenpred: a novel antimicrobial peptide predictor based on {BERT} feature extraction method and CNN-BiLSTM-Attention combination model}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad443}, doi = {10.1093/BIB/BBAD443}, timestamp = {Mon, 01 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/XingZLHD23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/XuCVLCZ23, author = {Ke Xu and Chinwang Cheong and Werner Pieter Veldsman and Aiping Lyu and William K. Cheung and Lu Zhang}, title = {Accurate and interpretable gene expression imputation on scRNA-seq data using IGSimpute}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad124}, doi = {10.1093/BIB/BBAD124}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/XuCVLCZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
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@article{DBLP:journals/bib/XuLHLLL23, author = {Chao Xu and Runduo Liu and Shuheng Huang and Wenchao Li and Zhe Li and Hai{-}Bin Luo}, title = {3D-SMGE: a pipeline for scaffold-based molecular generation and evaluation}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad327}, doi = {10.1093/BIB/BBAD327}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/XuLHLLL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/XuLLGLSPLIYAS23, author = {Jing Xu and Fuyi Li and Chen Li and Xudong Guo and Cornelia B. Landersdorfer and Hsin{-}Hui Shen and Anton Y. Peleg and Jian Li and Seiya Imoto and Jianhua Yao and Tatsuya Akutsu and Jiangning Song}, title = {iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activities}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad240}, doi = {10.1093/BIB/BBAD240}, timestamp = {Fri, 19 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/XuLLGLSPLIYAS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/XuWWZZJCN23, author = {Wei Xu and Teng Wang and Nan Wang and Haohong Zhang and Yuguo Zha and Lei Ji and Yuwen Chu and Kang Ning}, title = {Artificial intelligence-enabled microbiome-based diagnosis models for a broad spectrum of cancer types}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad178}, doi = {10.1093/BIB/BBAD178}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/XuWWZZJCN23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/XuYWML23, author = {Fanding Xu and Zhiwei Yang and Lizhuo Wang and Deyu Meng and Jiangang Long}, title = {MESPool: Molecular Edge Shrinkage Pooling for hierarchical molecular representation learning and property prediction}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad423}, doi = {10.1093/BIB/BBAD423}, timestamp = {Sat, 13 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/XuYWML23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/XuZLCZ23, author = {Jing Xu and Aidi Zhang and Fang Liu and Liang Chen and Xiujun Zhang}, title = {CIForm as a Transformer-based model for cell-type annotation of large-scale single-cell RNA-seq data}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad195}, doi = {10.1093/BIB/BBAD195}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/XuZLCZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/XuZLWJWLZLSJWRC23, author = {Yiming Xu and Bowen Zheng and Xiaohong Liu and Tao Wu and Jinxiu Ju and Shi{-}jie Wang and Yufan Lian and Hongjun Zhang and Tong Liang and Ye Sang and Rui Jiang and Guangyu Wang and Jie Ren and Ting Chen}, title = {Improving artificial intelligence pipeline for liver malignancy diagnosis using ultrasound images and video frames}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac569}, doi = {10.1093/BIB/BBAC569}, timestamp = {Wed, 08 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/XuZLWJWLZLSJWRC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YanFHW23, author = {Ke Yan and Jiawei Feng and Jing Huang and Hao Wu}, title = {iDRPro-SC: identifying DNA-binding proteins and RNA-binding proteins based on subfunction classifiers}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad251}, doi = {10.1093/BIB/BBAD251}, timestamp = {Mon, 22 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YanFHW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YanLZHZ23, author = {Junyu Yan and Shuai Li and Ying Zhang and Aimin Hao and Qinping Zhao}, title = {ZetaDesign: an end-to-end deep learning method for protein sequence design and side-chain packing}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad257}, doi = {10.1093/BIB/BBAD257}, timestamp = {Tue, 16 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/YanLZHZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YanYCW23, author = {Zi{-}Jun Yan and Chu{-}Ting Yu and Lei Chen and Hong{-}Yang Wang}, title = {Development of a TMErisk model based on immune infiltration in tumour microenvironment to predict prognosis of immune checkpoint inhibitor treatment in hepatocellular carcinoma}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad067}, doi = {10.1093/BIB/BBAD067}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YanYCW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YanYYLZLQ23, author = {Jiaxian Yan and Zhaofeng Ye and Ziyi Yang and Chengqiang Lu and Shengyu Zhang and Qi Liu and Jiezhong Qiu}, title = {Multi-task bioassay pre-training for protein-ligand binding affinity prediction}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad451}, doi = {10.1093/BIB/BBAD451}, timestamp = {Mon, 05 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/YanYYLZLQ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YangBXXWZ23, author = {Maohua Yang and Zonghua Bo and Tao Xu and Bo Xu and Dongdong Wang and Hang Zheng}, title = {Uni-GBSA: an open-source and web-based automatic workflow to perform {MM/GB(PB)SA} calculations for virtual screening}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad218}, doi = {10.1093/BIB/BBAD218}, timestamp = {Sun, 24 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YangBXXWZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YangC23, author = {Lu Yang and Jun Chen}, title = {Benchmarking differential abundance analysis methods for correlated microbiome sequencing data}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac607}, doi = {10.1093/BIB/BBAC607}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/YangC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YangC23a, author = {Bo Yang and Hailin Chen}, title = {Predicting circRNA-drug sensitivity associations by learning multimodal networks using graph auto-encoders and attention mechanism}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac596}, doi = {10.1093/BIB/BBAC596}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/YangC23a.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YangCRMSCT23, author = {Zikun Yang and Basilio Cieza and Dolly Reyes{-}Dumeyer and Rosa Montesinos and Marcio Soto{-}A{\~{n}}ari and Nilton Custodio and Giuseppe Tosto}, title = {A benchmark study on current {GWAS} models in admixed populations}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad437}, doi = {10.1093/BIB/BBAD437}, timestamp = {Sat, 13 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/YangCRMSCT23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YangGCLZW23, author = {Hai Yang and Lipeng Gan and Rui Chen and Dongdong Li and Jing Zhang and Zhe Wang}, title = {From multi-omics data to the cancer druggable gene discovery: a novel machine learning-based approach}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac528}, doi = {10.1093/BIB/BBAC528}, timestamp = {Sat, 18 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/YangGCLZW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YangGZSCZL23, author = {Shuang Yang and Weikang Gong and Tong Zhou and Xiaohan Sun and Lei Chen and Wenxue Zhou and Chunhua Li}, title = {emPDBA: protein-DNA binding affinity prediction by combining features from binding partners and interface learned with ensemble regression model}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad192}, doi = {10.1093/BIB/BBAD192}, timestamp = {Fri, 22 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YangGZSCZL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YangHCYL23, author = {Cheng{-}Hong Yang and Ming{-}Feng Hou and Li{-}Yeh Chuang and Cheng{-}San Yang and Yu{-}Da Lin}, title = {Dimensionality reduction approach for many-objective epistasis analysis}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac512}, doi = {10.1093/BIB/BBAC512}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/YangHCYL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YangLLZXC23, author = {Yongjian Yang and Yu{-}Te Lin and Guanxun Li and Yan Zhong and Qian Xu and James J. Cai}, title = {Interpretable modeling of time-resolved single-cell gene-protein expression with CrossmodalNet}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad342}, doi = {10.1093/BIB/BBAD342}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YangLLZXC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YangLLZZYMKLLP23, author = {Yifan Yang and Haoyuan Liu and Yi Liu and Liyuan Zhou and Xiaoqi Zheng and Rongxian Yue and David L. Mattson and Srividya Kidambi and Mingyu Liang and Pengyuan Liu and Xiaoqing Pan}, title = {\emph{E}-value: a superior alternative to \emph{P}-value and its adjustments in {DNA} methylation studies}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad241}, doi = {10.1093/BIB/BBAD241}, timestamp = {Wed, 04 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YangLLZZYMKLLP23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YangLY23, author = {Yang Yang and Yuwei Lu and Wenying Yan}, title = {A comprehensive review on knowledge graphs for complex diseases}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac543}, doi = {10.1093/BIB/BBAC543}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/YangLY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YangLYLW23, author = {Hai Yang and Yawen Liu and Yijing Yang and Dongdong Li and Zhe Wang}, title = {InDEP: an interpretable machine learning approach to predict cancer driver genes from multi-omics data}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad318}, doi = {10.1093/BIB/BBAD318}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YangLYLW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YangSLXDW23, author = {Minjian Yang and Hanyu Sun and Xue Liu and Xi Xue and Yafeng Deng and Xiaojian Wang}, title = {{CMGN:} a conditional molecular generation net to design target-specific molecules with desired properties}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad185}, doi = {10.1093/BIB/BBAD185}, timestamp = {Fri, 22 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YangSLXDW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YangXZWJJ23, author = {Qi Yang and Zhaochun Xu and Wenyang Zhou and Pingping Wang and Qinghua Jiang and Liran Juan}, title = {An interpretable single-cell {RNA} sequencing data clustering method based on latent Dirichlet allocation}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad199}, doi = {10.1093/BIB/BBAD199}, timestamp = {Sun, 24 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YangXZWJJ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YangYFXZDLLLZLGZLWZ23, author = {Kuo Yang and Yuxia Yang and Shuyue Fan and Jianan Xia and Qiguang Zheng and Xin Dong and Jun Liu and Qiong Liu and Lei Lei and Yingying Zhang and Bing Li and Zhuye Gao and Runshun Zhang and Baoyan Liu and Zhong Wang and Xuezhong Zhou}, title = {DRONet: effectiveness-driven drug repositioning framework using network embedding and ranking learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac518}, doi = {10.1093/BIB/BBAC518}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YangYFXZDLLLZLGZLWZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YangYHCL23, author = {Lifang Yang and Ye Yang and Luqi Huang and Xiuming Cui and Yuan Liu}, title = {From single- to multi-omics: future research trends in medicinal plants}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac485}, doi = {10.1093/BIB/BBAC485}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YangYHCL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YangZWLCLSZ23, author = {Xiaobo Yang and Bei Zhang and Siqi Wang and Ye Lu and Kaixian Chen and Cheng Luo and Aihua Sun and Hao Zhang}, title = {{OTTM:} an automated classification tool for translational drug discovery from omics data}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad301}, doi = {10.1093/BIB/BBAD301}, timestamp = {Wed, 01 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/YangZWLCLSZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YaoZSHL23, author = {Zhou Yao and Wenjing Zhang and Peng Song and Yuxue Hu and Jianxiao Liu}, title = {DeepFormer: a hybrid network based on convolutional neural network and flow-attention mechanism for identifying the function of {DNA} sequences}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad095}, doi = {10.1093/BIB/BBAD095}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YaoZSHL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YeLMSDDFSSX23, author = {Zheng Ye and Shaohao Li and Xue Mi and Baoyi Shao and Zhu Dai and Bo Ding and Songwei Feng and Bo Sun and Yang Shen and Zhongdang Xiao}, title = {STMHCpan, an accurate Star-Transformer-based extensible framework for predicting {MHC} {I} allele binding peptides}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad164}, doi = {10.1093/BIB/BBAD164}, timestamp = {Thu, 22 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YeLMSDDFSSX23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YeungZLK23, author = {Wayland Yeung and Zhongliang Zhou and Sheng Li and Natarajan Kannan}, title = {Alignment-free estimation of sequence conservation for identifying functional sites using protein sequence embeddings}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac599}, doi = {10.1093/BIB/BBAC599}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YeungZLK23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YeungZMGTOSVLLK23, author = {Wayland Yeung and Zhongliang Zhou and Liju Mathew and Nathan Gravel and Rahil Taujale and Brady O'boyle and Mariah Salcedo and Aarya Venkat and William Lanzilotta and Sheng Li and Natarajan Kannan}, title = {Tree visualizations of protein sequence embedding space enable improved functional clustering of diverse protein superfamilies}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac619}, doi = {10.1093/BIB/BBAC619}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YeungZMGTOSVLLK23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YiLCJ23, author = {Huiguang Yi and Yanling Lin and Qing Chang and Wenfei Jin}, title = {A fast and globally optimal solution for RNA-seq quantification}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad298}, doi = {10.1093/BIB/BBAD298}, timestamp = {Sat, 28 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YiLCJ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YiNJ23, author = {Dohun Yi and Jin{-}Wu Nam and Hyobin Jeong}, title = {Toward the functional interpretation of somatic structural variations: bulk- and single-cell approaches}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad297}, doi = {10.1093/BIB/BBAD297}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YiNJ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YinC23, author = {Qingyang Yin and Liang Chen}, title = {CellTICS: an explainable neural network for cell-type identification and interpretation based on single-cell RNA-seq data}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad449}, doi = {10.1093/BIB/BBAD449}, timestamp = {Mon, 01 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/YinC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YinLG23, author = {Zhen{-}Ning Yin and Fei{-}Liao Lai and Feng Gao}, title = {Unveiling human origins of replication using deep learning: accurate prediction and comprehensive analysis}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad432}, doi = {10.1093/BIB/BBAD432}, timestamp = {Sat, 13 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/YinLG23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YoonN23, author = {Sang{-}Ho Yoon and Jin{-}Wu Nam}, title = {Clustering malignant cell states using universally variable genes}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad460}, doi = {10.1093/BIB/BBAD460}, timestamp = {Sat, 13 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/YoonN23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YorkiSCWLMEW23, author = {Sosie Yorki and Terrance Shea and Christina Cuomo and Bruce J. Walker and Regina C. Larocque and Abigail L. Manson and Ashlee M. Earl and Colin J. Worby}, title = {Comparison of long- and short-read metagenomic assembly for low-abundance species and resistance genes}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad050}, doi = {10.1093/BIB/BBAD050}, timestamp = {Mon, 01 May 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YorkiSCWLMEW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YousefiYTKNBGBSG23, author = {Niloofar Yousefi and Mehdi Yazdani{-}Jahromi and Aida Tayebi and Elayaraja Kolanthai and Craig J. Neal and Tanumoy Banerjee and Agnivo Gosai and Ganesh Balasubramanian and Sudipta Seal and {\"{O}}zlem {\"{O}}zmen Garibay}, title = {BindingSite-AugmentedDTA: enabling a next-generation pipeline for interpretable prediction models in drug repurposing}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad136}, doi = {10.1093/BIB/BBAD136}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YousefiYTKNBGBSG23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YuAS23, author = {Runzhou Yu and Syed Muhammad Umer Abdullah and Yanni Sun}, title = {HMMPolish: a coding region polishing tool for TGS-sequenced {RNA} viruses}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad264}, doi = {10.1093/BIB/BBAD264}, timestamp = {Sat, 28 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YuAS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YuDGLZY23, author = {Yutong Yu and Pengju Ding and Hongli Gao and Guozhu Liu and Fa Zhang and Bin Yu}, title = {Cooperation of local features and global representations by a dual-branch network for transcription factor binding sites prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad036}, doi = {10.1093/BIB/BBAD036}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YuDGLZY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YuL23, author = {Han Yu and Xiaozhou Luo}, title = {{IPPF-FE:} an integrated peptide and protein function prediction framework based on fused features and ensemble models}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac476}, doi = {10.1093/BIB/BBAC476}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/YuL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YuLCLZLJZZKL23, author = {Kai Yu and Zekun Liu and Haoyang Cheng and Shihua Li and Qingfeng Zhang and Jia Liu and Huai{-}Qiang Ju and Zhixiang Zuo and Qi Zhao and Shiyang Kang and Zexian Liu}, title = {dSCOPE: a software to detect sequences critical for liquid-liquid phase separation}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac550}, doi = {10.1093/BIB/BBAC550}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/YuLCLZLJZZKL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YuLDSGS23, author = {Hui Yu and Kangkang Li and Wenmin Dong and Shuanghong Song and Chen Gao and Jianyu Shi}, title = {Attention-based cross domain graph neural network for prediction of drug-drug interactions}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad155}, doi = {10.1093/BIB/BBAD155}, timestamp = {Sun, 22 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YuLDSGS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YuLSD23, author = {Zhenhua Yu and Furui Liu and Fangyuan Shi and Fang Du}, title = {rcCAE: a convolutional autoencoder method for detecting intra-tumor heterogeneity and single-cell copy number alterations}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad108}, doi = {10.1093/BIB/BBAD108}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YuLSD23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YuanCYLC23, author = {Qitong Yuan and Keyi Chen and Yimin Yu and Nguyen{-}Quoc{-}Khanh Le and Matthew Chin Heng Chua}, title = {Prediction of anticancer peptides based on an ensemble model of deep learning and machine learning using ordinal positional encoding}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac630}, doi = {10.1093/BIB/BBAC630}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/YuanCYLC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YuanLLNK23, author = {Le Yuan and Hongzhong Lu and Feiran Li and Jens Nielsen and Eduard J. Kerkhoven}, title = {HGTphyloDetect: facilitating the identification and phylogenetic analysis of horizontal gene transfer}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad035}, doi = {10.1093/BIB/BBAD035}, timestamp = {Sat, 19 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YuanLLNK23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YuanWWY23, author = {Guo{-}Hua Yuan and Ying Wang and Guang{-}Zhong Wang and Li Yang}, title = {RNAlight: a machine learning model to identify nucleotide features determining {RNA} subcellular localization}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac509}, doi = {10.1093/BIB/BBAC509}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/YuanWWY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YuanXXZY23, author = {Qianmu Yuan and Junjie Xie and Jiancong Xie and Huiying Zhao and Yuedong Yang}, title = {Fast and accurate protein function prediction from sequence through pretrained language model and homology-based label diffusion}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad117}, doi = {10.1093/BIB/BBAD117}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YuanXXZY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YueLHLH23, author = {Yang Yue and Yongxuan Liu and Luoying Hao and Huangshu Lei and Shan He}, title = {Improving therapeutic synergy score predictions with adverse effects using multi-task heterogeneous network learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac564}, doi = {10.1093/BIB/BBAC564}, timestamp = {Mon, 09 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/YueLHLH23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/YueLWLTH23, author = {Yang Yue and Shu Li and Lingling Wang and Huanxiang Liu and Henry H. Y. Tong and Shan He}, title = {MpbPPI: a multi-task pre-training-based equivariant approach for the prediction of the effect of amino acid mutations on protein-protein interactions}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad310}, doi = {10.1093/BIB/BBAD310}, timestamp = {Sun, 12 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/YueLWLTH23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZengHZL23, author = {Yanping Zeng and Yongxin He and Ruiqing Zheng and Min Li}, title = {Inferring single-cell gene regulatory network by non-redundant mutual information}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad326}, doi = {10.1093/BIB/BBAD326}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZengHZL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZengYLCPLYY23, author = {Yuansong Zeng and Rui Yin and Mai Luo and Jianing Chen and Zixiang Pan and Yutong Lu and Weijiang Yu and Yuedong Yang}, title = {Identifying spatial domain by adapting transcriptomics with histology through contrastive learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad048}, doi = {10.1093/BIB/BBAD048}, timestamp = {Mon, 01 May 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZengYLCPLYY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhaiCD23, author = {Yuyao Zhai and Liang Chen and Minghua Deng}, title = {scGAD: a new task and end-to-end framework for generalized cell type annotation and discovery}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad045}, doi = {10.1093/BIB/BBAD045}, timestamp = {Mon, 01 May 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhaiCD23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhaiGWMS23, author = {Song Zhai and Bin Guo and Baolin Wu and Devan V. Mehrotra and Judong Shen}, title = {Integrating multiple traits for improving polygenic risk prediction in disease and pharmacogenomics {GWAS}}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad181}, doi = {10.1093/BIB/BBAD181}, timestamp = {Sun, 24 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhaiGWMS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhaiHSZ23, author = {Weiqi Zhai and Xiaodi Huang and Nan Shen and Shanfeng Zhu}, title = {Phen2Disease: a phenotype-driven model for disease and gene prioritization by bidirectional maximum matching semantic similarities}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad172}, doi = {10.1093/BIB/BBAD172}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhaiHSZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhanGCM23, author = {Yongkang Zhan and Jifeng Guo and C. L. Philip Chen and Xian{-}Bing Meng}, title = {iBT-Net: an incremental broad transformer network for cancer drug response prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad256}, doi = {10.1093/BIB/BBAD256}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhanGCM23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangCL23, author = {Zheng Zhang and Shengquan Chen and Zhixiang Lin}, title = {RefTM: reference-guided topic modeling of single-cell chromatin accessibility data}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac540}, doi = {10.1093/BIB/BBAC540}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangCL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangCL23a, author = {Qiyiwen Zhang and Changgee Chang and Qi Long}, title = {Robust knowledge-guided biclustering for multi-omics data}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad446}, doi = {10.1093/BIB/BBAD446}, timestamp = {Mon, 05 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhangCL23a.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangCYZCN23, author = {Haohong Zhang and Hui Chong and Qingyang Yu and Yuguo Zha and Mingyue Cheng and Kang Ning}, title = {Tracing human life trajectory using gut microbial communities by context-aware deep learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac629}, doi = {10.1093/BIB/BBAC629}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhangCYZCN23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangGLNGY23, author = {Mingxiang Zhang and Hongli Gao and Xin Liao and Baoxing Ning and Haiming Gu and Bin Yu}, title = {{DBGRU-SE:} predicting drug-drug interactions based on double BiGRU and squeeze-and-excitation attention mechanism}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad184}, doi = {10.1093/BIB/BBAD184}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangGLNGY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangGYWLLL23, author = {Ge Zhang and Zhijie Gao and Chaokun Yan and Jianlin Wang and Wenjuan Liang and Junwei Luo and Huimin Luo}, title = {KGANSynergy: knowledge graph attention network for drug synergy prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad167}, doi = {10.1093/BIB/BBAD167}, timestamp = {Fri, 07 Jul 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangGYWLLL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangJWYLWTZSL23, author = {Feng Zhang and Huiyuan Jiao and Yihao Wang and Chen Yang and Linying Li and Zhiming Wang and Ran Tong and Junmei Zhou and Jianfeng Shen and Lingjie Li}, title = {InferLoop: leveraging single-cell chromatin accessibility for the signal of chromatin loop}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad166}, doi = {10.1093/BIB/BBAD166}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangJWYLWTZSL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangJZXWLLLLLL23, author = {Wei Zhang and Jia Ju and Yong Zhou and Teng Xiong and Mengyao Wang and Chaohui Li and Shixin Lu and Zefeng Lu and Liya Lin and Xiao Liu and Shuaicheng Li}, title = {IMperm: a fast and comprehensive IMmune Paired-End Reads Merger for sequencing data}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad080}, doi = {10.1093/BIB/BBAD080}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangJZXWLLLLLL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangLBFUI23, author = {Yao{-}zhong Zhang and Yunjie Liu and Zeheng Bai and Kosuke Fujimoto and Satoshi Uematsu and Seiya Imoto}, title = {Zero-shot-capable identification of phage-host relationships with whole-genome sequence representation by contrastive learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad239}, doi = {10.1093/BIB/BBAD239}, timestamp = {Sat, 28 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangLBFUI23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangLD23, author = {Ying{-}Ying Zhang and De{-}Min Liang and Pu{-}Feng Du}, title = {iEssLnc: quantitative estimation of lncRNA gene essentialities with meta-path-guided random walks on the lncRNA-protein interaction network}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad097}, doi = {10.1093/BIB/BBAD097}, timestamp = {Fri, 07 Jul 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangLD23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangLDD23, author = {Guishan Zhang and Ye Luo and Xianhua Dai and Zhiming Dai}, title = {Benchmarking deep learning methods for predicting CRISPR/Cas9 sgRNA on- and off-target activities}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad333}, doi = {10.1093/BIB/BBAD333}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangLDD23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangLHWS23, author = {Chuanchao Zhang and Xinxing Li and Wendong Huang and Lequn Wang and Qianqian Shi}, title = {Spatially aware self-representation learning for tissue structure characterization and spatial functional genes identification}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad197}, doi = {10.1093/BIB/BBAD197}, timestamp = {Sun, 24 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangLHWS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangLLZZXZ23, author = {Hongning Zhang and Mingkun Lu and Gaole Lin and Lingyan Zheng and Wei Zhang and Zhijian Xu and Feng Zhu}, title = {SoCube: an innovative end-to-end doublet detection algorithm for analyzing scRNA-seq data}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad104}, doi = {10.1093/BIB/BBAD104}, timestamp = {Wed, 07 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangLLZZXZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangLSXW23, author = {Tianjiao Zhang and Liangyu Li and Hailong Sun and Dali Xu and Guohua Wang}, title = {DeepICSH: a complex deep learning framework for identifying cell-specific silencers and their strength from the human genome}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad316}, doi = {10.1093/BIB/BBAD316}, timestamp = {Thu, 09 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhangLSXW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangLZLW23, author = {Lishen Zhang and Chengqian Lu and Min Zeng and Yaohang Li and Jianxin Wang}, title = {{CRMSS:} predicting circRNA-RBP binding sites based on multi-scale characterizing sequence and structure features}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac530}, doi = {10.1093/BIB/BBAC530}, timestamp = {Sun, 12 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhangLZLW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangLZZ23, author = {Hui Zhang and Hongjia Li and Fa Zhang and Ping Zhu}, title = {A strategy combining denoising and cryo-EM single particle analysis}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad148}, doi = {10.1093/BIB/BBAD148}, timestamp = {Thu, 22 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangLZZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangMY23, author = {Jiawei Zhang and Wang Ma and Hui Yao}, title = {Accurate TCR-pMHC interaction prediction using a BERT-based transfer learning method}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad436}, doi = {10.1093/BIB/BBAD436}, timestamp = {Mon, 01 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhangMY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangSWDKLHP23, author = {Xujun Zhang and Chao Shen and Tianyue Wang and Yafeng Deng and Yu Kang and Dan Li and Tingjun Hou and Peichen Pan}, title = {{ML-PLIC:} a web platform for characterizing protein-ligand interactions and developing machine learning-based scoring functions}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad295}, doi = {10.1093/BIB/BBAD295}, timestamp = {Tue, 16 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangSWDKLHP23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangWWMC23, author = {Ran Zhang and Zhanjie Wang and Xuezhi Wang and Zhen Meng and Wenjuan Cui}, title = {{MHTAN-DTI:} Metapath-based hierarchical transformer and attention network for drug-target interaction prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad079}, doi = {10.1093/BIB/BBAD079}, timestamp = {Tue, 30 May 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangWWMC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangWWMCZ23, author = {Ran Zhang and Xuezhi Wang and Pengfei Wang and Zhen Meng and Wenjuan Cui and Yuanchun Zhou}, title = {{HTCL-DDI:} a hierarchical triple-view contrastive learning framework for drug-drug interaction prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad324}, doi = {10.1093/BIB/BBAD324}, timestamp = {Sat, 28 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangWWMCZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangWYZTLJKSCMW23, author = {Xin Zhang and Lesong Wei and Xiucai Ye and Kai Zhang and Saisai Teng and Zhongshen Li and Junru Jin and Min Jae Kim and Tetsuya Sakurai and Lizhen Cui and Balachandran Manavalan and Leyi Wei}, title = {SiameseCPP: a sequence-based Siamese network to predict cell-penetrating peptides by contrastive learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac545}, doi = {10.1093/BIB/BBAC545}, timestamp = {Sun, 12 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhangWYZTLJKSCMW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangXS23, author = {Pei{-}Dong Zhang and Chun{-}Qiu Xia and Hong{-}Bin Shen}, title = {High-accuracy protein model quality assessment using attention graph neural networks}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac614}, doi = {10.1093/BIB/BBAC614}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangXS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangXWCZ23, author = {Wentao Zhang and Yanchao Xu and Aowen Wang and Gang Chen and Junbo Zhao}, title = {Fuse feeds as one: cross-modal framework for general identification of AMPs}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad336}, doi = {10.1093/BIB/BBAD336}, timestamp = {Fri, 21 Jun 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangXWCZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangXWLWL23, author = {Ze{-}Qun Zhang and Junlin Xu and Yanan Wu and Nian{-}Nian Liu and Ying{-}Long Wang and Ying Liang}, title = {CapsNet-LDA: predicting lncRNA-disease associations using attention mechanism and capsule network based on multi-view data}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac531}, doi = {10.1093/BIB/BBAC531}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangXWLWL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangYLLYZL23, author = {Siqin Zhang and Kuo Yang and Zhenhong Liu and Xinxing Lai and Zhen Yang and Jianyang Zeng and Shao Li}, title = {DrugAI: a multi-view deep learning model for predicting drug-target activating/inhibiting mechanisms}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac526}, doi = {10.1093/BIB/BBAC526}, timestamp = {Wed, 02 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangYLLYZL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangYTAZC23, author = {Chengming Zhang and Yiwen Yang and Shijie Tang and Kazuyuki Aihara and Chuanchao Zhang and Luonan Chen}, title = {Contrastively generative self-expression model for single-cell and spatial multimodal data}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad265}, doi = {10.1093/BIB/BBAD265}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangYTAZC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangYVFZ23, author = {Zhenmiao Zhang and Chao Yang and Werner Pieter Veldsman and Xiaodong Fang and Lu Zhang}, title = {Benchmarking genome assembly methods on metagenomic sequencing data}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad087}, doi = {10.1093/BIB/BBAD087}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangYVFZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangZXL23, author = {Tong Zhang and Shao{-}Wu Zhang and Ming{-}Yu Xie and Yan Li}, title = {A novel heterophilic graph diffusion convolutional network for identifying cancer driver genes}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad137}, doi = {10.1093/BIB/BBAD137}, timestamp = {Thu, 22 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangZXL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhaoCCQ23, author = {Yuanchun Zhao and Xingqi Chen and Jiajia Chen and Xin Qi}, title = {Decoding Connectivity Map-based drug repurposing for oncotherapy}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad142}, doi = {10.1093/BIB/BBAD142}, timestamp = {Thu, 22 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhaoCCQ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhaoCJCW23, author = {Tingting Zhao and Lihua Cao and Jiafu Ji and David K. Chang and Jianmin Wu}, title = {ReProMSig: an integrative platform for development and application of reproducible multivariable models for cancer prognosis supporting guideline-based transparent reporting}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad267}, doi = {10.1093/BIB/BBAD267}, timestamp = {Wed, 01 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhaoCJCW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhaoCLFHZ23, author = {Ming{-}Xiao Zhao and Qiang Chen and Fulai Li and Songsen Fu and Biling Huang and Yufen Zhao}, title = {Protein phosphorylation database and prediction tools}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad090}, doi = {10.1093/BIB/BBAD090}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhaoCLFHZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhaoDYHZY23, author = {Hang Zhao and Pin{-}yuan Dai and Xiao{-}jin Yu and Jieyu He and Chao Zhao and Li{-}hong Yin}, title = {Evaluation of graphical models for multi-group metabolomics data}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad096}, doi = {10.1093/BIB/BBAD096}, timestamp = {Fri, 07 Jul 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhaoDYHZY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhaoFZN23, author = {Zhangxin Zhao and Qianjin Feng and Yu Zhang and Zhenyuan Ning}, title = {Adaptive risk-aware sharable and individual subspace learning for cancer survival analysis with multi-modality data}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac489}, doi = {10.1093/BIB/BBAC489}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhaoFZN23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhaoHXZZHYWDSY23, author = {Yu Zhao and Bing He and Zhimeng Xu and Yidan Zhang and Xuan Zhao and Zhi{-}An Huang and Fan Yang and Liang Wang and Lei Duan and Jiangning Song and Jianhua Yao}, title = {Interpretable artificial intelligence model for accurate identification of medical conditions using immune repertoire}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac555}, doi = {10.1093/BIB/BBAC555}, timestamp = {Fri, 15 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhaoHXZZHYWDSY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhaoQCQBWLWZZ23, author = {Lianhe Zhao and Xiaoning Qi and Yang Chen and Yixuan Qiao and Dechao Bu and Yang Wu and Yufan Luo and Sheng Wang and Rui Zhang and Yi Zhao}, title = {Biological knowledge graph-guided investigation of immune therapy response in cancer with graph neural network}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad023}, doi = {10.1093/BIB/BBAD023}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhaoQCQBWLWZZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhaoSSZS23, author = {Jingxuan Zhao and Jianqiang Sun and Stella C. Shuai and Qi Zhao and Jianwei Shuai}, title = {Predicting potential interactions between lncRNAs and proteins via combined graph auto-encoder methods}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac527}, doi = {10.1093/BIB/BBAC527}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhaoSSZS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhaoSZMXQYHY23, author = {Yu Zhao and Xiaona Su and Weitong Zhang and Sijie Mai and Zhimeng Xu and Chenchen Qin and Rongshan Yu and Bing He and Jianhua Yao}, title = {{SC-AIR-BERT:} a pre-trained single-cell model for predicting the antigen-binding specificity of the adaptive immune receptor}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad191}, doi = {10.1093/BIB/BBAD191}, timestamp = {Fri, 15 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhaoSZMXQYHY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhaoWCGLL23, author = {Yanpeng Zhao and Jingjing Wang and Fubin Chang and Weikang Gong and Yang Liu and Chunhua Li}, title = {Identification of metal ion-binding sites in {RNA} structures using deep learning method}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad049}, doi = {10.1093/BIB/BBAD049}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhaoWCGLL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhaoWH23, author = {Yanping Zhao and Kui Wang and Gang Hu}, title = {{DIST:} spatial transcriptomics enhancement using deep learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad013}, doi = {10.1093/BIB/BBAD013}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhaoWH23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhaoWZY23, author = {Xiaosa Zhao and Jun Wu and Xiaowei Zhao and Minghao Yin}, title = {Multi-view contrastive heterogeneous graph attention network for lncRNA-disease association prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac548}, doi = {10.1093/BIB/BBAC548}, timestamp = {Mon, 05 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhaoWZY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhaoYSJSHH23, author = {Weizhong Zhao and Xueling Yuan and Xianjun Shen and Xingpeng Jiang and Chuan Shi and Tingting He and Xiaohua Hu}, title = {Improving drug-drug interactions prediction with interpretability via meta-path-based information fusion}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad041}, doi = {10.1093/BIB/BBAD041}, timestamp = {Wed, 27 Dec 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhaoYSJSHH23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhaoYZYZ23, author = {Xingzhong Zhao and Anyi Yang and Zi{-}Chao Zhang and Yucheng T. Yang and Xing{-}Ming Zhao}, title = {Deciphering the genetic architecture of human brain structure and function: a brief survey on recent advances of neuroimaging genomics}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad060}, doi = {10.1093/BIB/BBAD060}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhaoYZYZ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhaoZDF23, author = {Tingting Zhao and Guangyu Zhu and Harsh Vardhan Dubey and Patrick Flaherty}, title = {Identification of significant gene expression changes in multiple perturbation experiments using knockoffs}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad084}, doi = {10.1093/BIB/BBAD084}, timestamp = {Mon, 05 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhaoZDF23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhaoZSLCXW23, author = {Jing Zhao and Bowen Zhao and Xiaotong Song and Chujun Lyu and Weizhi Chen and Yi Xiong and Dong{-}Qing Wei}, title = {Subtype-DCC: decoupled contrastive clustering method for cancer subtype identification based on multi-omics data}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad025}, doi = {10.1093/BIB/BBAD025}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhaoZSLCXW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhengHD23, author = {Rongtao Zheng and Zhijian Huang and Lei Deng}, title = {Large-scale predicting protein functions through heterogeneous feature fusion}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad243}, doi = {10.1093/BIB/BBAD243}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhengHD23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhengTWYLL23, author = {Zixi Zheng and Yanyan Tan and Hong Wang and Shengpeng Yu and Tianyu Liu and Cheng Liang}, title = {CasANGCL: pre-training and fine-tuning model based on cascaded attention network and graph contrastive learning for molecular property prediction}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac566}, doi = {10.1093/BIB/BBAC566}, timestamp = {Thu, 02 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhengTWYLL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhengYD23, author = {Jiahao Zheng and Yuedong Yang and Zhiming Dai}, title = {Subgraph extraction and graph representation learning for single cell Hi-C imputation and clustering}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad379}, doi = {10.1093/BIB/BBAD379}, timestamp = {Mon, 05 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhengYD23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhengZWYJLL23, author = {Kai Zheng and Xin{-}Lu Zhang and Lei Wang and Zhu{-}Hong You and Bo{-}Ya Ji and Xiao Liang and Zheng{-}Wei Li}, title = {{SPRDA:} a link prediction approach based on the structural perturbation to infer disease-associated Piwi-interacting RNAs}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac498}, doi = {10.1093/BIB/BBAC498}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhengZWYJLL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhongCLMS23, author = {Wujuan Zhong and Aparna Chhibber and Lan Luo and Devan V. Mehrotra and Judong Shen}, title = {A fast and powerful linear mixed model approach for genotype-environment interaction tests in large-scale {GWAS}}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac547}, doi = {10.1093/BIB/BBAC547}, timestamp = {Sat, 25 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhongCLMS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhongDLLC23, author = {Jiayuan Zhong and Dandan Ding and Juntan Liu and Rui Liu and Pei Chen}, title = {{SPNE:} sample-perturbed network entropy for revealing critical states of complex biological systems}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad028}, doi = {10.1093/BIB/BBAD028}, timestamp = {Mon, 01 May 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhongDLLC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhongWLZZG23, author = {Tengwei Zhong and Wenqing Wang and Houyan Liu and Maolin Zeng and Xinyu Zhao and Zhiyun Guo}, title = {eccDNA Atlas: a comprehensive resource of eccDNA catalog}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad037}, doi = {10.1093/BIB/BBAD037}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhongWLZZG23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhouDFJHZYCYZW23, author = {Bailing Zhou and Maolin Ding and Jing Feng and Baohua Ji and Pingping Huang and Junye Zhang and Xue Yu and Zanxia Cao and Yuedong Yang and Yaoqi Zhou and Jihua Wang}, title = {EVlncRNA-Dpred: improved prediction of experimentally validated lncRNAs by deep learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac583}, doi = {10.1093/BIB/BBAC583}, timestamp = {Sat, 13 May 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhouDFJHZYCYZW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhouJY23, author = {Yuting Zhou and Yongquan Jiang and Yan Yang}, title = {{AGAT-PPIS:} a novel protein-protein interaction site predictor based on augmented graph attention network with initial residual and identity mapping}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad122}, doi = {10.1093/BIB/BBAD122}, timestamp = {Sat, 20 Apr 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhouJY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhouST23, author = {Jiayin Zhou and Wen Song and Qichao Tu}, title = {To assemble or not to assemble: metagenomic profiling of microbially mediated biogeochemical pathways in complex communities}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac594}, doi = {10.1093/BIB/BBAC594}, timestamp = {Mon, 28 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhouST23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhouTS23, author = {Haiwei Zhou and Wenxi Tan and Shao{-}Ping Shi}, title = {DeepGpgs: a novel deep learning framework for predicting arginine methylation sites combined with Gaussian prior and gated self-attention mechanism}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad018}, doi = {10.1093/BIB/BBAD018}, timestamp = {Sat, 29 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhouTS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhouYYYQG23, author = {Zhi{-}Jian Zhou and Chen{-}Hui Yang and Sheng{-}Bao Ye and Xiao{-}Wei Yu and Ye Qiu and Xing{-}Yi Ge}, title = {VirusRecom: an information-theory-based method for recombination detection of viral lineages and its application on SARS-CoV-2}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac513}, doi = {10.1093/BIB/BBAC513}, timestamp = {Tue, 28 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhouYYYQG23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhouZLZJ23, author = {Shengming Zhou and Yetong Zhou and Tian Liu and Jia Zheng and Cangzhi Jia}, title = {PredLLPS{\_}PSSM: a novel predictor for liquid-liquid protein separation identification based on evolutionary information and a deep neural network}, journal = {Briefings Bioinform.}, volume = {24}, number = {5}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad299}, doi = {10.1093/BIB/BBAD299}, timestamp = {Fri, 27 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhouZLZJ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhuBXX23, author = {Xi{-}Liang Zhu and Lin{-}Xia Bao and Min{-}Qi Xue and Ying{-}Ying Xu}, title = {Automatic recognition of protein subcellular location patterns in single cells from immunofluorescence images based on deep learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac609}, doi = {10.1093/BIB/BBAC609}, timestamp = {Tue, 21 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhuBXX23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhuDDZMLHL23, author = {Fei Zhu and Lei Deng and Yuhao Dai and Guangyu Zhang and Fanwang Meng and Cheng Luo and Guang Hu and Zhongjie Liang}, title = {{PPICT:} an integrated deep neural network for predicting inter-protein {PTM} cross-talk}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad052}, doi = {10.1093/BIB/BBAD052}, timestamp = {Mon, 01 May 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhuDDZMLHL23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhuLGWCWSJ23, author = {Yan Zhu and Fuyi Li and Xudong Guo and Xiaoyu Wang and Lachlan J. M. Coin and Geoffrey I. Webb and Jiangning Song and Cangzhi Jia}, title = {{TIMER} is a Siamese neural network-based framework for identifying both general and species-specific bacterial promoters}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad209}, doi = {10.1093/BIB/BBAD209}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhuLGWCWSJ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhuLTLZWC23, author = {Junjie Zhu and Zhengxin Li and Haowei Tong and Zhouyu Lu and Ningjie Zhang and Ting Wei and Hai{-}Feng Chen}, title = {Phanto-IDP: compact model for precise intrinsically disordered protein backbone generation and enhanced sampling}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad429}, doi = {10.1093/BIB/BBAD429}, timestamp = {Sat, 13 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhuLTLZWC23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhuLW23, author = {Hao Zhu and Tong Liu and Zheng Wang}, title = {scHiMe: predicting single-cell {DNA} methylation levels based on single-cell Hi-C data}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad223}, doi = {10.1093/BIB/BBAD223}, timestamp = {Fri, 22 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhuLW23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZouLSXWWSWXZY23, author = {Min Zou and Honghao Li and Dongqing Su and Yuqiang Xiong and Haodong Wei and Shiyuan Wang and Hongmei Sun and Tao Wang and Qilemuge Xi and Yongchun Zuo and Lei Yang}, title = {Integrating somatic mutation profiles with structural deep clustering network for metabolic stratification in pancreatic cancer: a comprehensive analysis of prognostic and genomic landscapes}, journal = {Briefings Bioinform.}, volume = {25}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad430}, doi = {10.1093/BIB/BBAD430}, timestamp = {Sat, 13 Jan 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZouLSXWWSWXZY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AbeysingheYBZC22, author = {Rashmie Abeysinghe and Yuntao Yang and Mason Bartels and W. Jim Zheng and Licong Cui}, title = {An evidence-based lexical pattern approach for quality assurance of Gene Ontology relations}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac122}, doi = {10.1093/BIB/BBAC122}, timestamp = {Tue, 16 Aug 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/AbeysingheYBZC22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AdamowiczMBB22, author = {Klaudia Adamowicz and Andreas Maier and Jan Baumbach and David B. Blumenthal}, title = {Online \emph{in silico} validation of disease and gene sets, clusterings or subnetworks with {DIGEST}}, journal = {Briefings Bioinform.}, volume = {23}, number = {4}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac247}, doi = {10.1093/BIB/BBAC247}, timestamp = {Tue, 21 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/AdamowiczMBB22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AgapitoPNJ22, author = {Giuseppe Agapito and Chiara Pastrello and Yun Niu and Igor Jurisica}, title = {Pathway integration and annotation: building a puzzle with non-matching pieces and no reference picture}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac368}, doi = {10.1093/BIB/BBAC368}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/AgapitoPNJ22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AggarwalRKDY22, author = {Suruchi Aggarwal and Anurag Raj and Dhirendra Kumar and Debasis Dash and Amit Kumar Yadav}, title = {False discovery rate: the Achilles' heel of proteogenomics}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac163}, doi = {10.1093/BIB/BBAC163}, timestamp = {Tue, 18 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/AggarwalRKDY22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AhmedCWDSKLSP22, author = {Talal Ahmed and Mark A. Carty and Stephane Wenric and Jonathan R. Dry and Ameen A. Salahudeen and Aly A. Khan and Eric Lefkofsky and Martin C. Stumpe and Raphael Pelossof}, title = {Privacy preserving validation for multiomic prediction models}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac110}, doi = {10.1093/BIB/BBAC110}, timestamp = {Tue, 16 Aug 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/AhmedCWDSKLSP22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AlghamdiAAUK22, author = {Wajdi Alghamdi and Muhammad Attique and Ebraheem Alzahrani and Malik Zaka Ullah and Yaser Daanial Khan}, title = {LBCEPred: a machine learning model to predict linear B-cell epitopes}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac035}, doi = {10.1093/BIB/BBAC035}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/AlghamdiAAUK22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AlsaffarHMS22, author = {Muhalb M. Alsaffar and Mohammad Hasan and Gavin P. McStay and Mohamed Sedky}, title = {Digital {DNA} lifecycle security and privacy: an overview}, journal = {Briefings Bioinform.}, volume = {23}, number = {2}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab607}, doi = {10.1093/BIB/BBAB607}, timestamp = {Mon, 28 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/AlsaffarHMS22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AmerifarNG22, author = {Sare Amerifar and Mohammad Norouzi and Mahmoud Ghandi}, title = {A tool for feature extraction from biological sequences}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac108}, doi = {10.1093/BIB/BBAC108}, timestamp = {Thu, 20 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/AmerifarNG22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AnCYLG22, author = {Xin An and Xi Chen and Daiyao Yi and Hongyang Li and Yuanfang Guan}, title = {Representation of molecules for drug response prediction}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab393}, doi = {10.1093/BIB/BBAB393}, timestamp = {Tue, 15 Mar 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/AnCYLG22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AnEYP22, author = {Hyunsu An and Minho Eun and Jawoon Yi and Jihwan Park}, title = {{CRESSP:} a comprehensive pipeline for prediction of immunopathogenic SARS-CoV-2 epitopes using structural properties of proteins}, journal = {Briefings Bioinform.}, volume = {23}, number = {2}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac056}, doi = {10.1093/BIB/BBAC056}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/AnEYP22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AnchangMXACHPML22, author = {Benedict Anchang and Raul Mendez{-}Giraldez and Xiaojiang Xu and Trevor K. Archer and Qing Chen and Guang Hu and Sylvia K. Plevritis and Alison Anne Motsinger{-}Reif and Jian{-}Liang Li}, title = {Visualization, benchmarking and characterization of nested single-cell heterogeneity as dynamic forest mixtures}, journal = {Briefings Bioinform.}, volume = {23}, number = {2}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac017}, doi = {10.1093/BIB/BBAC017}, timestamp = {Mon, 28 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/AnchangMXACHPML22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AndradesM22, author = {Renan Andrades and Mariana Recamonde Mendoza}, title = {Machine learning methods for prediction of cancer driver genes: a survey paper}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac062}, doi = {10.1093/BIB/BBAC062}, timestamp = {Tue, 31 May 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/AndradesM22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AoZY22, author = {Chunyan Ao and Quan Zou and Liang Yu}, title = {NmRF: identification of multispecies {RNA} 2'-O-methylation modification sites from {RNA} sequences}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab480}, doi = {10.1093/BIB/BBAB480}, timestamp = {Tue, 15 Mar 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/AoZY22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ArendBMKLBBL22, author = {Lis Arend and Judith Bernett and Quirin Manz and Melissa Klug and Olga Lazareva and Jan Baumbach and Dario Bongiovanni and Markus List}, title = {A systematic comparison of novel and existing differential analysis methods for CyTOF data}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab471}, doi = {10.1093/BIB/BBAB471}, timestamp = {Mon, 05 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ArendBMKLBBL22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AromolaranAIO22, author = {Olufemi Aromolaran and Damilare Aromolaran and Itunuoluwa Isewon and Jelili Oyelade}, title = {Corrigendum to: Machine learning approach to gene essentiality prediction: a review}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab419}, doi = {10.1093/BIB/BBAB419}, timestamp = {Mon, 05 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/AromolaranAIO22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/AyyalaLO22, author = {Deepak Nag Ayyala and Jianan Lin and Zhengqing Ouyang}, title = {Differential {RNA} methylation using multivariate statistical methods}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab309}, doi = {10.1093/BIB/BBAB309}, timestamp = {Wed, 23 Feb 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/AyyalaLO22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BaiTAX22, author = {Jun Bai and Renbo Tan and Zheng An and Ying Xu}, title = {Quantitative estimation of intracellular oxidative stress in human tissues}, journal = {Briefings Bioinform.}, volume = {23}, number = {4}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac206}, doi = {10.1093/BIB/BBAC206}, timestamp = {Mon, 08 Aug 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BaiTAX22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/Balague-DobonCG22, author = {Laura Balagu{\'{e}}{-}Dob{\'{o}}n and Alejandro C{\'{a}}ceres and Juan R. Gonz{\'{a}}lez}, title = {Fully exploiting {SNP} arrays: a systematic review on the tools to extract underlying genomic structure}, journal = {Briefings Bioinform.}, volume = {23}, number = {2}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac043}, doi = {10.1093/BIB/BBAC043}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/Balague-DobonCG22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BaoLYZQZ22, author = {Siqi Bao and Ke Li and Congcong Yan and Zicheng Zhang and Jia Qu and Meng Zhou}, title = {Deep learning-based advances and applications for single-cell RNA-sequencing data analysis}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab473}, doi = {10.1093/BIB/BBAB473}, timestamp = {Tue, 15 Mar 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/BaoLYZQZ22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BartasVBPCBSBP22, author = {Martin Bartas and Adriana Voln{\'{a}} and Christopher A. Beaudoin and Ebbe Toftgaard Poulsen and Jir{\'{\i}} Cerven and V{\'{a}}clav Br{\'{a}}zda and Vladim{\'{\i}}r Spunda and Tom L. Blundell and Petr Pecinka}, title = {Unheeded SARS-CoV-2 proteins? {A} deep look into negative-sense {RNA}}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac045}, doi = {10.1093/BIB/BBAC045}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BartasVBPCBSBP22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BasithLM22, author = {Shaherin Basith and Gwang Lee and Balachandran Manavalan}, title = {{STALLION:} a stacking-based ensemble learning framework for prokaryotic lysine acetylation site prediction}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab376}, doi = {10.1093/BIB/BBAB376}, timestamp = {Sat, 08 Jun 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BasithLM22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/Ben-CohenDDLSR22, author = {Gil Ben{-}Cohen and Flora Doffe and Michal Devir and Bernard Leroy and Thierry Soussi and Shai Rosenberg}, title = {TP53{\_}PROF: a machine learning model to predict impact of missense mutations in \emph{TP53}}, journal = {Briefings Bioinform.}, volume = {23}, number = {2}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab524}, doi = {10.1093/BIB/BBAB524}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/Ben-CohenDDLSR22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BiLGWPGWYJS22, author = {Yue Bi and Fuyi Li and Xudong Guo and Zhikang Wang and Tong Pan and Yuming Guo and Geoffrey I. Webb and Jianhua Yao and Cangzhi Jia and Jiangning Song}, title = {Clarion is a multi-label problem transformation method for identifying mRNA subcellular localizations}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac467}, doi = {10.1093/BIB/BBAC467}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BiLGWPGWYJS22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BiLWWLX22, author = {Xia{-}an Bi and Lou Li and Zizheng Wang and Yu Wang and Xun Luo and Luyun Xu}, title = {{IHGC-GAN:} influence hypergraph convolutional generative adversarial network for risk prediction of late mild cognitive impairment based on imaging genetic data}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac093}, doi = {10.1093/BIB/BBAC093}, timestamp = {Thu, 02 Jun 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BiLWWLX22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BiMLWZLX22, author = {Xia{-}an Bi and Yuhua Mao and Sheng Luo and Hao Wu and Lixia Zhang and Xun Luo and Luyun Xu}, title = {A novel generation adversarial network framework with characteristics aggregation and diffusion for brain disease classification and feature selection}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac454}, doi = {10.1093/BIB/BBAC454}, timestamp = {Sun, 25 Dec 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/BiMLWZLX22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BiZLMHZX22, author = {Xia{-}an Bi and Wenyan Zhou and Sheng Luo and Yuhua Mao and Xi Hu and Bin Zeng and Luyun Xu}, title = {Feature aggregation graph convolutional network based on imaging genetic data for diagnosis and pathogeny identification of Alzheimer's disease}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac137}, doi = {10.1093/BIB/BBAC137}, timestamp = {Thu, 02 Jun 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BiZLMHZX22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BlecuaDVMMCE22, author = {Pedro Blecua and Veronica Davalos and Izar de Villasante and Angelika Merkel and Eva Musulen and Laia Coll{-}Sanmartin and Manel Esteller}, title = {Refinement of computational identification of somatic copy number alterations using {DNA} methylation microarrays illustrated in cancers of unknown primary}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac161}, doi = {10.1093/BIB/BBAC161}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BlecuaDVMMCE22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BommertWSR22, author = {Andrea Bommert and Thomas Welchowski and Matthias Schmid and J{\"{o}}rg Rahnenf{\"{u}}hrer}, title = {Benchmark of filter methods for feature selection in high-dimensional gene expression survival data}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab354}, doi = {10.1093/BIB/BBAB354}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BommertWSR22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BondhusVHA22, author = {Leroy Bondhus and Roshni Varma and Yenifer Hernandez and Valerie A. Arboleda}, title = {Balancing the transcriptome: leveraging sample similarity to improve measures of gene specificity}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac158}, doi = {10.1093/BIB/BBAC158}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BondhusVHA22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BonidiaAASRSC22, author = {Robson Bonidia and Anderson P. Avila{-}Santos and Breno L{\'{\i}}vio Silva de Almeida and Peter F. Stadler and Ulisses Nunes da Rocha and Danilo Sipoli Sanches and Andr{\'{e}} C. P. L. F. de Carvalho}, title = {BioAutoML: automated feature engineering and metalearning to predict noncoding RNAs in bacteria}, journal = {Briefings Bioinform.}, volume = {23}, number = {4}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac218}, doi = {10.1093/BIB/BBAC218}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BonidiaAASRSC22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BonidiaDSC22, author = {Robson Bonidia and Douglas Silva Domingues and Danilo Sipoli Sanches and Andr{\'{e}} C. P. L. F. de Carvalho}, title = {MathFeature: feature extraction package for DNA, {RNA} and protein sequences based on mathematical descriptors}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab434}, doi = {10.1093/BIB/BBAB434}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BonidiaDSC22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BonnerBYSEBHH22, author = {Stephen Bonner and Ian P. Barrett and Cheng Ye and Rowan Swiers and Ola Engkvist and Andreas Bender and Charles Tapley Hoyt and William L. Hamilton}, title = {A review of biomedical datasets relating to drug discovery: a knowledge graph perspective}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac404}, doi = {10.1093/BIB/BBAC404}, timestamp = {Mon, 28 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BonnerBYSEBHH22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BonnerKETB22, author = {Stephen Bonner and Ufuk Kirik and Ola Engkvist and Jian Tang and Ian P. Barrett}, title = {Implications of topological imbalance for representation learning on biomedical knowledge graphs}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac279}, doi = {10.1093/BIB/BBAC279}, timestamp = {Tue, 06 Dec 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/BonnerKETB22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BonomoGGR22, author = {Mariella Bonomo and Raffaele Giancarlo and Daniele Greco and Simona E. Rombo}, title = {Topological ranks reveal functional knowledge encoded in biological networks: a comparative analysis}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac101}, doi = {10.1093/BIB/BBAC101}, timestamp = {Thu, 23 Jun 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BonomoGGR22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BoyrazPEA22, author = {Asli Boyraz and Vera Pawlowsky{-}Glahn and Juan Jos{\'{e}} Egozcue and Aybar Can Acar}, title = {Principal microbial groups: compositional alternative to phylogenetic grouping of microbiome data}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac328}, doi = {10.1093/BIB/BBAC328}, timestamp = {Wed, 07 Dec 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/BoyrazPEA22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BuWWSSBC22, author = {Kevin Bu and David S. Wallach and Zach Wilson and Nan Shen and Leopoldo N. Segal and Emilia Bagiella and Jos{\'{e}} Carlos Clemente}, title = {Identifying correlations driven by influential observations in large datasets}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab482}, doi = {10.1093/BIB/BBAB482}, timestamp = {Tue, 15 Mar 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/BuWWSSBC22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BuckleyLMWWTSAS22, author = {Paul R. Buckley and Chloe H. Lee and Ruichong Ma and Isaac Woodhouse and Jeongmin Woo and Vasily Tsvetkov and Dmitrii S. Shcherbinin and Agne Antanaviciute and Mikhail Shughay and Margarida Rei and Alison Simmons and Hashem Koohy}, title = {Evaluating performance of existing computational models in predicting {CD8+} {T} cell pathogenic epitopes and cancer neoantigens}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac141}, doi = {10.1093/BIB/BBAC141}, timestamp = {Tue, 21 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/BuckleyLMWWTSAS22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BugnonEPGRFRCGA22, author = {Leandro A Bugnon and Alejandro A. Edera and Santiago Prochetto and Matias Gerard and Jonathan Raad and Emilio Fenoy and Mariano Rubiolo and Uciel Chorostecki and Toni Gabald{\'{o}}n and Federico Ariel and Leandro E. Di Persia and Diego H. Milone and Georgina Stegmayer}, title = {Secondary structure prediction of long noncoding {RNA:} review and experimental comparison of existing approaches}, journal = {Briefings Bioinform.}, volume = {23}, number = {4}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac205}, doi = {10.1093/BIB/BBAC205}, timestamp = {Fri, 16 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/BugnonEPGRFRCGA22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BurenHCWWSLW22, author = {Eric Van Buren and Ming Hu and Liang Cheng and John Wrobel and Kirk Wilhelmsen and Lishan Su and Yun Li and Di Wu}, title = {{TWO-SIGMA-G:} a new competitive gene set testing framework for scRNA-seq data accounting for inter-gene and cell-cell correlation}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac084}, doi = {10.1093/BIB/BBAC084}, timestamp = {Tue, 31 May 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BurenHCWWSLW22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BurnsSGHMBSFF22, author = {Josh J. R. Burns and Benjamin T. Shealy and Mitchell S. Greer and John A. Hadish and Matthew McGowan and Tyler Biggs and Melissa C. Smith and F. Alex Feltus and Stephen P. Ficklin}, title = {Addressing noise in co-expression network construction}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab495}, doi = {10.1093/BIB/BBAB495}, timestamp = {Sat, 08 Jun 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BurnsSGHMBSFF22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/CaiFQWZWJGZP22, author = {Zena Cai and Ping Fu and Ye Qiu and Aiping Wu and Gaihua Zhang and Yirong Wang and Taijiao Jiang and Xing{-}Yi Ge and Haizhen Zhu and Yousong Peng}, title = {vsRNAfinder: a novel method for identifying high-confidence viral small RNAs from small RNA-Seq data}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac496}, doi = {10.1093/BIB/BBAC496}, timestamp = {Tue, 21 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/CaiFQWZWJGZP22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/CaiVCLG22, author = {Menglan Cai and Anna Vesely and Xu Chen and Limin Li and Jelle J. Goeman}, title = {NetTDP: permutation-based true discovery proportions for differential co-expression network analysis}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac417}, doi = {10.1093/BIB/BBAC417}, timestamp = {Tue, 21 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/CaiVCLG22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/CaiZZWW22, author = {Hanxuan Cai and Huimin Zhang and Duancheng Zhao and Jingxing Wu and Ling Wang}, title = {{FP-GNN:} a versatile deep learning architecture for enhanced molecular property prediction}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac408}, doi = {10.1093/BIB/BBAC408}, timestamp = {Sun, 25 Dec 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/CaiZZWW22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/CaoHDJQZ22, author = {Zhen Cao and Yanting Huang and Ran Duan and Peng Jin and Zhaohui S. Qin and Shihua Zhang}, title = {Disease category-specific annotation of variants using an ensemble learning framework}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab438}, doi = {10.1093/BIB/BBAB438}, timestamp = {Tue, 15 Mar 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/CaoHDJQZ22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/CaoYZFWSWLW22, author = {Yi Cao and Zhen{-}Qun Yang and Xu{-}Lu Zhang and Wenqi Fan and Yaowei Wang and Jiajun Shen and Dong{-}Qing Wei and Qing Li and Xiao{-}Yong Wei}, title = {Identifying the kind behind {SMILES} - anatomical therapeutic chemical classification using structure-only representations}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac346}, doi = {10.1093/BIB/BBAC346}, timestamp = {Mon, 05 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/CaoYZFWSWLW22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/CarpiGHSV22, author = {Giovanna Carpi and Lev Gorenstein and Timothy T. Harkins and Mehrzad Samadi and Pankaj Vats}, title = {A GPU-accelerated compute framework for pathogen genomic variant identification to aid genomic epidemiology of infectious disease: a malaria case study}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac314}, doi = {10.1093/BIB/BBAC314}, timestamp = {Tue, 18 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/CarpiGHSV22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChaiGYLLCSYWXY22, author = {Mengya Chai and Yajuan Guo and Liu Yang and Jianhui Li and Shuo Liu and Lei Chen and Yuelei Shen and Yi Yang and Youchun Wang and Lida Xu and Changyuan Yu}, title = {A high-throughput single cell-based antibody discovery approach against the full-length SARS-CoV-2 spike protein suggests a lack of neutralizing antibodies targeting the highly conserved {S2} domain}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac070}, doi = {10.1093/BIB/BBAC070}, timestamp = {Thu, 02 Jun 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChaiGYLLCSYWXY22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChangZC22, author = {Wennan Chang and Chi Zhang and Sha Cao}, title = {Response to 'Letter to the Editor: on the stability and internal consistency of component-wise sparse mixture regression based clustering', Zhang \emph{et al.}}, journal = {Briefings Bioinform.}, volume = {23}, number = {4}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac262}, doi = {10.1093/BIB/BBAC262}, timestamp = {Mon, 08 Aug 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChangZC22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChatzigoulasC22, author = {Alexios Chatzigoulas and Zoe Cournia}, title = {Predicting protein-membrane interfaces of peripheral membrane proteins using ensemble machine learning}, journal = {Briefings Bioinform.}, volume = {23}, number = {2}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab518}, doi = {10.1093/BIB/BBAB518}, timestamp = {Fri, 01 Apr 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChatzigoulasC22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChelliahBKWEYSO22, author = {Ramachandran Chelliah and Eric Banan{-}Mwinedaliri and Imran Khan and Shuai Wei and Fazle Elahi and Su{-}Jung Yeon and Vijayalakshmi Selvakumar and Fred Kwame Ofosu and Momna Rubab and Hum Hun Ju and Harikrishna Reddy Rallabandi and Inamul Hasan Madar and Ghazala Sultan and Deog Hwan Oh}, title = {A review on the application of bioinformatics tools in food microbiome studies}, journal = {Briefings Bioinform.}, volume = {23}, number = {2}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac007}, doi = {10.1093/BIB/BBAC007}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChelliahBKWEYSO22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenGWM22, author = {Ziwei Chen and Fuzhou Gong and Lin Wan and Liang Ma}, title = {\emph{BiTSC} 2: Bayesian inference of tumor clonal tree by joint analysis of single-cell {SNV} and {CNA} data}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac092}, doi = {10.1093/BIB/BBAC092}, timestamp = {Tue, 16 Aug 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenGWM22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenH22, author = {Xing Chen and Li Huang}, title = {Computational model for ncRNA research}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac472}, doi = {10.1093/BIB/BBAC472}, timestamp = {Wed, 07 Dec 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ChenH22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenHMDHY22, author = {Yaowen Chen and Zhen He and Yahui Men and Guohua Dong and Shuofeng Hu and Xiaomin Ying}, title = {MetaLogo: a heterogeneity-aware sequence logo generator and aligner}, journal = {Briefings Bioinform.}, volume = {23}, number = {2}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab591}, doi = {10.1093/BIB/BBAB591}, timestamp = {Fri, 01 Apr 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenHMDHY22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenJZZQSZS22, author = {Zhao Chen and Yin Jiang and Xiaoyu Zhang and Rui Zheng and Ruijin Qiu and Yang Sun and Chen Zhao and Hongcai Shang}, title = {ResNet18DNN: prediction approach of drug-induced liver injury by deep neural network with ResNet18}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab503}, doi = {10.1093/BIB/BBAB503}, timestamp = {Wed, 23 Feb 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ChenJZZQSZS22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenJZZQSZS22a, author = {Zhao Chen and Yin Jiang and Xiaoyu Zhang and Rui Zheng and Ruijin Qiu and Yang Sun and Chen Zhao and Hongcai Shang}, title = {The prediction approach of drug-induced liver injury: response to the issues of reproducible science of artificial intelligence in real-world applications}, journal = {Briefings Bioinform.}, volume = {23}, number = {4}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac196}, doi = {10.1093/BIB/BBAC196}, timestamp = {Fri, 29 Jul 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenJZZQSZS22a.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenLLYJWGGZYL22, author = {Jiawen Chen and Weifang Liu and Tianyou Luo and Zhentao Yu and Minzhi Jiang and Jia Wen and Gaorav P. Gupta and Paola Giusti and Hongtu Zhu and Yuchen Yang and Yun Li}, title = {A comprehensive comparison on cell-type composition inference for spatial transcriptomics data}, journal = {Briefings Bioinform.}, volume = {23}, number = {4}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac245}, doi = {10.1093/BIB/BBAC245}, timestamp = {Mon, 28 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenLLYJWGGZYL22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenLYZJXL22, author = {Siqi Chen and Tiancheng Li and Luna Yang and Fei Zhai and Xiwei Jiang and Rongwu Xiang and Guixia Ling}, title = {Artificial intelligence-driven prediction of multiple drug interactions}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac427}, doi = {10.1093/BIB/BBAC427}, timestamp = {Wed, 17 May 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenLYZJXL22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenLZBZ22, author = {Shouzhi Chen and Qing Li and Jianping Zhao and Yannan Bin and Chunhou Zheng}, title = {NeuroPred-CLQ: incorporating deep temporal convolutional networks and multi-head attention mechanism to predict neuropeptides}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac319}, doi = {10.1093/BIB/BBAC319}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenLZBZ22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenQLLLFL22, author = {Lingxi Chen and Yuhao Qing and Ruikang Li and Chaohui Li and Hechen Li and Xikang Feng and Shuai Cheng Li}, title = {Somatic variant analysis suite: copy number variation clonal visualization online platform for large-scale single-cell genomics}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab452}, doi = {10.1093/BIB/BBAB452}, timestamp = {Thu, 08 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenQLLLFL22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenT22, author = {Jen{-}Hao Chen and Yufeng Jane Tseng}, title = {A general optimization protocol for molecular property prediction using a deep learning network}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab367}, doi = {10.1093/BIB/BBAB367}, timestamp = {Tue, 15 Mar 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ChenT22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenWRWZBZYZ22, author = {Qingjian Chen and Qi{-}Nian Wu and Yu{-}Ming Rong and Shixiang Wang and Zhixiang Zuo and Long Bai and Bei Zhang and Shuqiang Yuan and Qi Zhao}, title = {Deciphering clonal dynamics and metastatic routines in a rare patient of synchronous triple-primary tumors and multiple metastases with MPTevol}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac175}, doi = {10.1093/BIB/BBAC175}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenWRWZBZYZ22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenWWLZ22, author = {Yaojia Chen and Jiacheng Wang and Chuyu Wang and Mingxin Liu and Quan Zou}, title = {Deep learning models for disease-associated circRNA prediction: a review}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac364}, doi = {10.1093/BIB/BBAC364}, timestamp = {Wed, 12 Jun 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenWWLZ22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenXHJL22, author = {Ruolan Chen and Feng Xia and Bing Hu and Shuting Jin and Xiangrong Liu}, title = {Drug-target interactions prediction via deep collaborative filtering with multiembeddings}, journal = {Briefings Bioinform.}, volume = {23}, number = {2}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab520}, doi = {10.1093/BIB/BBAB520}, timestamp = {Tue, 26 Apr 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenXHJL22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenZ22, author = {Yurui Chen and Louxin Zhang}, title = {How much can deep learning improve prediction of the responses to drugs in cancer cell lines?}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab378}, doi = {10.1093/BIB/BBAB378}, timestamp = {Wed, 23 Feb 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ChenZ22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenZY22, author = {Ken Chen and Huiying Zhao and Yuedong Yang}, title = {Capturing large genomic contexts for accurately predicting enhancer-promoter interactions}, journal = {Briefings Bioinform.}, volume = {23}, number = {2}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab577}, doi = {10.1093/BIB/BBAB577}, timestamp = {Wed, 21 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ChenZY22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenZYZCL22, author = {Pei Chen and Jiayuan Zhong and Kun Yang and Xuhang Zhang and Yingqi Chen and Rui Liu}, title = {{TPD:} a web tool for tipping-point detection based on dynamic network biomarker}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac399}, doi = {10.1093/BIB/BBAC399}, timestamp = {Mon, 28 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenZYZCL22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/Cheng22, author = {Liang Cheng}, title = {Omics data analysis and integration for {COVID-19} patients - editorial}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac471}, doi = {10.1093/BIB/BBAC471}, timestamp = {Wed, 07 Dec 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/Cheng22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChengJXWXZZYMW22, author = {Qian Cheng and Shuqing Jiang and Feng Xu and Qian Wang and Yingjie Xiao and Ruyang Zhang and Jiuran Zhao and Jianbing Yan and Chuang Ma and Xiangfeng Wang}, title = {Genome optimization via virtual simulation to accelerate maize hybrid breeding}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab447}, doi = {10.1093/BIB/BBAB447}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChengJXWXZZYMW22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChengLSWWDSW22, author = {Shanshan Cheng and Jingjing Lyu and Xian Shi and Kai Wang and Zengmiao Wang and Minghua Deng and Baoluo Sun and Chaolong Wang}, title = {Rare variant association tests for ancestry-matched case-control data based on conditional logistic regression}, journal = {Briefings Bioinform.}, volume = {23}, number = {2}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab572}, doi = {10.1093/BIB/BBAB572}, timestamp = {Fri, 01 Apr 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChengLSWWDSW22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChengLWCRZJT22, author = {Xuanjin Cheng and Yongxing Liu and Jiahe Wang and Yujie Chen and Andrew Gordon Robertson and Xuekui Zhang and Steven J. M. Jones and Stefan Taubert}, title = {cSurvival: a web resource for biomarker interactions in cancer outcomes and in cell lines}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac090}, doi = {10.1093/BIB/BBAC090}, timestamp = {Tue, 16 Aug 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChengLWCRZJT22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChengSYDYZQLYX22, author = {Hang Cheng and Yuhong Sun and Qing Yang and Minggui Deng and Zhijian Yu and Gang Zhu and Jiuxin Qu and Lei Liu and Liang Yang and Yu Xia}, title = {A rapid bacterial pathogen and antimicrobial resistance diagnosis workflow using Oxford nanopore adaptive sequencing method}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac453}, doi = {10.1093/BIB/BBAC453}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChengSYDYZQLYX22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChengXLWCJZXJ22, author = {Rui Cheng and Zhaochun Xu and Meng Luo and Pingping Wang and Huimin Cao and Xiyun Jin and Wenyang Zhou and Lixing Xiao and Qinghua Jiang}, title = {Identification of alternative splicing-derived cancer neoantigens for mRNA vaccine development}, journal = {Briefings Bioinform.}, volume = {23}, number = {2}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab553}, doi = {10.1093/BIB/BBAB553}, timestamp = {Fri, 19 May 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChengXLWCJZXJ22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChiromMMSS22, author = {Keilash Chirom and Md. Zubbair Malik and Irengbam Rocky Mangangcha and Pallavi Somvanshi and R. K. Brojen Singh}, title = {Network medicine in ovarian cancer: topological properties to drug discovery}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac085}, doi = {10.1093/BIB/BBAC085}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChiromMMSS22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChongZYCXWHHSWC22, author = {Hui Chong and Yuguo Zha and Qingyang Yu and Mingyue Cheng and Guangzhou Xiong and Nan Wang and Xinhe Huang and Shijuan Huang and Chuqing Sun and Sicheng Wu and Wei{-}Hua Chen and Lu{\'{\i}}s Pedro Coelho and Kang Ning}, title = {{EXPERT:} transfer learning-enabled context-aware microbial community classification}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac396}, doi = {10.1093/BIB/BBAC396}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChongZYCXWHHSWC22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChuZSL22, author = {Shih{-}Kai Chu and Shilin Zhao and Yu Shyr and Qi Liu}, title = {Comprehensive evaluation of noise reduction methods for single-cell {RNA} sequencing data}, journal = {Briefings Bioinform.}, volume = {23}, number = {2}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab565}, doi = {10.1093/BIB/BBAB565}, timestamp = {Sun, 12 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ChuZSL22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/Dahal-KoiralaBN22, author = {Shiva Dahal{-}Koirala and Gabriel Balaban and Ralf Stefan Neumann and Lonneke Scheffer and Knut Erik Aslaksen Lundin and Victor Greiff and Ludvig Magne Sollid and Shuo{-}Wang Qiao and Geir Kjetil Sandve}, title = {TCRpower: quantifying the detection power of T-cell receptor sequencing with a novel computational pipeline calibrated by spike-in sequences}, journal = {Briefings Bioinform.}, volume = {23}, number = {2}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab566}, doi = {10.1093/BIB/BBAB566}, timestamp = {Tue, 16 Aug 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/Dahal-KoiralaBN22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DaiJPZL22, author = {Jianhua Dai and Chao Jiang and Ruoyao Peng and Daojian Zeng and Yangding Li}, title = {Chinese medical dialogue information extraction via contrastive multi-utterance inference}, journal = {Briefings Bioinform.}, volume = {23}, number = {4}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac284}, doi = {10.1093/BIB/BBAC284}, timestamp = {Fri, 29 Jul 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DaiJPZL22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DaiLWDG22, author = {Qiguo Dai and Ziqiang Liu and Zhaowei Wang and Xiaodong Duan and Maozu Guo}, title = {GraphCDA: a hybrid graph representation learning framework based on {GCN} and {GAT} for predicting disease-associated circRNAs}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac379}, doi = {10.1093/BIB/BBAC379}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DaiLWDG22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DaiPW22, author = {Min Dai and Xiaobing Pei and Xiu{-}Jie Wang}, title = {Accurate and fast cell marker gene identification with {COSG}}, journal = {Briefings Bioinform.}, volume = {23}, number = {2}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab579}, doi = {10.1093/BIB/BBAB579}, timestamp = {Fri, 01 Apr 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DaiPW22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DaiWLDSG22, author = {Qiguo Dai and Zhaowei Wang and Ziqiang Liu and Xiaodong Duan and Jinmiao Song and Maozu Guo}, title = {Predicting miRNA-disease associations using an ensemble learning framework with resampling method}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab543}, doi = {10.1093/BIB/BBAB543}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DaiWLDSG22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DanilevskyPS22, author = {Artem Danilevsky and Avital Luba Polsky and Noam Shomron}, title = {Adaptive sequencing using nanopores and deep learning of mitochondrial {DNA}}, journal = {Briefings Bioinform.}, volume = {23}, number = {4}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac251}, doi = {10.1093/BIB/BBAC251}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DanilevskyPS22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DasKGPLPK22, author = {Trishala Das and Harbinder Kaur and Pratibha Gour and Kartikay Prasad and Andrew M. Lynn and Amresh Prakash and Vijay Kumar}, title = {Intersection of network medicine and machine learning towards investigating the key biomarkers and pathways underlying amyotrophic lateral sclerosis: a systematic review}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac442}, doi = {10.1093/BIB/BBAC442}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DasKGPLPK22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DengCC22, author = {Yidi Deng and Jarny Choi and Kim{-}Anh L{\^{e}} Cao}, title = {Sincast: a computational framework to predict cell identities in single-cell transcriptomes using bulk atlases as references}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac088}, doi = {10.1093/BIB/BBAC088}, timestamp = {Thu, 23 Jun 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DengCC22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DengQXLZZZ22, author = {Yifan Deng and Yang Qiu and Xinran Xu and Shichao Liu and Zhongfei Zhang and Shanfeng Zhu and Wen Zhang}, title = {{META-DDIE:} predicting drug-drug interaction events with few-shot learning}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab514}, doi = {10.1093/BIB/BBAB514}, timestamp = {Fri, 01 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/DengQXLZZZ22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DengYOSW22, author = {Jianyuan Deng and Zhibo Yang and Iwao Ojima and Dimitris Samaras and Fusheng Wang}, title = {Artificial intelligence in drug discovery: applications and techniques}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab430}, doi = {10.1093/BIB/BBAB430}, timestamp = {Mon, 04 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/DengYOSW22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DeySM22, author = {Ashmita Dey and Sagnik Sen and Ujjwal Maulik}, title = {Study of transcription factor druggabilty for prostate cancer using structure information, gene regulatory networks and protein moonlighting}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab465}, doi = {10.1093/BIB/BBAB465}, timestamp = {Wed, 23 Feb 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/DeySM22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DhakalMTC22, author = {Ashwin Dhakal and Cole McKay and John J. Tanner and Jianlin Cheng}, title = {Artificial intelligence in the prediction of protein-ligand interactions: recent advances and future directions}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab476}, doi = {10.1093/BIB/BBAB476}, timestamp = {Tue, 15 Mar 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/DhakalMTC22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DhallPR22, author = {Anjali Dhall and Sumeet Patiyal and Gajendra P. S. Raghava}, title = {HLAncPred: a method for predicting promiscuous non-classical {HLA} binding sites}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac192}, doi = {10.1093/BIB/BBAC192}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DhallPR22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DhandaMG22, author = {Sandeep Kumar Dhanda and Jitendra Malviya and Sudheer Gupta}, title = {Not all {T} cell epitopes are equally desired: a review of \emph{in silico} tools for the prediction of cytokine-inducing potential of T-cell epitopes}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac382}, doi = {10.1093/BIB/BBAC382}, timestamp = {Tue, 18 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DhandaMG22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DingL22, author = {Hongyu Ding and Junwei Luo}, title = {MAMnet: detecting and genotyping deletions and insertions based on long reads and a deep learning approach}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac195}, doi = {10.1093/BIB/BBAC195}, timestamp = {Tue, 18 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DingL22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DingLLW22, author = {Yulian Ding and Xiujuan Lei and Bo Liao and Fang{-}Xiang Wu}, title = {{MLRDFM:} a multi-view Laplacian regularized DeepFM model for predicting miRNA-disease associations}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac079}, doi = {10.1093/BIB/BBAC079}, timestamp = {Tue, 31 May 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DingLLW22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DingNG22, author = {Wenze Ding and Kenta Nakai and Haipeng Gong}, title = {Protein design via deep learning}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac102}, doi = {10.1093/BIB/BBAC102}, timestamp = {Tue, 16 Aug 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DingNG22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DingTGZ22, author = {Yijie Ding and Jijun Tang and Fei Guo and Quan Zou}, title = {Identification of drug-target interactions via multiple kernel-based triple collaborative matrix factorization}, journal = {Briefings Bioinform.}, volume = {23}, number = {2}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab582}, doi = {10.1093/BIB/BBAB582}, timestamp = {Mon, 28 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DingTGZ22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DingYLXXPCASCJ22, author = {Qian Ding and Wenyi Yang and Meng Luo and Chang Xu and Zhaochun Xu and Fenglan Pang and Yideng Cai and Anastasia A. Anashkina and Xi Su and Na Chen and Qinghua Jiang}, title = {{CBLRR:} a cauchy-based bounded constraint low-rank representation method to cluster single-cell RNA-seq data}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac300}, doi = {10.1093/BIB/BBAC300}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DingYLXXPCASCJ22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DongCCWCDWHHH22, author = {Xin Dong and Ke Chen and Wenbo Chen and Jun Wang and Liuping Chang and Jin Deng and Lei Wei and Leng Han and Chunhua Huang and Chunjiang He}, title = {circRIP: an accurate tool for identifying circRNA-RBP interactions}, journal = {Briefings Bioinform.}, volume = {23}, number = {4}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac186}, doi = {10.1093/BIB/BBAC186}, timestamp = {Mon, 05 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DongCCWCDWHHH22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DongZFZ22, author = {Guiying Dong and Zi{-}Chao Zhang and Jianfeng Feng and Xing{-}Ming Zhao}, title = {MorbidGCN: prediction of multimorbidity with a graph convolutional network based on integration of population phenotypes and disease network}, journal = {Briefings Bioinform.}, volume = {23}, number = {4}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac255}, doi = {10.1093/BIB/BBAC255}, timestamp = {Mon, 28 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DongZFZ22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DongZLSZ22, author = {Jingxin Dong and Mingyi Zhao and Yuansheng Liu and Yansen Su and Xiangxiang Zeng}, title = {Deep learning in retrosynthesis planning: datasets, models and tools}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab391}, doi = {10.1093/BIB/BBAB391}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DongZLSZ22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DongZWCXGLYZWLT22, author = {Ji Dong and Peijie Zhou and Yichong Wu and Yidong Chen and Haoling Xie and Yuan Gao and Jiansen Lu and Jingwei Yang and Xiannian Zhang and Lu Wen and Tiejun Li and Fuchou Tang}, title = {Integrating single-cell datasets with ambiguous batch information by incorporating molecular network features}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab366}, doi = {10.1093/BIB/BBAB366}, timestamp = {Mon, 03 Jun 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DongZWCXGLYZWLT22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DuWHCPHYL22, author = {Zhihua Du and Yang{-}Han Wu and Yu{-}An Huang and Jie Chen and Gui{-}Qing Pan and Lun Hu and Zhu{-}Hong You and Jian{-}Qiang Li}, title = {GraphTGI: an attention-based graph embedding model for predicting TF-target gene interactions}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac148}, doi = {10.1093/BIB/BBAC148}, timestamp = {Sun, 03 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DuWHCPHYL22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DubocPMBDPB22, author = {V{\'{e}}ronique Duboc and David Pratella and Marco Milanesio and John Boudjarane and St{\'{e}}phane Descombes and V{\'{e}}ronique Paquis{-}Flucklinger and Silvia Bottini}, title = {NiPTUNE: an automated pipeline for noninvasive prenatal testing in an accurate, integrative and flexible framework}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab380}, doi = {10.1093/BIB/BBAB380}, timestamp = {Tue, 15 Mar 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/DubocPMBDPB22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DuhanNK22, author = {Naveen Duhan and Jeanette M. Norton and Rakesh Kaundal}, title = {deepNEC: a novel alignment-free tool for the identification and classification of nitrogen biochemical network-related enzymes using deep learning}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac071}, doi = {10.1093/BIB/BBAC071}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DuhanNK22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/EderaMS22, author = {Alejandro A. Edera and Diego H. Milone and Georgina Stegmayer}, title = {Anc2vec: embedding gene ontology terms by preserving ancestors relationships}, journal = {Briefings Bioinform.}, volume = {23}, number = {2}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac003}, doi = {10.1093/BIB/BBAC003}, timestamp = {Fri, 25 Mar 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/EderaMS22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FanCP22, author = {Yongxian Fan and Meijun Chen and Xiaoyong Pan}, title = {{GCRFLDA:} scoring lncRNA-disease associations using graph convolution matrix completion with conditional random field}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab361}, doi = {10.1093/BIB/BBAB361}, timestamp = {Tue, 15 Mar 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/FanCP22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FanKDMSW22, author = {Peihao Fan and Julia Kofler and Ying Ding and Michael Marks and Robert A. Sweet and Lirong Wang}, title = {Efficacy difference of antipsychotics in Alzheimer's disease and schizophrenia: explained with network efficiency and pathway analysis methods}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac394}, doi = {10.1093/BIB/BBAC394}, timestamp = {Wed, 20 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/FanKDMSW22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FanLZWLX22, author = {Jiaxin Fan and Yafei Lyu and Qihuang Zhang and Xuran Wang and Mingyao Li and Rui Xiao}, title = {MuSiC2: cell-type deconvolution for multi-condition bulk RNA-seq data}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac430}, doi = {10.1093/BIB/BBAC430}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/FanLZWLX22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FangLL22, author = {Yiming Fang and Xuejun Liu and Hui Liu}, title = {Attention-aware contrastive learning for predicting {T} cell receptor-antigen binding specificity}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac378}, doi = {10.1093/BIB/BBAC378}, timestamp = {Mon, 28 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/FangLL22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FangSAIJH22, author = {Mingyan Fang and Zheng Su and Hassan Abolhassani and Yuval Itan and Xin Jin and Lennart Hammarstr{\"{o}}m}, title = {{VIPPID:} a gene-specific single nucleotide variant pathogenicity prediction tool for primary immunodeficiency diseases}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac176}, doi = {10.1093/BIB/BBAC176}, timestamp = {Tue, 06 Dec 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/FangSAIJH22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FengHLZZ22, author = {Qiongqiong Feng and Minghua Hou and Jun Liu and Kai{-}Long Zhao and Guijun Zhang}, title = {Construct a variable-length fragment library for de novo protein structure prediction}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac086}, doi = {10.1093/BIB/BBAC086}, timestamp = {Tue, 31 May 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/FengHLZZ22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FengSLL22, author = {Ziyan Feng and Zihao Shen and Honglin Li and Shiliang Li}, title = {e-TSN: an interactive visual exploration platform for target-disease knowledge mapping from literature}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac465}, doi = {10.1093/BIB/BBAC465}, timestamp = {Tue, 16 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/FengSLL22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FengWYAQXG22, author = {Jitong Feng and Shengbo Wu and Hongpeng Yang and Chengwei Ai and Jianjun Qiao and Junhai Xu and Fei Guo}, title = {Microbe-bridged disease-metabolite associations identification by heterogeneous graph fusion}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac423}, doi = {10.1093/BIB/BBAC423}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/FengWYAQXG22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FengYFS22, author = {Yi{-}Yang Feng and Hui Yu and Yue{-}Hua Feng and Jian{-}Yu Shi}, title = {Directed graph attention networks for predicting asymmetric drug-drug interactions}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac151}, doi = {10.1093/BIB/BBAC151}, timestamp = {Thu, 27 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/FengYFS22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FenoyES22, author = {Emilio Fenoy and Alejandro A. Edera and Georgina Stegmayer}, title = {Transfer learning in proteins: evaluating novel protein learned representations for bioinformatics tasks}, journal = {Briefings Bioinform.}, volume = {23}, number = {4}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac232}, doi = {10.1093/BIB/BBAC232}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/FenoyES22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/Fernandez-OrthR22, author = {Dietmar Fern{\'{a}}ndez{-}Orth and Manuel Rueda and Babita Singh and Mauricio Moldes and Aina Jene and Marta Ferri and Claudia Vasallo and Lauren A. Fromont and Arcadi Navarro and Jordi Rambla}, title = {A quality control portal for sequencing data deposited at the European genome-phenome archive}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac136}, doi = {10.1093/BIB/BBAC136}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/Fernandez-OrthR22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FiroozbakhtYS22, author = {Farzaneh Firoozbakht and Behnam Yousefi and Benno Schwikowski}, title = {An overview of machine learning methods for monotherapy drug response prediction}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab408}, doi = {10.1093/BIB/BBAB408}, timestamp = {Tue, 15 Mar 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/FiroozbakhtYS22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/FloresLZHCYPJZG22, author = {Mario Flores and Zhentao Liu and Tinghe Zhang and Md Musaddaqui Hasib and Yu{-}Chiao Chiu and Zhenqing Ye and Karla Paniagua and Sumin Jo and Jianqiu Zhang and Shou{-}Jiang Gao and Yu{-}Fang Jin and Yidong Chen and Yufei Huang}, title = {Deep learning tackles single-cell analysis - a survey of deep learning for scRNA-seq analysis}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab531}, doi = {10.1093/BIB/BBAB531}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/FloresLZHCYPJZG22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ForniCPCS22, author = {Diego Forni and Rachele Cagliani and Chiara Pontremoli and Mario Clerici and Manuela Sironi}, title = {The substitution spectra of coronavirus genomes}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab382}, doi = {10.1093/BIB/BBAB382}, timestamp = {Sat, 09 Apr 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ForniCPCS22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GabellaDD22, author = {Chiara Gabella and Severine Duvaud and Christine Durinx}, title = {Managing the life cycle of a portfolio of open data resources at the {SIB} Swiss Institute of Bioinformatics}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab478}, doi = {10.1093/BIB/BBAB478}, timestamp = {Tue, 15 Mar 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/GabellaDD22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GableSLRM22, author = {Annika L. Gable and Damian Szklarczyk and David Lyon and Jo{\~{a}}o F. Matias Rodrigues and Christian von Mering}, title = {Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac355}, doi = {10.1093/BIB/BBAC355}, timestamp = {Tue, 18 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GableSLRM22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GaffoBMB22, author = {Enrico Gaffo and Alessia Buratin and Anna Dal Molin and Stefania Bortoluzzi}, title = {Sensitive, reliable and robust circRNA detection from RNA-seq with CirComPara2}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab418}, doi = {10.1093/BIB/BBAB418}, timestamp = {Sat, 13 May 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GaffoBMB22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GanGGXZ22, author = {Yanglan Gan and Cheng Guo and Wenjing Guo and Guangwei Xu and Guobing Zou}, title = {Entropy-based inference of transition states and cellular trajectory for single-cell transcriptomics}, journal = {Briefings Bioinform.}, volume = {23}, number = {4}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac225}, doi = {10.1093/BIB/BBAC225}, timestamp = {Fri, 29 Jul 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GanGGXZ22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GanHZZG22, author = {Yanglan Gan and Xingyu Huang and Guobing Zou and Shuigeng Zhou and Jihong Guan}, title = {Deep structural clustering for single-cell RNA-seq data jointly through autoencoder and graph neural network}, journal = {Briefings Bioinform.}, volume = {23}, number = {2}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac018}, doi = {10.1093/BIB/BBAC018}, timestamp = {Fri, 25 Mar 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/GanHZZG22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GanYZ22, author = {Dailin Gan and Guosheng Yin and Yan Dora Zhang}, title = {The {GR2D2} estimator for the precision matrices}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac426}, doi = {10.1093/BIB/BBAC426}, timestamp = {Tue, 21 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/GanYZ22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GaoCZSX22, author = {Ling Gao and Hui Cui and Tiangang Zhang and Nan Sheng and Ping Xuan}, title = {Prediction of drug-disease associations by integrating common topologies of heterogeneous networks and specific topologies of subnets}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab467}, doi = {10.1093/BIB/BBAB467}, timestamp = {Mon, 28 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GaoCZSX22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GaoLQGS22, author = {Meihong Gao and Shuhui Liu and Yang Qi and Xinpeng Guo and Xuequn Shang}, title = {{GAE-LGA:} integration of multi-omics data with graph autoencoders to identify lncRNA-PCG associations}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac452}, doi = {10.1093/BIB/BBAC452}, timestamp = {Sun, 12 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/GaoLQGS22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GaoSGWZSGZLNZ22, author = {Yue Gao and Shipeng Shang and Shuang Guo and Xinyue Wang and Hanxiao Zhou and Yue Sun and Jing Gan and Yakun Zhang and Xia Li and Shangwei Ning and Yunpeng Zhang}, title = {AgingBank: a manually curated knowledgebase and high-throughput analysis platform that provides experimentally supported multi-omics data relevant to aging in multiple species}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac438}, doi = {10.1093/BIB/BBAC438}, timestamp = {Thu, 29 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/GaoSGWZSGZLNZ22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GaoYLC22, author = {Rong Gao and Jinling Yan and Peiluan Li and Luonan Chen}, title = {Detecting the critical states during disease development based on temporal network flow entropy}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac164}, doi = {10.1093/BIB/BBAC164}, timestamp = {Tue, 18 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GaoYLC22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GaoZSW22, author = {Qian Gao and Yu Zhang and Hongwei Sun and Tong Wang}, title = {Evaluation of propensity score methods for causal inference with high-dimensional covariates}, journal = {Briefings Bioinform.}, volume = {23}, number = {4}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac227}, doi = {10.1093/BIB/BBAC227}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GaoZSW22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/Garcia-JacasGMT22, author = {C{\'{e}}sar R. Garc{\'{\i}}a{-}Jacas and Luis A. Garc{\'{\i}}a{-}Gonz{\'{a}}lez and Felix Martinez{-}Rios and Issac P. Tapia{-}Contreras and Carlos A. Brizuela}, title = {Handcrafted versus non-handcrafted (self-supervised) features for the classification of antimicrobial peptides: complementary or redundant?}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac428}, doi = {10.1093/BIB/BBAC428}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/Garcia-JacasGMT22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/Garcia-JacasPGB22, author = {C{\'{e}}sar R. Garc{\'{\i}}a{-}Jacas and Sergio Alejandro Pinacho{-}Castellanos and Luis A. Garc{\'{\i}}a{-}Gonz{\'{a}}lez and Carlos A. Brizuela}, title = {Do deep learning models make a difference in the identification of antimicrobial peptides?}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac094}, doi = {10.1093/BIB/BBAC094}, timestamp = {Fri, 15 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/Garcia-JacasPGB22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GautamGGRMMAGSS22, author = {Vishakha Gautam and Rahul Gupta and Deepti Gupta and Anubhav Ruhela and Aayushi Mittal and Sanjay Kumar Mohanty and Sakshi Arora and Ria Gupta and Chandan Saini and Debarka Sengupta and Natarajan Arul Murugan and Gaurav Ahuja}, title = {\emph{deepGraphh}: AI-driven web service for graph-based quantitative structure-activity relationship analysis}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac288}, doi = {10.1093/BIB/BBAC288}, timestamp = {Mon, 28 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GautamGGRMMAGSS22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GeZXASY22, author = {Fang Ge and Ying Zhang and Jian Xu and Muhammad Arif and Jiangning Song and Dong{-}Jun Yu}, title = {Prediction of disease-associated nsSNPs by integrating multi-scale ResNet models with deep feature fusion}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab530}, doi = {10.1093/BIB/BBAB530}, timestamp = {Tue, 15 Nov 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/GeZXASY22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GelhausenMSASEB22, author = {Rick Gelhausen and Teresa M{\"{u}}ller and Sarah L. Svensson and Omer S. Alkhnbashi and Cynthia M. Sharma and Florian Eggenhofer and Rolf Backofen}, title = {RiboReport - benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria}, journal = {Briefings Bioinform.}, volume = {23}, number = {2}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab549}, doi = {10.1093/BIB/BBAB549}, timestamp = {Tue, 21 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/GelhausenMSASEB22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GliozzoMNPPGPVC22, author = {Jessica Gliozzo and Marco Mesiti and Marco Notaro and Alessandro Petrini and Alex Patak and Antonio Puertas Gallardo and Alberto Paccanaro and Giorgio Valentini and Elena Casiraghi}, title = {Heterogeneous data integration methods for patient similarity networks}, journal = {Briefings Bioinform.}, volume = {23}, number = {4}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac207}, doi = {10.1093/BIB/BBAC207}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GliozzoMNPPGPVC22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/Gomez-GonzalezC22, author = {Paula J. G{\'{o}}mez{-}Gonz{\'{a}}lez and Susana G. Campino and Jody Phelan and Taane G. Clark}, title = {Portable sequencing of \emph{Mycobacterium tuberculosis} for clinical and epidemiological applications}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac256}, doi = {10.1093/BIB/BBAC256}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/Gomez-GonzalezC22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GongWWSLX22, author = {Weikang Gong and Junjie Wee and Min{-}Chun Wu and Xiaohan Sun and Chunhua Li and Kelin Xia}, title = {Persistent spectral simplicial complex-based machine learning for chromosomal structural analysis in cellular differentiation}, journal = {Briefings Bioinform.}, volume = {23}, number = {4}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac168}, doi = {10.1093/BIB/BBAC168}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GongWWSLX22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GoossensHVDVWR22, author = {Sander N. Goossens and Tim H. Heupink and Elise De Vos and Anzaan Dippenaar and Margaretha De Vos and Rob Warren and Annelies Van Rie}, title = {Detection of minor variants in Mycobacterium tuberculosis whole genome sequencing data}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab541}, doi = {10.1093/BIB/BBAB541}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GoossensHVDVWR22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GoudeyGVZ22, author = {Benjamin Goudey and Nicholas Geard and Karin Verspoor and Justin Zobel}, title = {Propagation, detection and correction of errors using the sequence database network}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac416}, doi = {10.1093/BIB/BBAC416}, timestamp = {Sun, 12 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/GoudeyGVZ22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GrzesikAWM22, author = {Piotr Grzesik and Dariusz Rafal Augustyn and Lukasz Wycislik and Dariusz Mrozek}, title = {Serverless computing in omics data analysis and integration}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab349}, doi = {10.1093/BIB/BBAB349}, timestamp = {Sat, 09 Apr 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GrzesikAWM22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
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@article{DBLP:journals/bib/GuanWSLHZ22, author = {Xiaoyu Guan and Yuqin Wang and Wei Shao and Zhongnian Li and Shuo Huang and Daoqiang Zhang}, title = {S2Snet: deep learning for low molecular weight {RNA} identification with nanopore}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac098}, doi = {10.1093/BIB/BBAC098}, timestamp = {Sun, 22 Oct 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GuanWSLHZ22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GuoESSTXZ22, author = {Yang Guo and Fatemeh Esfahani and Xiaojian Shao and Venkatesh Srinivasan and Alex Thomo and Li Xing and Xuekui Zhang}, title = {Integrative {COVID-19} biological network inference with probabilistic core decomposition}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab455}, doi = {10.1093/BIB/BBAB455}, timestamp = {Mon, 25 Apr 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GuoESSTXZ22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GuoHYS22, author = {Xinyun Guo and Huan He and Jialin Yu and Shaoping Shi}, title = {{PKSPS:} a novel method for predicting kinase of specific phosphorylation sites based on maximum weighted bipartite matching algorithm and phosphorylation sequence enrichment analysis}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab436}, doi = {10.1093/BIB/BBAB436}, timestamp = {Tue, 22 Mar 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/GuoHYS22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GuoJZ22, author = {Xiaoyi Guo and Yizhang Jiang and Quan Zou}, title = {Structured Sparse Regularized {TSK} Fuzzy System for predicting therapeutic peptides}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac135}, doi = {10.1093/BIB/BBAC135}, timestamp = {Mon, 09 Jan 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/GuoJZ22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GuoSA22, author = {Margaret G. Guo and Daniel N. Sosa and Russ B. Altman}, title = {Challenges and opportunities in network-based solutions for biological questions}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab437}, doi = {10.1093/BIB/BBAB437}, timestamp = {Tue, 15 Mar 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/GuoSA22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GuoYWYZRP22, author = {Lu{-}Xiang Guo and Zhu{-}Hong You and Lei Wang and Changqing Yu and Bo{-}Wei Zhao and Zhong{-}Hao Ren and Jie Pan}, title = {A novel circRNA-miRNA association prediction model based on structural deep neural network embedding}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac391}, doi = {10.1093/BIB/BBAC391}, timestamp = {Thu, 11 Apr 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GuoYWYZRP22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GuptaVM22, author = {Priya Gupta and Sureshkumar Venkadesan and Debasisa Mohanty}, title = {Pf-Phospho: a machine learning-based phosphorylation sites prediction tool for \emph{Plasmodium} proteins}, journal = {Briefings Bioinform.}, volume = {23}, number = {4}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac249}, doi = {10.1093/BIB/BBAC249}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GuptaVM22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GuzziPM22, author = {Pietro Hiram Guzzi and Francesco Petrizzelli and Tommaso Mazza}, title = {Disease spreading modeling and analysis: a survey}, journal = {Briefings Bioinform.}, volume = {23}, number = {4}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac230}, doi = {10.1093/BIB/BBAC230}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GuzziPM22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GwakR22, author = {Ho{-}Jin Gwak and Mina Rho}, title = {ViBE: a hierarchical {BERT} model to identify eukaryotic viruses using metagenome sequencing data}, journal = {Briefings Bioinform.}, volume = {23}, number = {4}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac204}, doi = {10.1093/BIB/BBAC204}, timestamp = {Mon, 08 Aug 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GwakR22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HaberSP22, author = {Anna Christine Haber and Ulrich Sax and Fabian Prasser}, title = {Open tools for quantitative anonymization of tabular phenotype data: literature review}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac440}, doi = {10.1093/BIB/BBAC440}, timestamp = {Sun, 12 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HaberSP22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HamamotoTMKTBSS22, author = {Ryuji Hamamoto and Ken Takasawa and Hidenori Machino and Kazuma Kobayashi and Satoshi Takahashi and Amina Bolatkan and Norio Shinkai and Akira Sakai and Rina Aoyama and Masayoshi Yamada and Ken Asada and Masaaki Komatsu and Koji Okamoto and Hirokazu Kameoka and Syuzo Kaneko}, title = {Application of non-negative matrix factorization in oncology: one approach for establishing precision medicine}, journal = {Briefings Bioinform.}, volume = {23}, number = {4}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac246}, doi = {10.1093/BIB/BBAC246}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HamamotoTMKTBSS22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HanCCZHCZHCKGL22, author = {Wenkai Han and Yuqi Cheng and Jiayang Chen and Huawen Zhong and Zhihang Hu and Siyuan Chen and Licheng Zong and Liang Hong and Ting{-}Fung Chan and Irwin King and Xin Gao and Yu Li}, title = {Self-supervised contrastive learning for integrative single cell RNA-seq data analysis}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac377}, doi = {10.1093/BIB/BBAC377}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HanCCZHCZHCKGL22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HanHFPASLMSGPW22, author = {Siyu Han and Jialing Huang and Francesco Foppiano and Cornelia Prehn and Jerzy Adamski and Karsten Suhre and Ying Li and Giuseppe Matullo and Freimut Schliess and Christian Gieger and Annette Peters and Rui Wang{-}Sattler}, title = {{TIGER:} technical variation elimination for metabolomics data using ensemble learning architecture}, journal = {Briefings Bioinform.}, volume = {23}, number = {2}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab535}, doi = {10.1093/BIB/BBAB535}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HanHFPASLMSGPW22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HanSZXSY22, author = {Ke Han and Long{-}Chen Shen and Yi{-}Heng Zhu and Jian Xu and Jiangning Song and Dong{-}Jun Yu}, title = {MAResNet: predicting transcription factor binding sites by combining multi-scale bottom-up and top-down attention and residual network}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab445}, doi = {10.1093/BIB/BBAB445}, timestamp = {Tue, 15 Mar 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HanSZXSY22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HanWCACYL22, author = {Yanqiang Han and Zhilong Wang and An Chen and Imran Ali and Junfei Cai and Simin Ye and Jin{-}Jin Li}, title = {An inductive transfer learning force field {(ITLFF)} protocol builds protein force fields in seconds}, journal = {Briefings Bioinform.}, volume = {23}, number = {2}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab590}, doi = {10.1093/BIB/BBAB590}, timestamp = {Mon, 18 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HanWCACYL22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HanYSYZPFL22, author = {Siyu Han and Xiao Yang and Hang Sun and Hu Yang and Qi Zhang and Cheng Peng and Wensi Fang and Ying Li}, title = {{LION:} an integrated {R} package for effective prediction of ncRNA-protein interaction}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac420}, doi = {10.1093/BIB/BBAC420}, timestamp = {Tue, 23 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HanYSYZPFL22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HaoLLLXKLLXQLL22, author = {Yangyang Hao and Liang Lu and Anna Liu and Xue Lin and Li Xiao and Xiaoyue Kong and Kai Li and Fengji Liang and Jianghui Xiong and Lina Qu and Yinghui Li and Jian Li}, title = {Integrating bioinformatic strategies in spatial life science research}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac415}, doi = {10.1093/BIB/BBAC415}, timestamp = {Sun, 25 Dec 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HaoLLLXKLLXQLL22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HeCC22, author = {Haohuai He and Guanxing Chen and Calvin Yu{-}Chian Chen}, title = {3DGT-DDI: 3D graph and text based neural network for drug-drug interaction prediction}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac134}, doi = {10.1093/BIB/BBAC134}, timestamp = {Tue, 21 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HeCC22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HeJJLZMSGW22, author = {Wenjia He and Yi Jiang and Junru Jin and Zhongshen Li and Jiaojiao Zhao and Balachandran Manavalan and Ran Su and Xin Gao and Leyi Wei}, title = {Accelerating bioactive peptide discovery via mutual information-based meta-learning}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab499}, doi = {10.1093/BIB/BBAB499}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HeJJLZMSGW22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HeWXBTTGXY22, author = {Binsheng He and Kun Wang and Ju Xiang and Pingping Bing and Min Tang and Geng Tian and Cheng Guo and Miao Xu and Jialiang Yang}, title = {{DGHNE:} network enhancement-based method in identifying disease-causing genes through a heterogeneous biomedical network}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac405}, doi = {10.1093/BIB/BBAC405}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HeWXBTTGXY22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HeYJ22, author = {Qifan He and Jian Yang and Yonghai Jin}, title = {Immune infiltration and clinical significance analyses of the coagulation-related genes in hepatocellular carcinoma}, journal = {Briefings Bioinform.}, volume = {23}, number = {4}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac291}, doi = {10.1093/BIB/BBAC291}, timestamp = {Mon, 08 Aug 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HeYJ22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HicklQWMH22, author = {Oskar Hickl and Pedro Queir{\'{o}}s and Paul Wilmes and Patrick May and Anna Heintz{-}Buschart}, title = {\emph{binny}: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac431}, doi = {10.1093/BIB/BBAC431}, timestamp = {Sun, 15 Jan 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HicklQWMH22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HippeLBPKDHSC22, author = {Kyle Hippe and Cade Lilley and Joshua William Berkenpas and Ciri Chandana Pocha and Kiyomi Kishaba and Hui Ding and Jie Hou and Dong Si and Renzhi Cao}, title = {ZoomQA: residue-level protein model accuracy estimation with machine learning on sequential and 3D structural features}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab384}, doi = {10.1093/BIB/BBAB384}, timestamp = {Tue, 27 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HippeLBPKDHSC22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HoLO22, author = {Quang{-}Thai Ho and Nguyen{-}Quoc{-}Khanh Le and Yu{-}Yen Ou}, title = {mCNN-ETC: identifying electron transporters and their functional families by using multiple windows scanning techniques in convolutional neural networks with evolutionary information of protein sequences}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab352}, doi = {10.1093/BIB/BBAB352}, timestamp = {Tue, 15 Mar 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HoLO22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HongFSPJCE22, author = {Ye Hong and Dani Flinkman and Tomi Suomi and Sami Pietil{\"{a}} and Peter James and Eleanor Coffey and Laura L. Elo}, title = {PhosPiR: an automated phosphoproteomic pipeline in {R}}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab510}, doi = {10.1093/BIB/BBAB510}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HongFSPJCE22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HongFSPJCE22a, author = {Ye Hong and Dani Flinkman and Tomi Suomi and Sami Pietil{\"{a}} and Peter James and Eleanor Coffey and Laura L. Elo}, title = {Correction to: PhosPiR: an automated phosphoproteomic pipeline in {R}}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac153}, doi = {10.1093/BIB/BBAC153}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HongFSPJCE22a.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HouPZZZ22, author = {Minghua Hou and Chunxiang Peng and Xiaogen Zhou and Biao Zhang and Guijun Zhang}, title = {Multi contact-based folding method for de novo protein structure prediction}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab463}, doi = {10.1093/BIB/BBAB463}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HouPZZZ22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HouZYWMLL22, author = {Siyu Hou and Peng Zhang and Kuo Yang and Lan Wang and Changzheng Ma and Yanda Li and Shao Li}, title = {Decoding multilevel relationships with the human tissue-cell-molecule network}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac170}, doi = {10.1093/BIB/BBAC170}, timestamp = {Wed, 07 Dec 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HouZYWMLL22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuCZSX22, author = {Kaimiao Hu and Hui Cui and Tiangang Zhang and Chang Sun and Ping Xuan}, title = {{ALDPI:} adaptively learning importance of multi-scale topologies and multi-modality similarities for drug-protein interaction prediction}, journal = {Briefings Bioinform.}, volume = {23}, number = {2}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab606}, doi = {10.1093/BIB/BBAB606}, timestamp = {Mon, 28 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HuCZSX22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuGFLWHWZ22, author = {Jing Hu and Jie Gao and Xiaomin Fang and Zijing Liu and Fan Wang and Weili Huang and Hua Wu and Guodong Zhao}, title = {DTSyn: a dual-transformer-based neural network to predict synergistic drug combinations}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac302}, doi = {10.1093/BIB/BBAC302}, timestamp = {Thu, 08 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HuGFLWHWZ22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuLLYP22, author = {Hang Hu and Zhong Li and Xiangjie Li and Minzhe Yu and Xiutao Pan}, title = {ScCAEs: deep clustering of single-cell RNA-seq via convolutional autoencoder embedding and soft K-means}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab321}, doi = {10.1093/BIB/BBAB321}, timestamp = {Tue, 15 Mar 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HuLLYP22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuRGJTCDY22, author = {Wei{-}Xin Hu and Yu Rong and Yan Guo and Feng Jiang and Wen Tian and Hao Chen and Shan{-}Shan Dong and Tie{-}Lin Yang}, title = {ExsgRNA: reduce off-target efficiency by on-target mismatched sgRNA}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac183}, doi = {10.1093/BIB/BBAC183}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HuRGJTCDY22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuXLMYWWCLXZ22, author = {Congxue Hu and Yingqi Xu and Feng Li and Wanqi Mi and He Yu and Xinran Wang and Xin Wen and Shuaijun Chen and Xia Li and Yanjun Xu and Yunpeng Zhang}, title = {Identifying and characterizing drug sensitivity-related lncRNA-TF-gene regulatory triplets}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac366}, doi = {10.1093/BIB/BBAC366}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HuXLMYWWCLXZ22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuZS22, author = {Jialu Hu and Yuanke Zhong and Xuequn Shang}, title = {A versatile and scalable single-cell data integration algorithm based on domain-adversarial and variational approximation}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab400}, doi = {10.1093/BIB/BBAB400}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HuZS22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuangJGW22, author = {Xiaotai Huang and Songwei Jia and Lin Gao and Jing Wu}, title = {Reconstruction of human protein-coding gene functional association network based on machine learning}, journal = {Briefings Bioinform.}, volume = {23}, number = {2}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab552}, doi = {10.1093/BIB/BBAB552}, timestamp = {Fri, 25 Mar 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HuangJGW22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuangKWCW22, author = {Kai{-}Yao Huang and Hui{-}Ju Kao and Tzu{-}Hsiang Weng and Chia{-}Hung Chen and Shun{-}Long Weng}, title = {iDVIP: identification and characterization of viral integrase inhibitory peptides}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac406}, doi = {10.1093/BIB/BBAC406}, timestamp = {Wed, 17 May 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HuangKWCW22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuangLJL22, author = {Yuyao Huang and Jiesi Luo and Runyu Jing and Menglong Li}, title = {Multi-model predictive analysis of {RNA} solvent accessibility based on modified residual attention mechanism}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac470}, doi = {10.1093/BIB/BBAC470}, timestamp = {Sun, 25 Dec 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HuangLJL22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuangLLSZW22, author = {Lei Huang and Jiecong Lin and Xiangtao Li and Linqi Song and Zetian Zheng and Ka{-}Chun Wong}, title = {{EGFI:} drug-drug interaction extraction and generation with fusion of enriched entity and sentence information}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab451}, doi = {10.1093/BIB/BBAB451}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HuangLLSZW22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuangLLZMCLW22, author = {Lei Huang and Jiecong Lin and Rui Liu and Zetian Zheng and Lingkuan Meng and Xingjian Chen and Xiangtao Li and Ka{-}Chun Wong}, title = {CoaDTI: multi-modal co-attention based framework for drug-target interaction annotation}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac446}, doi = {10.1093/BIB/BBAC446}, timestamp = {Wed, 07 Dec 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HuangLLZMCLW22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuangNNGLW22, author = {Neng Huang and Fan Nie and Peng Ni and Xin Gao and Feng Luo and Jianxin Wang}, title = {BlockPolish: accurate polishing of long-read assembly via block divide-and-conquer}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab405}, doi = {10.1093/BIB/BBAB405}, timestamp = {Wed, 14 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HuangNNGLW22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuangWYG22, author = {Zimo Huang and Jun Wang and Zhongmin Yan and Maozu Guo}, title = {Differentially expressed genes prediction by multiple self-attention on epigenetics data}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac117}, doi = {10.1093/BIB/BBAC117}, timestamp = {Fri, 10 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HuangWYG22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuangYLJWARHL22, author = {Le Huang and Yuchen Yang and Gang Li and Minzhi Jiang and Jia Wen and Armen Abnousi and Jonathan D. Rosen and Ming Hu and Yun Li}, title = {A systematic evaluation of Hi-C data enhancement methods for enhancing PLAC-seq and HiChIP data}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac145}, doi = {10.1093/BIB/BBAC145}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HuangYLJWARHL22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuangZC22, author = {Li Huang and Li Zhang and Xing Chen}, title = {Updated review of advances in microRNAs and complex diseases: taxonomy, trends and challenges of computational models}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac358}, doi = {10.1093/BIB/BBAC358}, timestamp = {Tue, 18 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HuangZC22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuangZC22a, author = {Li Huang and Li Zhang and Xing Chen}, title = {Updated review of advances in microRNAs and complex diseases: experimental results, databases, webservers and data fusion}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac397}, doi = {10.1093/BIB/BBAC397}, timestamp = {Sun, 25 Dec 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HuangZC22a.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuangZC22b, author = {Li Huang and Li Zhang and Xing Chen}, title = {Updated review of advances in microRNAs and complex diseases: towards systematic evaluation of computational models}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac407}, doi = {10.1093/BIB/BBAC407}, timestamp = {Sun, 25 Dec 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HuangZC22b.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuangZLDWZL22, author = {Haojie Huang and Gongming Zhou and Xuejun Liu and Lei Deng and Chen Wu and Dachuan Zhang and Hui Liu}, title = {Contrastive learning-based computational histopathology predict differential expression of cancer driver genes}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac294}, doi = {10.1093/BIB/BBAC294}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/HuangZLDWZL22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/HuffmanOHDTH22, author = {Anthony Huffman and Edison Ong and Junguk Hur and Adonis D'mello and Herv{\'{e}} Tettelin and Yongqun He}, title = {{COVID-19} vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning}, journal = {Briefings Bioinform.}, volume = {23}, number = {4}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac190}, doi = {10.1093/BIB/BBAC190}, timestamp = {Tue, 21 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/HuffmanOHDTH22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/Hussain22, author = {Waqar Hussain}, title = {sAMP-PFPDeep: Improving accuracy of short antimicrobial peptides prediction using three different sequence encodings and deep neural networks}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab487}, doi = {10.1093/BIB/BBAB487}, timestamp = {Tue, 15 Mar 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/Hussain22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JaakkolaE22, author = {Maria K. Jaakkola and Laura L. Elo}, title = {Estimating cell type-specific differential expression using deconvolution}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab433}, doi = {10.1093/BIB/BBAB433}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JaakkolaE22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JacobsenKCRS22, author = {Julius O. B. Jacobsen and Catherine Kelly and Valentina Cipriani and Peter N. Robinson and Damian Smedley}, title = {Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac188}, doi = {10.1093/BIB/BBAC188}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JacobsenKCRS22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JarnotZGG22, author = {Patryk Jarnot and Joanna Ziemska{-}Legiecka and Marcin Grynberg and Aleksandra Gruca}, title = {Insights from analyses of low complexity regions with canonical methods for protein sequence comparison}, journal = {Briefings Bioinform.}, volume = {23}, number = {5}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac299}, doi = {10.1093/BIB/BBAC299}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JarnotZGG22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JeonHPLM22, author = {Young{-}Jun Jeon and Md. Mehedi Hasan and Hyun Woo Park and Ki Wook Lee and Balachandran Manavalan}, title = {{TACOS:} a novel approach for accurate prediction of cell-specific long noncoding RNAs subcellular localization}, journal = {Briefings Bioinform.}, volume = {23}, number = {4}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac243}, doi = {10.1093/BIB/BBAC243}, timestamp = {Sat, 13 May 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JeonHPLM22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JeongSTTGBPL22, author = {Yunhee Jeong and Lisa Barros de Andrade e Sousa and Dominik Thalmeier and Reka Toth and Marlene Ganslmeier and Kersten Breuer and Christoph Plass and Pavlo Lutsik}, title = {Systematic evaluation of cell-type deconvolution pipelines for sequencing-based bulk {DNA} methylomes}, journal = {Briefings Bioinform.}, volume = {23}, number = {4}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac248}, doi = {10.1093/BIB/BBAC248}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JeongSTTGBPL22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JiAPES22, author = {Jiahui Ji and Maryam Anwar and Enrico Petretto and Costanza Emanueli and Prashant Kumar Srivastava}, title = {{PPMS:} {A} framework to Profile Primary MicroRNAs from Single-cell RNA-sequencing datasets}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac419}, doi = {10.1093/BIB/BBAC419}, timestamp = {Sun, 12 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/JiAPES22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JiLZST22, author = {Hongchao Ji and Xue Lu and Zhenxiang Zheng and Siyuan Sun and Chris Soon Heng Tan}, title = {ProSAP: a {GUI} software tool for statistical analysis and assessment of thermal stability data}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac057}, doi = {10.1093/BIB/BBAC057}, timestamp = {Tue, 16 Aug 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JiLZST22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JiaYJLWLHLCZ22, author = {Lihua Jia and Wen Yao and Yingru Jiang and Yang Li and Zhizhan Wang and Haoran Li and Fangfang Huang and Jiaming Li and Tiantian Chen and Huiyong Zhang}, title = {Development of interactive biological web applications with R/Shiny}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab415}, doi = {10.1093/BIB/BBAB415}, timestamp = {Tue, 16 Aug 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JiaYJLWLHLCZ22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JiangCLLHX22, author = {Peiran Jiang and Ying Chi and Xiao{-}Shuang Li and Xiang Liu and Xian{-}Sheng Hua and Kelin Xia}, title = {Molecular persistent spectral image (Mol-PSI) representation for machine learning models in drug design}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab527}, doi = {10.1093/BIB/BBAB527}, timestamp = {Tue, 21 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/JiangCLLHX22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JiangHL22, author = {Han{-}Jing Jiang and Yabing Huang and Qianpeng Li}, title = {Spectral clustering of single cells using Siamese nerual network combined with improved affinity matrix}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac113}, doi = {10.1093/BIB/BBAC113}, timestamp = {Tue, 31 May 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JiangHL22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JiangJYFJL22, author = {Likun Jiang and Changzhi Jiang and Xinyu Yu and Rao Fu and Shuting Jin and Xiangrong Liu}, title = {DeepTTA: a transformer-based model for predicting cancer drug response}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac100}, doi = {10.1093/BIB/BBAC100}, timestamp = {Thu, 02 Jun 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JiangJYFJL22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JiangLLWXDYCS22, author = {Zhonghua Jiang and Yongmei Lu and Zhuochong Liu and Wei Wu and Xinyi Xu and Andr{\'{a}}s Dinny{\'{e}}s and Zhonghua Yu and Li Chen and Qun Sun}, title = {Drug resistance prediction and resistance genes identification in \emph{Mycobacterium tuberculosis} based on a hierarchical attentive neural network utilizing genome-wide variants}, journal = {Briefings Bioinform.}, volume = {23}, number = {3}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac041}, doi = {10.1093/BIB/BBAC041}, timestamp = {Wed, 06 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JiangLLWXDYCS22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JiangNWWZLLCS22, author = {Mengyun Jiang and Weidong Ning and Shishi Wu and Xingwei Wang and Kun Zhu and Aomei Li and Yongyao Li and Shifeng Cheng and Bo Song}, title = {Three-nucleotide periodicity of nucleotide diversity in a population enables the identification of open reading frames}, journal = {Briefings Bioinform.}, volume = {23}, number = {4}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac210}, doi = {10.1093/BIB/BBAC210}, timestamp = {Mon, 08 Aug 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/JiangNWWZLLCS22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
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