default search action
Google
Google Scholar
Semantic Scholar
Internet Archive Scholar
CiteSeerX
ORCIDBriefings in Bioinformatics, Volume 25
Volume 25, Number 1, November 2023
- Junjie Zhu, Zhengxin Li, Haowei Tong, Zhouyu Lu, Ningjie Zhang, Ting Wei, Hai-Feng Chen
:
Phanto-IDP: compact model for precise intrinsically disordered protein backbone generation and enhanced sampling. - Dong Liu, Biao Zhang, Jun Liu, Hui Li, Le Song, Guijun Zhang:
Assessing protein model quality based on deep graph coupled networks using protein language model. - Milos Musil, Andrej Jezik, Jana Horackova, Simeon Borko, Petr Kabourek, Jirí Damborský, David Bednar:
FireProt 2.0: web-based platform for the fully automated design of thermostable proteins. - Francis Yew Fu Tieng, Muhammad Redha Abdullah Zawawi, Nur Alyaa Afifah Md Shahri, Zeti-Azura Mohamed-Hussein, Learn-Han Lee, Nurul-Syakima Ab Mutalib:
A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools. - Jiawei Zhang, Wang Ma, Hui Yao:
Accurate TCR-pMHC interaction prediction using a BERT-based transfer learning method. - Miles McGibbon, Steven R. Shave, Jie Dong, Yumiao Gao, Douglas R. Houston, Jiancong Xie, Yuedong Yang, Philippe Schwaller, Vincent Blay:
From intuition to AI: evolution of small molecule representations in drug discovery. - Nhat Truong Pham, Le Thi Phan, Jimin Seo, Yeonwoo Kim, Minkyung Song, Sukchan Lee, Young-Jun Jeon, Balachandran Manavalan:
Advancing the accuracy of SARS-CoV-2 phosphorylation site detection via meta-learning approach. - Wenxuan Xing, Jie Zhang, Chen Li, Yujia Huo, Gaifang Dong:
iAMP-Attenpred: a novel antimicrobial peptide predictor based on BERT feature extraction method and CNN-BiLSTM-Attention combination model. - Qingyang Yin, Liang Chen:
CellTICS: an explainable neural network for cell-type identification and interpretation based on single-cell RNA-seq data. - Zikun Yang, Basilio Cieza, Dolly Reyes-Dumeyer, Rosa Montesinos, Marcio Soto-Añari, Nilton Custodio, Giuseppe Tosto:
A benchmark study on current GWAS models in admixed populations. - Yajie Meng, Yi Wang, Junlin Xu, Changcheng Lu, Xianfang Tang, Tao Peng, Ben-gong Zhang, Geng Tian, Jialiang Yang:
Drug repositioning based on weighted local information augmented graph neural network. - Elena Lucy Carter, Chrystala Constantinidou, Mohammad Tauqeer Alam:
Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations. - Ping Fu, Yifan Wu, Zhiyuan Zhang, Ye Qiu, Yirong Wang, Yousong Peng:
VIGA: a one-stop tool for eukaryotic virus identification and genome assembly from next-generation-sequencing data. - Yu Mei Wang, Yuzhi Sun, Beiying Wang, Zhiping Wu, Xiao-Ying He, Yuansong Zhao:
Transfer learning for clustering single-cell RNA-seq data crossing-species and batch, case on uterine fibroids. - Peilong Li, Junfeng Wei, Ying Zhu:
CellGO: a novel deep learning-based framework and webserver for cell-type-specific gene function interpretation. - Correction to: Breaking the barriers of data scarcity in drug-target affinity prediction.
- Daniel Toro-Domínguez, Jordi Martorell-Marugan, Manuel Martínez-Bueno, Raúl López-Domínguez, Elena Carnero-Montoro, Guillermo Barturen, Daniel Goldman, Michelle Petri, Pedro Carmona-Saez, Marta E. Alarcón-Riquelme:
Response to the letter 'testing the effectiveness of MyPROSLE in classifying patients with lupus nephritis'. - Sang-Ho Yoon, Jin-Wu Nam:
Clustering malignant cell states using universally variable genes. - Jiaxian Yan, Zhaofeng Ye, Ziyi Yang, Chengqiang Lu, Shengyu Zhang, Qi Liu, Jiezhong Qiu:
Multi-task bioassay pre-training for protein-ligand binding affinity prediction. - Pavel Akhtyamov, Layal Shaheen, Mikhail Raevskiy, Alexey Stupnikov, Yulia A. Medvedeva:
scATAC-seq preprocessing and imputation evaluation system for visualization, clustering and digital footprinting. - Jie Dong, Zheng Wu, Huanle Xu, Defang Ouyang:
FormulationAI: a novel web-based platform for drug formulation design driven by artificial intelligence. - So-Ra Han, Mingyu Park, Sai Kosaraju, Jeungmin Lee, Hyun Lee, Jun Hyuck Lee, Tae-Jin Oh, Mingon Kang:
Evidential deep learning for trustworthy prediction of enzyme commission number. - Jorge Beltrán, Lisandra Herrera Belén, Jorge G. Farias, Mauricio Zamorano, Nicolás Lefin, Javiera Miranda, Fernanda Parraguez Contreras:
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. - Cuiling Wu, Yiyi Zhang, Zhiwen Ying, Ling Li, Jun Wang, Hui Yu, Mengchen Zhang, Xianzhong Feng, Xinghua Wei, Xiaogang Xu:
A transformer-based genomic prediction method fused with knowledge-guided module. - Min Zou, Honghao Li, Dongqing Su, Yuqiang Xiong, Haodong Wei, Shiyuan Wang, Hongmei Sun, Tao Wang, Qilemuge Xi, Yongchun Zuo, Lei Yang:
Integrating somatic mutation profiles with structural deep clustering network for metabolic stratification in pancreatic cancer: a comprehensive analysis of prognostic and genomic landscapes. - Hao Qian, Wenjing Huang, Shikui Tu, Lei Xu:
KGDiff: towards explainable target-aware molecule generation with knowledge guidance. - Jan Stourac, Simeon Borko, Rayyan T. Khan, Petra Pokorna, Adam Dobias, Joan Planas-Iglesias, Stanislav Mazurenko, Gaspar R. P. Pinto, Veronika Szotkowska, Jaroslav Sterba, Ondrej Slaby, Jirí Damborský, David Bednar:
PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning. - Lei Chen, Yuwei Chen:
RMTLysPTM: recognizing multiple types of lysine PTM sites by deep analysis on sequences. - Zhen-Ning Yin, Fei-Liao Lai, Feng Gao:
Unveiling human origins of replication using deep learning: accurate prediction and comprehensive analysis. - Qiyiwen Zhang, Changgee Chang, Qi Long:
Robust knowledge-guided biclustering for multi-omics data. - Ruofan Ding, Xudong Zou, Yangmei Qin, Lihai Gong, Hui Chen, Xuelian Ma, Shouhong Guang, Chen Yu, Gao Wang, Lei Li:
xQTLbiolinks: a comprehensive and scalable tool for integrative analysis of molecular QTLs. - Qisheng Pan, Stephanie Portelli, Thanh-Binh Nguyen, David B. Ascher:
Characterization on the oncogenic effect of the missense mutations of p53 via machine learning. - Stavros Makrodimitris, Bram Pronk, Tamim Abdelaal, Marcel J. T. Reinders:
An in-depth comparison of linear and non-linear joint embedding methods for bulk and single-cell multi-omics. - Shuheng Pan, Xinyi Jiang, Kai Zhang:
WSGMB: weight signed graph neural network for microbial biomarker identification. - Qilin Wang, Junyou Zhang, Zhaoshuo Liu, Yingying Duan, Chunyan Li:
Integrative approaches based on genomic techniques in the functional studies on enhancers. - Fanding Xu, Zhiwei Yang, Lizhuo Wang, Deyu Meng, Jiangang Long:
MESPool: Molecular Edge Shrinkage Pooling for hierarchical molecular representation learning and property prediction. - Juntao Li, Hongmei Zhang, Bingyu Mu, Hongliang Zuo, Kanglei Zhou:
Identifying phenotype-associated subpopulations through LP_SGL. - Jiahao Zheng, Yuedong Yang, Zhiming Dai:
Subgraph extraction and graph representation learning for single cell Hi-C imputation and clustering. - Zhen Wang, Zheng Feng, Yanjun Li, Bowen Li, Yongrui Wang, Chulin Sha, Min He, Xiaolin Li:
BatmanNet: bi-branch masked graph transformer autoencoder for molecular representation. - Benzhe Su, Weiwei Wang, Xiaohui Lin, Shenglan Liu, Xin Huang:
Identifying the potential miRNA biomarkers based on multi-view networks and reinforcement learning for diseases. - Kevin Tippenhauer, Marwin Philips, Carlo R. Largiadèr, Murat Sariyar:
Using the PharmCAT tool for Pharmacogenetic clinical decision support.
Volume 25, Number 2, January 2024
- Rajesh Kumar Pathak, Jun-Mo Kim:
Veterinary systems biology for bridging the phenotype-genotype gap via computational modeling for disease epidemiology and animal welfare. - Fengjuan Huang, Xinjie Fan, Ying Wang, Yu Zou, Jiangfang Lian, Chuang Wang, Feng Ding, Yunxiang Sun:
Computational insights into the cross-talk between medin and Aβ: implications for age-related vascular risk factors in Alzheimer's disease. - Sheng-Yong Xu, Shanshan Cai, Zhi-Qiang Han:
Evaluating the efficacy of MEANGS for mitochondrial genome assembly of cartilaginous and ray-finned fish species. - Minghao Fang, Jingwen Fang, Songwen Luo, Ke Liu, Qiaoni Yu, Jiaxuan Yang, Youyang Zhou, Zongkai Li, Ruoming Sun, Chuang Guo, Kun Qu:
eccDNA-pipe: an integrated pipeline for identification, analysis and visualization of extrachromosomal circular DNA from high-throughput sequencing data. - Yi-Heng Zhu, Zi Liu, Yan Liu, Zhiwei Ji, Dong-Jun Yu:
ULDNA: integrating unsupervised multi-source language models with LSTM-attention network for high-accuracy protein-DNA binding site prediction. - Hangjia Zhao, Michael Baudis:
labelSeg: segment annotation for tumor copy number alteration profiles. - Simone Maestri, Mattia Furlan, Logan Mulroney, Lucia Coscujuela Tarrero, Camilla Ugolini, Fabio Dalla Pozza, Tommaso Leonardi, Ewan Birney, Francesco Nicassio, Mattia Pelizzola:
Benchmarking of computational methods for m6A profiling with Nanopore direct RNA sequencing. - Ariadna Llop-Peiró, Gerard Pujadas, Santiago Garcia-Vallvé:
Challenges in distinguishing functional proteins from polyproteins in databases: implications for drug discovery. - Yuyao Zhai, Liang Chen, Minghua Deng:
scEVOLVE: cell-type incremental annotation without forgetting for single-cell RNA-seq data. - Sowmya Ramaswamy Krishnan, Arijit Roy, M. Michael Gromiha:
Reliable method for predicting the binding affinity of RNA-small molecule interactions using machine learning. - Wang Xu, Houfang Zhang, Wenhan Guo, Lijun Jiang, Yunjie Zhao, Yunhui Peng:
Deciphering principles of nucleosome interactions and impact of cancer-associated mutations from comprehensive interaction network analysis. - Xinyu Guo, Liang Chen:
From G1 to M: a comparative study of methods for identifying cell cycle phases. - Musu Yuan, Hui Wan, Zihao Wang, Qirui Guo, Minghua Deng:
SPANN: annotating single-cell resolution spatial transcriptome data with scRNA-seq data. - Mengting Niu, Chunyu Wang, Yaojia Chen, Quan Zou, Lei Xu:
Identification, characterization and expression analysis of circRNA encoded by SARS-CoV-1 and SARS-CoV-2. - Qiuchen Meng, Lei Wei, Kun Ma, Ming Shi, Xinyi Lin, Joshua W. K. Ho, Yinqing Li, Xuegong Zhang:
scDecouple: decoupling cellular response from infected proportion bias in scCRISPR-seq. - Songqi Zhou, Yang Li, Wenyuan Wu, Li Li:
scMMT: a multi-use deep learning approach for cell annotation, protein prediction and embedding in single-cell RNA-seq data. - Mona Nourbakhsh, Kristine Degn, Astrid Saksager, Matteo Tiberti, Elena Papaleo:
Prediction of cancer driver genes and mutations: the potential of integrative computational frameworks. - Jiaxuan Liu, Yonggang Lu, Li Zhu:
A kinetic model for solving a combination optimization problem in ab-initio Cryo-EM 3D reconstruction. - Yury A Barbitoff, Mikhail O. Ushakov, Tatyana E. Lazareva, Yulia A Nasykhova, Andrey S. Glotov, Alexander V. Predeus:
Bioinformatics of germline variant discovery for rare disease diagnostics: current approaches and remaining challenges. - Yaofeng Hu, Kai Xiao, Hengyu Yang, Xiaoping Liu, Chuanchao Zhang, Qianqian Shi:
Spatially contrastive variational autoencoder for deciphering tissue heterogeneity from spatially resolved transcriptomics. - Lu-Xiang Guo, Lei Wang, Zhu-Hong You, Chang-Qing Yu, Meng-Lei Hu, Bo-Wei Zhao, Yang Li:
Likelihood-based feature representation learning combined with neighborhood information for predicting circRNA-miRNA associations. - Junxiang Zeng, Xiupan Gao, Limei Gao, Youyou Yu, Lisong Shen, Xiujun Pan:
Recognition of rare antinuclear antibody patterns based on a novel attention-based enhancement framework. - Merve Vural-Ozdeniz, Kubra Calisir, Rana Acar, Aysenur Yavuz, Mustafa M. Ozgur, Ertugrul Dalgic, Ozlen Konu:
CAP-RNAseq: an integrated pipeline for functional annotation and prioritization of co-expression clusters. - Lijuan Wang, Ying Lu, Doudou Li, Yajing Zhou, Lili Yu, Ines Mesa Eguiagaray, Harry Campbell, Xue Li, Evropi Theodoratou:
The landscape of the methodology in drug repurposing using human genomic data: a systematic review. - Min Sun, Jing Chen, Chang Zhao, Lihua Zhang, Maili Liu, Yukui Zhang, Qun Zhao, Zhou Gong:
Enhancing protein dynamics analysis with hydrophilic polyethylene glycol cross-linkers. - Jing Meng, Jingze Liu, Wenkai Song, Honglei Li, Jiangyuan Wang, Le Zhang, Yousong Peng, Aiping Wu, Taijiao Jiang:
PREDAC-CNN: predicting antigenic clusters of seasonal influenza A viruses with convolutional neural network. - Gulam Sarwar Chuwdhury, Yunshan Guo, Chi-Leung Chiang, Ka-On Lam, Ngar-Woon Kam, Zhonghua Liu, Wei Dai:
ImmuneMirror: A machine learning-based integrative pipeline and web server for neoantigen prediction. - Yue Guo, Haitao Hu, Wenbo Chen, Hao Yin, Jian Wu, Chang-Yu Hsieh, Qiaojun He, Ji Cao:
SynergyX: a multi-modality mutual attention network for interpretable drug synergy prediction. - Giovanni Visonà, Emmanuelle Bouzigon, Florence Demenais, Gabriele Beate Schweikert:
Network propagation for GWAS analysis: a practical guide to leveraging molecular networks for disease gene discovery. - Céline Brouard, Raphaël Mourad, Nathalie Vialaneix:
Should we really use graph neural networks for transcriptomic prediction? - Chengcheng Zhang, Tianyi Zang, Tianyi Zhao:
KGE-UNIT: toward the unification of molecular interactions prediction based on knowledge graph and multi-task learning on drug discovery. - Jici Jiang, Hongdi Pei, Jiayu Li, Mingxin Li, Quan Zou, Zhibin Lv:
FEOpti-ACVP: identification of novel anti-coronavirus peptide sequences based on feature engineering and optimization. - Zhen-Hao Guo, Yan-Bin Wang, Siguo Wang, Qinhu Zhang, De-Shuang Huang:
scCorrector: a robust method for integrating multi-study single-cell data. - Youngjune Park, Nils P. Muttray, Anne-Christin Hauschild:
Species-agnostic transfer learning for cross-species transcriptomics data integration without gene orthology. - Olivier Cinquin:
ChIP-GPT: a managed large language model for robust data extraction from biomedical database records. - Yibo Zhang, Wenyu Liu, Junbo Duan:
On the core segmentation algorithms of copy number variation detection tools. - Yan Miao, Zhenyuan Sun, Chenjing Ma, Chen Lin, Guohua Wang, Chunxue Yang:
VirGrapher: a graph-based viral identifier for long sequences from metagenomes. - Qingyue Wei, Md Tauhidul Islam, Yuyin Zhou, Lei Xing:
Self-supervised deep learning of gene-gene interactions for improved gene expression recovery. - Aleksandra E. Badaczewska-Dawid, Karol Wroblewski, Mateusz Kurcinski, Sebastian Kmiecik:
Structure prediction of linear and cyclic peptides using CABS-flex. - Lingyan Zheng, Shuiyang Shi, Xiuna Sun, Mingkun Lu, Yang Liao, Sisi Zhu, Hongning Zhang, Ziqi Pan, Pan Fang, Zhenyu Zeng, Honglin Li, Zhaorong Li, Weiwei Xue, Feng Zhu:
MoDAFold: a strategy for predicting the structure of missense mutant protein based on AlphaFold2 and molecular dynamics. - Seokjin Han, Ji Eun Lee, Seolhee Kang, Minyoung So, Hee Jin, Jang Ho Lee, Sunghyeob Baek, Hyungjin Jun, Tae Yong Kim, Yun-Sil Lee:
Standigm ASK™: knowledge graph and artificial intelligence platform applied to target discovery in idiopathic pulmonary fibrosis. - Jin Zhang, Zikang Ma, Yan Yang, Lei Guo, Lei Du:
Modeling genotype-protein interaction and correlation for Alzheimer's disease: a multi-omics imaging genetics study. - Shuang Gu, Chaoliang Wen, Zhen Xiao, Qiang Huang, Zheyi Jiang, Honghong Liu, Jia Gao, Junying Li, Congjiao Sun, Ning Yang:
MyoV: a deep learning-based tool for the automated quantification of muscle fibers. - Fabio N. de Mello, Ana C. Tahira, Maria Gabriela Berzoti-Coelho, Sergio Verjovski-Almeida:
The CUT&RUN greenlist: genomic regions of consistent noise are effective normalizing factors for quantitative epigenome mapping. - Yue Zang, Xia Ran, Jie Yuan, Hao Wu, Youya Wang, He Li, Huajing Teng, Zhongsheng Sun:
Genomic hallmarks and therapeutic targets of ribosome biogenesis in cancer. - Zeyu Luo, Rui Wang, Yawen Sun, Junhao Liu, Herman Z. Q. Chen, Yu-Juan Zhang:
Interpretable feature extraction and dimensionality reduction in ESM2 for protein localization prediction. - Shi Zhang, Rui Zhang, Kai Yuan, Lu Yang, Chang Liu, Yuting Liu, Xumin Ni, Shuhua Xu:
Reconstructing complex admixture history using a hierarchical model. - Shuo Li, Yan Liu, Long-Chen Shen, He Yan, Jiangning Song, Dong-Jun Yu:
GMFGRN: a matrix factorization and graph neural network approach for gene regulatory network inference. - Albert Katchborian-Neto, Matheus F. Alves, Paula C. P. Bueno, Karen de Jesus Nicácio, Miller S. Ferreira, Tiago B. Oliveira, Henrique Barbosa, Michael Murgu, Ana C. C. de Paula Ladvocat, Danielle F. Dias, Marisi G. Soares, João Henrique Ghilardi Lago, Daniela A Chagas-Paula:
Integrative open workflow for confident annotation and molecular networking of metabolomics MSE/DIA data. - Xiaodi Yang, Stefan Wuchty, Zeyin Liang, Li Ji, Bingjie Wang, Jialin Zhu, Ziding Zhang, Yujun Dong:
Multi-modal features-based human-herpesvirus protein-protein interaction prediction by using LightGBM. - Kandarp Joshi, Dan O. Wang:
epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation. - Yantong Cai, Jia Lv, Rui Li, Xiaowen Huang, Shi Wang, Zhenmin Bao, Qifan Zeng:
Deqformer: high-definition and scalable deep learning probe design method. - Jingxuan Qiu, Wanchun Nie, Hao Ding, Jia Dai, Yiwen Wei, Dezhi Li, Yuxi Zhang, Junting Xie, Xinxin Tian, Nannan Wu, Tianyi Qiu:
PB-LKS: a python package for predicting phage-bacteria interaction through local K-mer strategy. - Wenyuan Ma, Hui Wu, Yiran Chen, Hongxia Xu, Junjie Jiang, Bang Du, Mingyu Wan, Xiaolu Ma, Xiaoyu Chen, Lili Lin, Xinhui Su, Xuanwen Bao, Yifei Shen, Nong Xu, Jian Ruan, Haiping Jiang, Yongfeng Ding:
New techniques to identify the tissue of origin for cancer of unknown primary in the era of precision medicine: progress and challenges. - Tingpeng Yang, Tianze Ling, Boyan Sun, Zhendong Liang, Fan Xu, Xiansong Huang, Linhai Xie, Yonghong He, Leyuan Li, Fuchu He, Yu Wang, Cheng Chang:
Introducing π-HelixNovo for practical large-scale de novo peptide sequencing.
Volume 25, Number 3, 2024
- Hui Wang, Dong Liu, Kailong Zhao, Yajun Wang, Guijun Zhang:
SPDesign: protein sequence designer based on structural sequence profile using ultrafast shape recognition. - Pengyong Li, Zhengxiang Jiang, Tianxiao Liu, Xinyu Liu, Hui Qiao, Xiaojun Yao:
Improving drug response prediction via integrating gene relationships with deep learning. - Haoquan Liu, Yunjie Zhao:
Integrated modeling of protein and RNA. - Zhenyu Wei, Chengkui Zhao, Min Zhang, Jiayu Xu, Nan Xu, Shiwei Wu, Xiaohui Xin, Lei Yu, Weixing Feng:
Meta-DHGNN: method for CRS-related cytokines analysis in CAR-T therapy based on meta-learning directed heterogeneous graph neural network. - Junxi Mu, Zhengxin Li, Bo Zhang, Qi Zhang, Jamshed Iqbal, Abdul Wadood, Ting Wei, Yan Feng, Hai-Feng Chen:
Graphormer supervised de novo protein design method and function validation. - Seunghyun Wang, Doheon Lee:
Community cohesion looseness in gene networks reveals individualized drug targets and resistance. - Zhen Gao, Yansen Su, Junfeng Xia, Rui-Fen Cao, Yun Ding, Chun-Hou Zheng, Pi-Jing Wei:
DeepFGRN: inference of gene regulatory network with regulation type based on directed graph embedding. - Xinyan Wang, Kuo Yang, Ting Jia, Fanghui Gu, Chongyu Wang, Kuan Xu, Zixin Shu, Jianan Xia, Qiang Zhu, Xuezhong Zhou:
KDGene: knowledge graph completion for disease gene prediction using interactional tensor decomposition. - Akram Vasighizaker, Sheena Hora, Raymond Zeng, Luis Rueda:
SEGCECO: Subgraph Embedding of Gene expression matrix for prediction of CEll-cell COmmunication. - Zhen Tian, Chenguang Han, Lewen Xu, Zhixia Teng, Wei Song:
MGCNSS: miRNA-disease association prediction with multi-layer graph convolution and distance-based negative sample selection strategy. - Priyotosh Sil, Ajay Subbaroyan, Saumitra Kulkarni, Olivier C. Martin, Areejit Samal:
Biologically meaningful regulatory logic enhances the convergence rate in Boolean networks and bushiness of their state transition graph.