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@article{DBLP:journals/bioinformatics/AbanadesGBD22,
author = {Brennan Abanades and
Guy Georges and
Alexander Bujotzek and
Charlotte M. Deane},
title = {ABlooper: fast accurate antibody {CDR} loop structure prediction with
accuracy estimation},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {1877--1880},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac016},
doi = {10.1093/BIOINFORMATICS/BTAC016},
timestamp = {Fri, 13 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AbanadesGBD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AbdelmoulaSRRAS22,
author = {Walid M. Abdelmoula and
Sylwia Stopka and
Elizabeth C. Randall and
Michael Regan and
Jeffrey N. Agar and
Jann N. Sarkaria and
William M. Wells III and
Tina Kapur and
Nathalie Y. R. Agar},
title = {massNet: integrated processing and classification of spatially resolved
mass spectrometry data using deep learning for rapid tumor delineation},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {2015--2021},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac032},
doi = {10.1093/BIOINFORMATICS/BTAC032},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AbdelmoulaSRRAS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AbebePHMWWD22,
author = {Jonathan S. Abebe and
Alexander M. Price and
Katharina E. Hayer and
Ian Mohr and
Matthew D. Weitzman and
Angus C. Wilson and
Daniel P. Depledge},
title = {{DRUMMER} - rapid detection of {RNA} modifications through comparative
nanopore sequencing},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3113--3115},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac274},
doi = {10.1093/BIOINFORMATICS/BTAC274},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AbebePHMWWD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AcharyyaZB22,
author = {Satwik Acharyya and
Xiang Zhou and
Veerabhadran Baladandayuthapani},
title = {SpaceX: gene co-expression network estimation for spatial transcriptomics},
journal = {Bioinform.},
volume = {38},
number = {22},
pages = {5033--5041},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac645},
doi = {10.1093/BIOINFORMATICS/BTAC645},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/AcharyyaZB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AdamczykAS22,
author = {Bartosz Adamczyk and
Maciej Antczak and
Marta Szachniuk},
title = {RNAsolo: a repository of cleaned PDB-derived {RNA} 3D structures},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3668--3670},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac386},
doi = {10.1093/BIOINFORMATICS/BTAC386},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AdamczykAS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AdamsNKBJ22,
author = {Tim Adams and
Marcin Namysl and
Alpha Tom Kodamullil and
Sven Behnke and
Marc Jacobs},
title = {Benchmarking table recognition performance on biomedical literature
on neurological disorders},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1624--1630},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab843},
doi = {10.1093/BIOINFORMATICS/BTAB843},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AdamsNKBJ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AgmonSSPPMC22,
author = {Eran Agmon and
Ryan K. Spangler and
Christopher J. Skalnik and
William Poole and
Shayn M. Peirce and
Jerry H. Morrison and
Markus W. Covert},
title = {Vivarium: an interface and engine for integrative multiscale modeling
in computational biology},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {1972--1979},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac049},
doi = {10.1093/BIOINFORMATICS/BTAC049},
timestamp = {Wed, 27 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AgmonSSPPMC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AinciburuMDLPG22,
author = {Marina Ainciburu and
Duncan M. Morgan and
Erica A. K. Depasquale and
J. Christopher Love and
Felipe Pr{\'{o}}sper and
Peter van Galen},
title = {{WAT3R:} recovery of T-cell receptor variable regions from 3{\({'}\)}
single-cell RNA-sequencing},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3645--3647},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac382},
doi = {10.1093/BIOINFORMATICS/BTAC382},
timestamp = {Mon, 08 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AinciburuMDLPG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AkgunPK22,
author = {Mete Akg{\"{u}}n and
Nico Pfeifer and
Oliver Kohlbacher},
title = {Efficient privacy-preserving whole-genome variant queries},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2202--2210},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac070},
doi = {10.1093/BIOINFORMATICS/BTAC070},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AkgunPK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Al-AnziKF22,
author = {Bader F. Al{-}Anzi and
Mohammad Khajah and
Saja A. Fakhraldeen},
title = {Predicting and explaining the impact of genetic disruptions and interactions
on organismal viability},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4088--4099},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac519},
doi = {10.1093/BIOINFORMATICS/BTAC519},
timestamp = {Mon, 24 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Al-AnziKF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AlameerC22,
author = {Abbas Alameer and
Davide Chicco},
title = {geoCancerPrognosticDatasetsRetriever: a bioinformatics tool to easily
identify cancer prognostic datasets on Gene Expression Omnibus {(GEO)}},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1761--1763},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab852},
doi = {10.1093/BIOINFORMATICS/BTAB852},
timestamp = {Fri, 01 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AlameerC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AlcorizaBalaguerGRRL22,
author = {Mar{\'{\i}}a Isabel Alcoriza{-}Balaguer and
Juan Carlos Garc{\'{\i}}a{-}Ca{\~{n}}averas and
Francisco Javier Ripoll{-}Esteve and
Marta Roca and
Agust{\'{\i}}n Lahoz},
title = {LipidMS 3.0: an R-package and a web-based tool for {LC-MS/MS} data
processing and lipid annotation},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4826--4828},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac581},
doi = {10.1093/BIOINFORMATICS/BTAC581},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AlcorizaBalaguerGRRL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AlmeidaTD22,
author = {Hayda Almeida and
Adrian Tsang and
Abdoulaye Banir{\'{e}} Diallo},
title = {Improving candidate Biosynthetic Gene Clusters in fungi through reinforcement
learning},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {3984--3991},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac420},
doi = {10.1093/BIOINFORMATICS/BTAC420},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AlmeidaTD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AlmodaresiKMFJP22,
author = {Fatemeh Almodaresi and
Jamshed Khan and
Sergey Madaminov and
Michael Ferdman and
Rob Johnson and
Prashant Pandey and
Rob Patro},
title = {An incrementally updatable and scalable system for large-scale sequence
search using the Bentley-Saxe transformation},
journal = {Bioinform.},
volume = {38},
number = {12},
pages = {3155--3163},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac142},
doi = {10.1093/BIOINFORMATICS/BTAC142},
timestamp = {Wed, 23 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AlmodaresiKMFJP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AlthagafiAKMAMA22,
author = {Azza Althagafi and
Lamia Alsubaie and
Nagarajan Kathiresan and
Katsuhiko Mineta and
Taghrid Aloraini and
Fuad Al Mutairi and
Majid Alfadhel and
Takashi Gojobori and
Ahmad Alfares and
Robert Hoehndorf},
title = {DeepSVP: integration of genotype and phenotype for structural variant
prioritization using deep learning},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1677--1684},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab859},
doi = {10.1093/BIOINFORMATICS/BTAB859},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AlthagafiAKMAMA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AluruSCSA22,
author = {Maneesha Aluru and
Harsh Shrivastava and
Sriram P. Chockalingam and
Shruti Shivakumar and
Srinivas Aluru},
title = {EnGRaiN: a supervised ensemble learning method for recovery of large-scale
gene regulatory networks},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1312--1319},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab829},
doi = {10.1093/BIOINFORMATICS/BTAB829},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/AluruSCSA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AmblardBCSZ22,
author = {Elise Amblard and
Jonathan Bac and
Alexander Chervov and
Vassili Soumelis and
Andrei Yu. Zinovyev},
title = {Hubness reduction improves clustering and trajectory inference in
single-cell transcriptomic data},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1045--1051},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab795},
doi = {10.1093/BIOINFORMATICS/BTAB795},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AmblardBCSZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AmgadAHMHEMMGEC22,
author = {Mohamed Amgad and
Lamees A. Atteya and
Hagar Hussein and
Kareem Hosny Mohammed and
Ehab Hafiz and
Maha A. T. Elsebaie and
Pooya Mobadersany and
David Manthey and
David A. Gutman and
Habiba Elfandy and
Lee A. D. Cooper},
title = {Explainable nucleus classification using Decision Tree Approximation
of Learned Embeddings},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {513--519},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab670},
doi = {10.1093/BIOINFORMATICS/BTAB670},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AmgadAHMHEMMGEC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AmiryousefiWJT22,
author = {Ali Amiryousefi and
Bernardo Williams and
Mohieddin Jafari and
Jing Tang},
title = {The {ENDS} of assumptions: an online tool for the epistemic non-parametric
drug-response scoring},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3132--3133},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac217},
doi = {10.1093/BIOINFORMATICS/BTAC217},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AmiryousefiWJT22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AngaroniCDCGR22,
author = {Fabrizio Angaroni and
Kevin Chen and
Chiara Damiani and
Giulio Caravagna and
Alex Graudenzi and
Daniele Ramazzotti},
title = {{PMCE:} efficient inference of expressive models of cancer evolution
with high prognostic power},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {754--762},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab717},
doi = {10.1093/BIOINFORMATICS/BTAB717},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AngaroniCDCGR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AnsaloniGEGS22,
author = {Federico Ansaloni and
Nicol{\`{o}} Gualandi and
Mauro Esposito and
Stefano Gustincich and
Remo Sanges},
title = {TEspeX: consensus-specific quantification of transposable element
expression preventing biases from exonized fragments},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4430--4433},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac526},
doi = {10.1093/BIOINFORMATICS/BTAC526},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AnsaloniGEGS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AnthonCG22,
author = {Christian Anthon and
Giulia Ilaria Corsi and
Jan Gorodkin},
title = {CRISPRon/off: CRISPR/Cas9 on- and off-target gRNA design},
journal = {Bioinform.},
volume = {38},
number = {24},
pages = {5437--5439},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac697},
doi = {10.1093/BIOINFORMATICS/BTAC697},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AnthonCG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AptekmannBGGFB22,
author = {Ariel A. Aptekmann and
J. Buongiorno and
D. Giovannelli and
M. Glamoclija and
Diego U. Ferreiro and
Yana Bromberg},
title = {\emph{mebipred}: identifying metal-binding potential in protein sequence},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3532--3540},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac358},
doi = {10.1093/BIOINFORMATICS/BTAC358},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AptekmannBGGFB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ArefBH22,
author = {Layla Aref and
Lisa Bastarache and
Jacob J. Hughey},
title = {The phers {R} package: using phenotype risk scores based on electronic
health records to study Mendelian disease and rare genetic variants},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4972--4974},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac619},
doi = {10.1093/BIOINFORMATICS/BTAC619},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ArefBH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AttaSF22,
author = {Lyla Atta and
Arpan Sahoo and
Jean Fan},
title = {VeloViz: {RNA} velocity-informed embeddings for visualizing cellular
trajectories},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {391--396},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab653},
doi = {10.1093/BIOINFORMATICS/BTAB653},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/AttaSF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AyatiYCK22,
author = {Marzieh Ayati and
Serhan Yilmaz and
Mark R. Chance and
Mehmet Koyut{\"{u}}rk},
title = {Functional characterization of co-phosphorylation networks},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3785--3793},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac406},
doi = {10.1093/BIOINFORMATICS/BTAC406},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/AyatiYCK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Badaczewska-Dawid22,
author = {Aleksandra E. Badaczewska{-}Dawid and
Javier Garcia{-}Pardo and
Aleksander Kuriata and
Jordi Pujols and
Salvador Ventura and
Sebastian Kmiecik},
title = {{A3D} database: structure-based predictions of protein aggregation
for the human proteome},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3121--3123},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac215},
doi = {10.1093/BIOINFORMATICS/BTAC215},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Badaczewska-Dawid22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BaiLSYZC22,
author = {Yang Bai and
Yang Li and
Yu Shen and
Mingyu Yang and
Wentao Zhang and
Bin Cui},
title = {AutoDC: an automatic machine learning framework for disease classification},
journal = {Bioinform.},
volume = {38},
number = {13},
pages = {3415--3421},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac334},
doi = {10.1093/BIOINFORMATICS/BTAC334},
timestamp = {Wed, 24 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BaiLSYZC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BaiXZGL22,
author = {Tian Bai and
Jiayu Xu and
Zhenting Zhang and
Shuyu Guo and
Xiao Luo},
title = {Context-aware learning for cancer cell nucleus recognition in pathology
images},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2892--2898},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac167},
doi = {10.1093/BIOINFORMATICS/BTAC167},
timestamp = {Mon, 13 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BaiXZGL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BaiZMYFUI22,
author = {Zeheng Bai and
Yao{-}zhong Zhang and
Satoru Miyano and
Rui Yamaguchi and
Kosuke Fujimoto and
Satoshi Uematsu and
Seiya Imoto},
title = {Identification of bacteriophage genome sequences with representation
learning},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4264--4270},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac509},
doi = {10.1093/BIOINFORMATICS/BTAC509},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BaiZMYFUI22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BalabinHBGBKPHD22,
author = {Helena Balabin and
Charles Tapley Hoyt and
Colin Birkenbihl and
Benjamin M. Gyori and
John A. Bachman and
Alpha Tom Kodamullil and
Paul G. Pl{\"{o}}ger and
Martin Hofmann{-}Apitius and
Daniel Domingo{-}Fern{\'{a}}ndez},
title = {STonKGs: a sophisticated transformer trained on biomedical text and
knowledge graphs},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1648--1656},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac001},
doi = {10.1093/BIOINFORMATICS/BTAC001},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BalabinHBGBKPHD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BaltzisMJLEN22,
author = {Athanasios Baltzis and
Leila Mansouri and
Suzanne Jin and
Bj{\"{o}}rn E. Langer and
Ionas Erb and
C{\'{e}}dric Notredame},
title = {Highly significant improvement of protein sequence alignments with
AlphaFold2},
journal = {Bioinform.},
volume = {38},
number = {22},
pages = {5007--5011},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac625},
doi = {10.1093/BIOINFORMATICS/BTAC625},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BaltzisMJLEN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BandyopadhyayDD22,
author = {Hmrishav Bandyopadhyay and
Zihao Deng and
Leiting Ding and
Sinuo Liu and
Mostofa Rafid Uddin and
Xiangrui Zeng and
Sima Behpour and
Min Xu},
title = {Cryo-shift: reducing domain shift in cryo-electron subtomograms with
unsupervised domain adaptation and randomization},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {977--984},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab794},
doi = {10.1093/BIOINFORMATICS/BTAB794},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BandyopadhyayDD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BaoZLCLZRZ22,
author = {Xiaoqiong Bao and
Kaiyu Zhu and
Xuefei Liu and
Zhihang Chen and
Ziwei Luo and
Qi Zhao and
Jian Ren and
Zhixiang Zuo},
title = {MeRIPseqPipe: an integrated analysis pipeline for MeRIP-seq data based
on Nextflow},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {2054--2056},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac025},
doi = {10.1093/BIOINFORMATICS/BTAC025},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BaoZLCLZRZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BarbonORBGATW22,
author = {Luca Barbon and
Victoria Offord and
Elizabeth J. Radford and
Adam P. Butler and
Sebastian S. Gerety and
David J. Adams and
Hong Kee Tan and
Andrew J. Waters},
title = {Variant Library Annotation Tool (VaLiAnT): an oligonucleotide library
design and annotation tool for saturation genome editing and other
deep mutational scanning experiments},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {892--899},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab776},
doi = {10.1093/BIOINFORMATICS/BTAB776},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BarbonORBGATW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BarozetMVZFSC22,
author = {Am{\'{e}}lie Barozet and
Kevin Molloy and
Marc Vaisset and
Christophe Zanon and
Pierre Fauret and
Thierry Sim{\'{e}}on and
Juan Cort{\'{e}}s},
title = {MoMA-LoopSampler: a web server to exhaustively sample protein loop
conformations},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {552--553},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab584},
doi = {10.1093/BIOINFORMATICS/BTAB584},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BarozetMVZFSC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BaruzzoCC22,
author = {Giacomo Baruzzo and
Giulia Cesaro and
Barbara Di Camillo},
title = {Identify, quantify and characterize cellular communication from single-cell
{RNA} sequencing data with \emph{scSeqComm}},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {1920--1929},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac036},
doi = {10.1093/BIOINFORMATICS/BTAC036},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BaruzzoCC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BayarriAHOG22,
author = {Genis Bayarri and
Pau Andrio and
Adam Hospital and
Modesto Orozco and
Josep Lluis Gelp{\'{\i}}},
title = {BioExcel Building Blocks {REST} {API} (BioBB {REST} API), programmatic
access to interoperable biomolecular simulation tools},
journal = {Bioinform.},
volume = {38},
number = {12},
pages = {3302--3303},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac316},
doi = {10.1093/BIOINFORMATICS/BTAC316},
timestamp = {Thu, 25 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BayarriAHOG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BehbahaniCLC22,
author = {Yasser Mohseni Behbahani and
Simon Crouzet and
Elodie Laine and
Alessandra Carbone},
title = {Deep Local Analysis evaluates protein docking conformations with locally
oriented cubes},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4505--4512},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac551},
doi = {10.1093/BIOINFORMATICS/BTAC551},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BehbahaniCLC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BehkamalNPSN22,
author = {Bahareh Behkamal and
Mahmoud Naghibzadeh and
Andrea Pagnani and
Mohammad Reza Saberi and
Kamal Al Nasr},
title = {{LPTD:} a novel linear programming-based topology determination method
for cryo-EM maps},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2734--2741},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac170},
doi = {10.1093/BIOINFORMATICS/BTAC170},
timestamp = {Mon, 13 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BehkamalNPSN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BenesBHPSS22,
author = {Nikola Benes and
Lubos Brim and
Ondrej Huvar and
Samuel Pastva and
David Safr{\'{a}}nek and
Eva Smij{\'{a}}kov{\'{a}}},
title = {AEON.py: Python library for attractor analysis in asynchronous Boolean
networks},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4978--4980},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac624},
doi = {10.1093/BIOINFORMATICS/BTAC624},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BenesBHPSS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BennettTPHZMK22,
author = {Christopher Bennett and
Micah Thornton and
Chanhee Park and
Gervaise Henry and
Yun Zhang and
Venkat S. Malladi and
Daehwan Kim},
title = {SeqWho: reliable, rapid determination of sequence file identity using
\emph{k}-mer frequencies in Random Forest classifiers},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {1830--1837},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac050},
doi = {10.1093/BIOINFORMATICS/BTAC050},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BennettTPHZMK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BergstromKTA22,
author = {Erik N. Bergstrom and
Mousumy Kundu and
Noura Tbeileh and
Ludmil B. Alexandrov},
title = {Examining clustered somatic mutations with SigProfilerClusters},
journal = {Bioinform.},
volume = {38},
number = {13},
pages = {3470--3473},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac335},
doi = {10.1093/BIOINFORMATICS/BTAC335},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BergstromKTA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BernalSBGHG22,
author = {Victor Bernal and
Venustiano Soancatl{-}Aguilar and
Jonas Bulthuis and
Victor Guryev and
Peter Horvatovich and
Marco Grzegorczyk},
title = {GeneNetTools: tests for Gaussian graphical models with shrinkage},
journal = {Bioinform.},
volume = {38},
number = {22},
pages = {5049--5054},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac657},
doi = {10.1093/BIOINFORMATICS/BTAC657},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BernalSBGHG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BernettKSBFKLB22,
author = {Judith Bernett and
Dominik Krupke and
Sepideh Sadegh and
Jan Baumbach and
S{\'{a}}ndor P. Fekete and
Tim Kacprowski and
Markus List and
David B. Blumenthal},
title = {Robust disease module mining via enumeration of diverse prize-collecting
Steiner trees},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1600--1606},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab876},
doi = {10.1093/BIOINFORMATICS/BTAB876},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BernettKSBFKLB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BevilacquaPTP22,
author = {Martina Bevilacqua and
Lisanna Paladin and
Silvio C. E. Tosatto and
Damiano Piovesan},
title = {ProSeqViewer: an interactive, responsive and efficient TypeScript
library for visualization of sequences and alignments in web applications},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1129--1130},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab764},
doi = {10.1093/BIOINFORMATICS/BTAB764},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BevilacquaPTP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BiroloT22,
author = {Giovanni Birolo and
Andrea Telatin},
title = {BamToCov: an efficient toolkit for sequence coverage calculations},
journal = {Bioinform.},
volume = {38},
number = {9},
pages = {2617--2618},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac125},
doi = {10.1093/BIOINFORMATICS/BTAC125},
timestamp = {Wed, 18 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BiroloT22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BittrichRSLWDB22,
author = {Sebastian Bittrich and
Yana Rose and
Joan Segura and
Robert Lowe and
John D. Westbrook and
Jose M. Duarte and
Stephen K. Burley},
title = {{RCSB} Protein Data Bank: improved annotation, search and visualization
of membrane protein structures archived in the {PDB}},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1452--1454},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab813},
doi = {10.1093/BIOINFORMATICS/BTAB813},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BittrichRSLWDB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BizzarriRBSA22,
author = {Daniele Bizzarri and
Marcel J. T. Reinders and
Marian Beekman and
P. Eline Slagboom and
Erik van den Akker},
title = {MiMIR: R-shiny application to infer risk factors and endpoints from
Nightingale Health's 1H-NMR metabolomics data},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3847--3849},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac388},
doi = {10.1093/BIOINFORMATICS/BTAC388},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BizzarriRBSA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BodeinSPCD22,
author = {Antoine Bodein and
Marie{-}Pier Scott{-}Boyer and
Olivier P{\'{e}}rin and
Kim{-}Anh L{\^{e}} Cao and
Arnaud Droit},
title = {timeOmics: an {R} package for longitudinal multi-omics data integration},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {577--579},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab664},
doi = {10.1093/BIOINFORMATICS/BTAB664},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BodeinSPCD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BoggyMMVHPB22,
author = {Gregory J. Boggy and
GW McElfresh and
Eisa Mahyari and
Abigail B. Ventura and
Scott G. Hansen and
Louis J. Picker and
Benjamin N. Bimber},
title = {{BFF} and cellhashR: analysis tools for accurate demultiplexing of
cell hashing data},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2791--2801},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac213},
doi = {10.1093/BIOINFORMATICS/BTAC213},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BoggyMMVHPB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BoldinaFRBLA22,
author = {Galina Boldina and
Paul Fogel and
Corinne Rocher and
Charles Bettembourg and
George Luta and
Franck Aug{\'{e}}},
title = {A2Sign: Agnostic Algorithms for Signatures - a universal method for
identifying molecular signatures from transcriptomic datasets prior
to cell-type deconvolution},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1015--1021},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab773},
doi = {10.1093/BIOINFORMATICS/BTAB773},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BoldinaFRBLA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BonetCDHGLL22,
author = {Jos{\'{e}} Bonet and
Mandi Chen and
Marc Dabad and
Simon Heath and
Abel Gonzalez{-}Perez and
N{\'{u}}ria L{\'{o}}pez{-}Bigas and
Jens Lagergren},
title = {DeepMP: a deep learning tool to detect {DNA} base modifications on
Nanopore sequencing data},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1235--1243},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab745},
doi = {10.1093/BIOINFORMATICS/BTAB745},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BonetCDHGLL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Bonfield22,
author = {James K. Bonfield},
title = {{CRAM} 3.1: advances in the {CRAM} file format},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1497--1503},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac010},
doi = {10.1093/BIOINFORMATICS/BTAC010},
timestamp = {Fri, 13 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Bonfield22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BowlesHAR22,
author = {Jonathan R. Bowles and
Caroline Hoppe and
Hilary L. Ashe and
Magnus Rattray},
title = {Scalable inference of transcriptional kinetic parameters from {MS2}
time series data},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1030--1036},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab765},
doi = {10.1093/BIOINFORMATICS/BTAB765},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BowlesHAR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BradburyCJJMMRS22,
author = {Peter J. Bradbury and
Terry M. Casstevens and
Sarah E. Jensen and
L. C. Johnson and
Z. R. Miller and
Brandon Monier and
M. C. Romay and
B. Song and
Edward S. Buckler},
title = {The Practical Haplotype Graph, a platform for storing and using pangenomes
for imputation},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3698--3702},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac410},
doi = {10.1093/BIOINFORMATICS/BTAC410},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BradburyCJJMMRS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BrandesOPRL22,
author = {Nadav Brandes and
Dan Ofer and
Yam Peleg and
Nadav Rappoport and
Michal Linial},
title = {ProteinBERT: a universal deep-learning model of protein sequence and
function},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2102--2110},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac020},
doi = {10.1093/BIOINFORMATICS/BTAC020},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BrandesOPRL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BreitenbachSD22,
author = {Tim Breitenbach and
Matthias J{\"{u}}rgen Schmitt and
Thomas Dandekar},
title = {Optimization of synthetic molecular reporters for a mesenchymal glioblastoma
transcriptional program by integer programing},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4162--4171},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac488},
doi = {10.1093/BIOINFORMATICS/BTAC488},
timestamp = {Thu, 22 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BreitenbachSD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BreitwieserHMVI22,
author = {Lukas Breitwieser and
Ahmad Hesam and
Jean de Montigny and
Vasileios Vavourakis and
Alexandros Iosif and
Jack Jennings and
Marcus Kaiser and
Marco Manca and
Alberto Di Meglio and
Zaid Al{-}Ars and
Fons Rademakers and
Onur Mutlu and
Roman Bauer},
title = {BioDynaMo: a modular platform for high-performance agent-based simulation},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {453--460},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab649},
doi = {10.1093/BIOINFORMATICS/BTAB649},
timestamp = {Thu, 11 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BreitwieserHMVI22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BrewerGPB22,
author = {Kenneth I Brewer and
Glenn J. Gaffield and
Malavika Puri and
Ronald R. Breaker},
title = {{DIMPL:} a bioinformatics pipeline for the discovery of structured
noncoding {RNA} motifs in bacteria},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {533--535},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab624},
doi = {10.1093/BIOINFORMATICS/BTAB624},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BrewerGPB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BrezovskyTSSMSF22,
author = {Jan Brezovsky and
Aravind Selvaram Thirunavukarasu and
Bartlomiej Surpeta and
Carlos Eduardo Sequeiros{-}Borja and
Nishita Mandal and
Dheeraj Kumar Sarkar and
Cedrix Jurgal Dongmo Foumthuim and
Nikhil Agrawal},
title = {TransportTools: a library for high-throughput analyses of internal
voids in biomolecules and ligand transport through them},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1752--1753},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab872},
doi = {10.1093/BIOINFORMATICS/BTAB872},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BrezovskyTSSMSF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BuchnerML22,
author = {Dominik Buchner and
Till{-}Hendrik Macher and
Florian Leese},
title = {{APSCALE:} advanced pipeline for simple yet comprehensive analyses
of {DNA} metabarcoding data},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4817--4819},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac588},
doi = {10.1093/BIOINFORMATICS/BTAC588},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BuchnerML22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BueschlDVSFWZ22,
author = {Christoph Bueschl and
Maria Doppler and
Elisabeth Varga and
Bernhard Seidl and
Mira Flasch and
Benedikt Warth and
J{\"{u}}rgen Zanghellini},
title = {PeakBot: machine-learning-based chromatographic peak picking},
journal = {Bioinform.},
volume = {38},
number = {13},
pages = {3422--3428},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac344},
doi = {10.1093/BIOINFORMATICS/BTAC344},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BueschlDVSFWZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BuitronCGHPFP22,
author = {Martin Gonzalez Buitron and
Ronaldo Romario Tunque Cahui and
Emilio Garcia{-}Rios and
Layla Hirsh and
Gustavo D. Parisi and
Mar{\'{\i}}a Silvina Fornasari and
Nicolas Palopoli},
title = {CoDNaS-RNA: a database of conformational diversity in the native state
of {RNA}},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1745--1748},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab858},
doi = {10.1093/BIOINFORMATICS/BTAB858},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BuitronCGHPFP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ButerezBTAL22,
author = {David Buterez and
Ioana Bica and
Ifrah Tariq and
Helena Andr{\'{e}}s{-}Terr{\'{e}} and
Pietro Li{\`{o}}},
title = {CellVGAE: an unsupervised scRNA-seq analysis workflow with graph attention
networks},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1277--1286},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab804},
doi = {10.1093/BIOINFORMATICS/BTAB804},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ButerezBTAL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BuyukozkanSK22,
author = {Mustafa Buyukozkan and
Karsten Suhre and
Jan Krumsiek},
title = {{SGI:} automatic clinical subgroup identification in omics datasets},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {573--576},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab656},
doi = {10.1093/BIOINFORMATICS/BTAB656},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BuyukozkanSK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CaceresG22,
author = {Alejandro C{\'{a}}ceres and
Juan R. Gonz{\'{a}}lez},
title = {\emph{teff}: estimation of Treatment EFFects on transcriptomic data
using causal random forest},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3124--3125},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac269},
doi = {10.1093/BIOINFORMATICS/BTAC269},
timestamp = {Tue, 28 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CaceresG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CaiS22,
author = {Dehan Cai and
Yanni Sun},
title = {Reconstructing viral haplotypes using long reads},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2127--2134},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac089},
doi = {10.1093/BIOINFORMATICS/BTAC089},
timestamp = {Wed, 18 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CaiS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CaiSS22,
author = {Dehan Cai and
Jiayu Shang and
Yanni Sun},
title = {HaploDMF: viral haplotype reconstruction from long reads via deep
matrix factorization},
journal = {Bioinform.},
volume = {38},
number = {24},
pages = {5360--5367},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac708},
doi = {10.1093/BIOINFORMATICS/BTAC708},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CaiSS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CaiYCLFLBCMCW22,
author = {Manqi Cai and
Molin Yue and
Tianmeng Chen and
Jinling Liu and
Erick Forno and
Xinghua Lu and
Timothy Billiar and
Juan C. Celed{\'{o}}n and
Chris McKennan and
Wei Chen and
Jiebiao Wang},
title = {Robust and accurate estimation of cellular fraction from tissue omics
data via ensemble deconvolution},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3004--3010},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac279},
doi = {10.1093/BIOINFORMATICS/BTAC279},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CaiYCLFLBCMCW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CakmakciKBPPNC22,
author = {Doruk Cakmakci and
Gun Kaynar and
Caroline Bund and
Martial Piotto and
Francois Proust and
Izzie{-}Jacques Namer and
A. Erc{\"{u}}ment {\c{C}}i{\c{c}}ek},
title = {Targeted metabolomics analyses for brain tumor margin assessment during
surgery},
journal = {Bioinform.},
volume = {38},
number = {12},
pages = {3238--3244},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac309},
doi = {10.1093/BIOINFORMATICS/BTAC309},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CakmakciKBPPNC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CameleMCMHBA22,
author = {Genaro Camele and
Sebastian Menazzi and
Hern{\'{a}}n Chanfreau and
Agustin Marraco and
Waldo Hasperu{\'{e}} and
Matias D. Butti and
Martin C. Abba},
title = {Multiomix: a cloud-based platform to infer cancer genomic and epigenomic
events associated with gene expression modulation},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {866--868},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab678},
doi = {10.1093/BIOINFORMATICS/BTAB678},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CameleMCMHBA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CameronDP22,
author = {Daniel Cameron and
Ruining Dong and
Anthony T. Papenfuss},
title = {StructuralVariantAnnotation: a R/Bioconductor foundation for a caller-agnostic
structural variant software ecosystem},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {2046--2048},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac042},
doi = {10.1093/BIOINFORMATICS/BTAC042},
timestamp = {Fri, 13 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CameronDP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CaneteIOBHP22,
author = {Nicolas P. Canete and
Sourish S. Iyengar and
John T. Ormerod and
Heeva Baharlou and
Andrew N. Harman and
Ellis Patrick},
title = {spicyR: spatial analysis of \emph{in situ} cytometry data in {R}},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3099--3105},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac268},
doi = {10.1093/BIOINFORMATICS/BTAC268},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CaneteIOBHP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CaoDWZLN22,
author = {Yang Cao and
Qingyang Dong and
Dan Wang and
Pengcheng Zhang and
Ying Liu and
Chao Niu},
title = {microbiomeMarker: an R/Bioconductor package for microbiome marker
identification and visualization},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {4027--4029},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac438},
doi = {10.1093/BIOINFORMATICS/BTAC438},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CaoDWZLN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CaoLPYY22,
author = {Yue Cao and
Yingxin Lin and
Ellis Patrick and
Pengyi Yang and
Jean Yee Hwa Yang},
title = {scFeatures: multi-view representations of single-cell and spatial
data for disease outcome prediction},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4745--4753},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac590},
doi = {10.1093/BIOINFORMATICS/BTAC590},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CaoLPYY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CaoZBBDKMMRRRSHS22,
author = {Han Cao and
Youcheng Zhang and
Jan Baumbach and
Paul R. Burton and
Dominic B. Dwyer and
Nikolaos Koutsouleris and
Julian O. Matschinske and
Yannick Marcon and
Sivanesan Rajan and
Thilo Rieg and
Patricia Ryser{-}Welch and
Julian Sp{\"{a}}th and
Carl Herrmann and
Emanuel Schwarz},
title = {dsMTL: a computational framework for privacy-preserving, distributed
multi-task machine learning},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4919--4926},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac616},
doi = {10.1093/BIOINFORMATICS/BTAC616},
timestamp = {Thu, 15 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CaoZBBDKMMRRRSHS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CaptierMMSZNBKZ22,
author = {Nicolas Captier and
Jane Merlevede and
Askhat Molkenov and
Ainur Seisenova and
Altynbek Zhubanchaliyev and
Petr V. Nazarov and
Emmanuel Barillot and
Ulykbek Kairov and
Andrei Yu. Zinovyev},
title = {{BIODICA:} a computational environment for Independent Component Analysis
of omics data},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2963--2964},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac204},
doi = {10.1093/BIOINFORMATICS/BTAC204},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CaptierMMSZNBKZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Caraballo-Ortiz22,
author = {Marcos A. Caraballo{-}Ortiz and
Sayaka Miura and
Maxwell D. Sanderford and
Tenzin Dolker and
Qiqing Tao and
Steven Weaver and
Sergei L. Kosakovsky Pond and
Sudhir Kumar},
title = {TopHap: rapid inference of key phylogenetic structures from common
haplotypes in large genome collections with limited diversity},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2719--2726},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac186},
doi = {10.1093/BIOINFORMATICS/BTAC186},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Caraballo-Ortiz22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CardosoRKGTMDPM22,
author = {Milena A. Cardoso and
Luis E. A. Rizzardi and
Leonardo W. Kume and
Clarice S. Groeneveld and
Sheyla Trefflich and
Diego A. A. Morais and
Rodrigo J. S. Dalmolin and
Bruce A. J. Ponder and
Kerstin B. Meyer and
Mauro A. A. Castro},
title = {TreeAndLeaf: an R/Bioconductor package for graphs and trees with focus
on the leaves},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1463--1464},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab819},
doi = {10.1093/BIOINFORMATICS/BTAB819},
timestamp = {Wed, 16 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CardosoRKGTMDPM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CarenzoPSLLC22,
author = {Andrea Carenzo and
Federico Pistore and
Mara S. Serafini and
Deborah Lenoci and
Armando G. Licata and
Loris De Cecco},
title = {hacksig: a unified and tidy {R} framework to easily compute gene expression
signature scores},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2940--2942},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac161},
doi = {10.1093/BIOINFORMATICS/BTAC161},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CarenzoPSLLC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CarlucciKLGKPO22,
author = {Matthew Carlucci and
Algimantas Krisciunas and
Haohan Li and
Povilas Gibas and
Karolis Koncevicius and
Art Petronis and
Gabriel Oh},
title = {DiscoRhythm: an easy-to-use web application and {R} package for discovering
rhythmicity},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {882},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab517},
doi = {10.1093/BIOINFORMATICS/BTAB517},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CarlucciKLGKPO22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CascaranoCSMPM22,
author = {Pasquale Cascarano and
Maria Colomba Comes and
Andrea Sebastiani and
Arianna Mencattini and
Elena Loli Piccolomini and
Eugenio Martinelli},
title = {DeepCEL0 for 2D single-molecule localization in fluorescence microscopy},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1411--1419},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab808},
doi = {10.1093/BIOINFORMATICS/BTAB808},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CascaranoCSMPM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CascarinaR22,
author = {Sean M. Cascarina and
Eric D. Ross},
title = {The LCD-Composer webserver: high-specificity identification and functional
analysis of low-complexity domains in proteins},
journal = {Bioinform.},
volume = {38},
number = {24},
pages = {5446--5448},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac699},
doi = {10.1093/BIOINFORMATICS/BTAC699},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CascarinaR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CastroHMSL22,
author = {Giovanni Marques de Castro and
Zandora Hastenreiter and
Thiago Augusto Silva Monteiro and
Thieres Tayroni Martins da Silva and
Francisco Pereira Lobo},
title = {Cross-species prediction of essential genes in insects},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1504--1513},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac009},
doi = {10.1093/BIOINFORMATICS/BTAC009},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CastroHMSL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CattaneoPGPR22,
author = {Giuseppe Cattaneo and
Umberto Ferraro Petrillo and
Raffaele Giancarlo and
Francesco Palini and
Chiara Romualdi},
title = {The power of word-frequency-based alignment-free functions: a comprehensive
large-scale experimental analysis},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {925--932},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab747},
doi = {10.1093/BIOINFORMATICS/BTAB747},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CattaneoPGPR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChaguzaTLHCHB22,
author = {Chrispin Chaguza and
Gerry Tonkin{-}Hill and
Stephanie W. Lo and
James Hadfield and
Nicholas J. Croucher and
Simon R. Harris and
Stephen D. Bentley},
title = {RCandy: an {R} package for visualizing homologous recombinations in
bacterial genomes},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1450--1451},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab814},
doi = {10.1093/BIOINFORMATICS/BTAB814},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChaguzaTLHCHB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChatzigoulasC22,
author = {Alexios Chatzigoulas and
Zoe Cournia},
title = {{DREAMM:} a web-based server for drugging protein-membrane interfaces
as a novel workflow for targeted drug design},
journal = {Bioinform.},
volume = {38},
number = {24},
pages = {5449--5451},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac680},
doi = {10.1093/BIOINFORMATICS/BTAC680},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChatzigoulasC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChaumeilMHP22,
author = {Pierre{-}Alain Chaumeil and
Aaron J. Mussig and
Philip Hugenholtz and
Donovan H. Parks},
title = {GTDB-Tk v2: memory friendly classification with the genome taxonomy
database},
journal = {Bioinform.},
volume = {38},
number = {23},
pages = {5315--5316},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac672},
doi = {10.1093/BIOINFORMATICS/BTAC672},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChaumeilMHP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Chaves-UrbanoHG22,
author = {Blas Chaves{-}Urbano and
Barbara Hernando and
Maria J. Garcia and
Geoff MacIntyre},
title = {CNpare: matching {DNA} copy number profiles},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3638--3641},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac371},
doi = {10.1093/BIOINFORMATICS/BTAC371},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Chaves-UrbanoHG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CheethamKE22,
author = {Seth W. Cheetham and
Michaela Kindlova and
Adam D. Ewing},
title = {Methylartist: tools for visualizing modified bases from nanopore sequence
data},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3109--3112},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac292},
doi = {10.1093/BIOINFORMATICS/BTAC292},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CheethamKE22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenBLLRV22,
author = {Brian Y. Chen and
William Bone and
Kim Lorenz and
Michael Levin and
Marylyn D. Ritchie and
Benjamin F. Voight},
title = {ColocQuiaL: a {QTL-GWAS} colocalization pipeline},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4409--4411},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac512},
doi = {10.1093/BIOINFORMATICS/BTAC512},
timestamp = {Fri, 23 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenBLLRV22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenCL22,
author = {Yang Chen and
Shue Chen and
Elissa P. Lei},
title = {DiffChIPL: a differential peak analysis method for high-throughput
sequencing data with biological replicates based on limma},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4062--4069},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac498},
doi = {10.1093/BIOINFORMATICS/BTAC498},
timestamp = {Thu, 22 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenCL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenFSZME22,
author = {Yi{-}Pei Chen and
Laura B. Ferguson and
Nihal A. Salem and
George Zheng and
R. Dayne Mayfield and
Mohammed Eslami},
title = {{RNA} Solutions: Synthesizing Information to Support Transcriptomics
{(RNASSIST)}},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {397--403},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab673},
doi = {10.1093/BIOINFORMATICS/BTAB673},
timestamp = {Tue, 20 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenFSZME22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenHHFC22,
author = {Yuhao Chen and
Yanshi Hu and
Xiaotian Hu and
Cong Feng and
Ming Chen},
title = {CoGO: a contrastive learning framework to predict disease similarity
based on gene network and ontology structure},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4380--4386},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac520},
doi = {10.1093/BIOINFORMATICS/BTAC520},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenHHFC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenKLSR22,
author = {Athena Chen and
Kai Kammers and
H. Benjamin Larman and
Robert B. Scharpf and
Ingo Ruczinski},
title = {Detecting and quantifying antibody reactivity in PhIP-Seq data with
{BEER}},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4647--4649},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac555},
doi = {10.1093/BIOINFORMATICS/BTAC555},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenKLSR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenL22,
author = {Guangyi Chen and
Zhi{-}Ping Liu},
title = {Graph attention network for link prediction of gene regulations from
single-cell RNA-sequencing data},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4522--4529},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac559},
doi = {10.1093/BIOINFORMATICS/BTAC559},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenLCZEZ22,
author = {Zhong Chen and
You Lu and
Bo Cao and
Wensheng Zhang and
Andrea Edwards and
Kun Zhang},
title = {Driver gene detection through Bayesian network integration of mutation
and expression profiles},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2781--2790},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac203},
doi = {10.1093/BIOINFORMATICS/BTAC203},
timestamp = {Mon, 13 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenLCZEZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenLIWL22,
author = {Chixiang Chen and
Yuk Yee Leung and
Matei Ionita and
Li{-}San Wang and
Mingyao Li},
title = {Omnibus and robust deconvolution scheme for bulk {RNA} sequencing
data integrating multiple single-cell reference sets and prior biological
knowledge},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4530--4536},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac563},
doi = {10.1093/BIOINFORMATICS/BTAC563},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenLIWL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenNYVXRS22,
author = {Chaoran Chen and
Sarah Nadeau and
Michael Yared and
Philippe Voinov and
Ning Xie and
Cornelius Roemer and
Tanja Stadler},
title = {CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify
and characterize new variants},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1735--1737},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab856},
doi = {10.1093/BIOINFORMATICS/BTAB856},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenNYVXRS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenOM22,
author = {Yi{-}An Chen and
Rodolfo S. Allendes Osorio and
Kenji Mizuguchi},
title = {TargetMine 2022: a new vision into drug target analysis},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4454--4456},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac507},
doi = {10.1093/BIOINFORMATICS/BTAC507},
timestamp = {Tue, 06 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenOM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenW22,
author = {Yuhao Chen and
Xiaowei Wang},
title = {Evaluation of efficiency prediction algorithms and development of
ensemble model for CRISPR/Cas9 gRNA selection},
journal = {Bioinform.},
volume = {38},
number = {23},
pages = {5175--5181},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac681},
doi = {10.1093/BIOINFORMATICS/BTAC681},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenWLDLCYEHW22,
author = {Lulu Chen and
Chiung{-}Ting Wu and
Chia{-}Hsiang Lin and
Rujia Dai and
Chunyu Liu and
Robert Clarke and
Guoqiang Yu and
Jennifer E. Van Eyk and
David M. Herrington and
Yue Wang},
title = {swCAM: estimation of subtype-specific expressions in individual samples
with unsupervised sample-wise deconvolution},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1403--1410},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab839},
doi = {10.1093/BIOINFORMATICS/BTAB839},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenWLDLCYEHW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenWZ22,
author = {Li Chen and
Ye Wang and
Fengdi Zhao},
title = {Exploiting deep transfer learning for the prediction of functional
non-coding variants using genomic sequence},
journal = {Bioinform.},
volume = {38},
number = {12},
pages = {3164--3172},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac214},
doi = {10.1093/BIOINFORMATICS/BTAC214},
timestamp = {Wed, 11 Sep 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenWZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenZ22,
author = {Jun Chen and
Xianyang Zhang},
title = {dICC: distance-based intraclass correlation coefficient for metagenomic
reproducibility studies},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4969--4971},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac618},
doi = {10.1093/BIOINFORMATICS/BTAC618},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenZCMQ22,
author = {Duoyuan Chen and
Taikui Zhang and
Yamao Chen and
Hong Ma and
Ji Qi},
title = {Tree2GD: a phylogenomic method to detect large-scale gene duplication
events},
journal = {Bioinform.},
volume = {38},
number = {23},
pages = {5317--5321},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac669},
doi = {10.1093/BIOINFORMATICS/BTAC669},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenZCMQ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChengD22,
author = {Xiaoheng Cheng and
Michael Degiorgio},
title = {BalLeRMix +: mixture model approaches for robust joint identification
of both positive selection and long-term balancing selection},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {861--863},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab720},
doi = {10.1093/BIOINFORMATICS/BTAB720},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChengD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChengM22,
author = {Yi Cheng and
Xiuli Ma},
title = {scGAC: a graph attentional architecture for clustering single-cell
RNA-seq data},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2187--2193},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac099},
doi = {10.1093/BIOINFORMATICS/BTAC099},
timestamp = {Wed, 18 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChengM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChengQCSXSL22,
author = {Qing Cheng and
Tingting Qiu and
Xiaoran Chai and
Baoluo Sun and
Yingcun Xia and
Xingjie Shi and
Jin Liu},
title = {MR-Corr2: a two-sample Mendelian randomization method that accounts
for correlated horizontal pleiotropy using correlated instrumental
variants},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {303--310},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab646},
doi = {10.1093/BIOINFORMATICS/BTAB646},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChengQCSXSL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChengZLW22,
author = {Zhongjian Cheng and
Qichang Zhao and
Yaohang Li and
Jianxin Wang},
title = {{IIFDTI:} predicting drug-target interactions through interactive
and independent features based on attention mechanism},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4153--4161},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac485},
doi = {10.1093/BIOINFORMATICS/BTAC485},
timestamp = {Thu, 22 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChengZLW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CherifTSRJDBDGC22,
author = {Emira Cherif and
Fatou Seck Thiam and
Mohammad Salma and
Georgina Rivera{-}Ingraham and
Fabienne Justy and
Theo Deremarque and
Damien Breugnot and
Jean{-}Claude Doudou and
Rodolphe E. Gozlan and
Marine Combe},
title = {ONTdeCIPHER: an amplicon-based nanopore sequencing pipeline for tracking
pathogen variants},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {2033--2035},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac043},
doi = {10.1093/BIOINFORMATICS/BTAC043},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CherifTSRJDBDGC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChetnikBGSBBWAZ22,
author = {Kelsey Chetnik and
Elisa Benedetti and
Daniel P. Gomari and
Annalise Schweickart and
Richa Batra and
Mustafa Buyukozkan and
Zeyu Wang and
Matthias Arnold and
Jonas Zierer and
Karsten Suhre and
Jan Krumsiek},
title = {maplet: an extensible {R} toolbox for modular and reproducible metabolomics
pipelines},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1168--1170},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab741},
doi = {10.1093/BIOINFORMATICS/BTAB741},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChetnikBGSBBWAZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChilinskiP22,
author = {Mateusz Chilinski and
Dariusz Plewczynski},
title = {ConsensuSV - from the whole-genome sequencing data to the complete
variant list},
journal = {Bioinform.},
volume = {38},
number = {24},
pages = {5440--5442},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac709},
doi = {10.1093/BIOINFORMATICS/BTAC709},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChilinskiP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChitpinSNTXAOTC22,
author = {Justin G. Chitpin and
Anuradha Surendra and
Thao T. Nguyen and
Graeme Taylor and
Hongbin Xu and
Irina Alecu and
Roberto Ortega and
Julianna J. Tomlinson and
Angela M. Crawley and
Michaeline McGuinty and
Michael G. Schlossmacher and
Rachel Saunders{-}Pullman and
Miroslava Cuperlovic{-}Culf and
Steffany A. L. Bennett and
Theodore J. Perkins},
title = {{BATL:} Bayesian annotations for targeted lipidomics},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1593--1599},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab854},
doi = {10.1093/BIOINFORMATICS/BTAB854},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChitpinSNTXAOTC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChoiCCLW22,
author = {Ji{-}Hye Choi and
Hui{-}Seon Choi and
Seong{-}Ho Cho and
Ji{-}Hye Lee and
Hyun Goo Woo},
title = {{CGV:} Cancer Genome Viewer, a web service for integrative cancer
genome and pharmacogenomic data analysis},
journal = {Bioinform.},
volume = {38},
number = {22},
pages = {5116--5118},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac642},
doi = {10.1093/BIOINFORMATICS/BTAC642},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChoiCCLW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChristensenDMPS22,
author = {Niels Johan Christensen and
Samuel Demharter and
Meera Vieira Machado and
Lykke Pedersen and
Marco Salvatore and
Valdemar Stentoft{-}Hansen and
Miquel Triana Iglesias},
title = {Identifying interactions in omics data for clinical biomarker discovery
using symbolic regression},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3749--3758},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac405},
doi = {10.1093/BIOINFORMATICS/BTAC405},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChristensenDMPS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChuahLDFA22,
author = {Aaron Chuah and
Sean Li and
Andrea Do and
Matthew A. Field and
Dan Andrews},
title = {StabilitySort: assessment of protein stability changes on a genome-wide
scale to prioritize potentially pathogenic genetic variation},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4220--4222},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac465},
doi = {10.1093/BIOINFORMATICS/BTAC465},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChuahLDFA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CiaKRP22,
author = {Gabriel Cia and
Jean Marc Kwasigroch and
Marianne Rooman and
Fabrizio Pucci},
title = {SpikePro: a webserver to predict the fitness of SARS-CoV-2 variants},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4418--4419},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac517},
doi = {10.1093/BIOINFORMATICS/BTAC517},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CiaKRP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CilibrasiPBCCC22,
author = {Luca Cilibrasi and
Pietro Pinoli and
Anna Bernasconi and
Arif Canakoglu and
Matteo Chiara and
Stefano Ceri},
title = {ViruClust: direct comparison of SARS-CoV-2 genomes and genetic variants
in space and time},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {1988--1994},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac030},
doi = {10.1093/BIOINFORMATICS/BTAC030},
timestamp = {Wed, 27 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CilibrasiPBCCC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CiortanD22,
author = {Madalina Ciortan and
Matthieu Defrance},
title = {GNN-based embedding for clustering scRNA-seq data},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1037--1044},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab787},
doi = {10.1093/BIOINFORMATICS/BTAB787},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CiortanD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ClasenKSLLGBC22,
author = {Milan A. Clasen and
Louise U. Kurt and
Marlon D. M. Santos and
Diogo B. Lima and
Fan Liu and
F{\'{a}}bio C. Gozzo and
Valmir C. Barbosa and
Paulo C. Carvalho},
title = {Increasing confidence in proteomic spectral deconvolution through
mass defect},
journal = {Bioinform.},
volume = {38},
number = {22},
pages = {5119--5120},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac638},
doi = {10.1093/BIOINFORMATICS/BTAC638},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ClasenKSLLGBC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CooperCR22,
author = {Brendon H. Cooper and
Tsu{-}Pei Chiu and
Remo Rohs},
title = {Top-Down Crawl: a method for the ultra-rapid and motif-free alignment
of sequences with associated binding metrics},
journal = {Bioinform.},
volume = {38},
number = {22},
pages = {5121--5123},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac653},
doi = {10.1093/BIOINFORMATICS/BTAC653},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CooperCR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CopeAFJMKLMSTWX22,
author = {Alexander Cope and
Felicity Anderson and
John Favate and
Michael Jackson and
Amanda Mok and
Anna Kurowska and
Junchen Liu and
Emma Mackenzie and
Vikram Shivakumar and
Peter Tilton and
Sophie M. Winterbourne and
Siyin Xue and
Kostas Kavoussanakis and
Liana F. Lareau and
Premal Shah and
Edward W. J. Wallace},
title = {riboviz 2: a flexible and robust ribosome profiling data analysis
and visualization workflow},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2358--2360},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac093},
doi = {10.1093/BIOINFORMATICS/BTAC093},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CopeAFJMKLMSTWX22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CoxPKWWCGK22,
author = {Andrew Cox and
Chanhee Park and
Prasad Koduru and
Kathleen Wilson and
Olga Weinberg and
Weina Chen and
Rolando Garc{\'{\i}}a and
Daehwan Kim},
title = {Automated classification of cytogenetic abnormalities in hematolymphoid
neoplasms},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1420--1426},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab822},
doi = {10.1093/BIOINFORMATICS/BTAB822},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CoxPKWWCGK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CrownTNB22,
author = {Matthew Crown and
Nat{\'{a}}lia Teruel and
Rafael Najmanovich and
Matthew Bashton},
title = {{SPEAR:} Systematic ProtEin AnnotatoR},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3827--3829},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac391},
doi = {10.1093/BIOINFORMATICS/BTAC391},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CrownTNB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CrysupBW22,
author = {Benjamin Crysup and
Bruce Budowle and
August E. Woerner},
title = {ProSynAR: a reference aware read merger},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {2052--2053},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac022},
doi = {10.1093/BIOINFORMATICS/BTAC022},
timestamp = {Wed, 27 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CrysupBW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CuiSWL22,
author = {Elvis Han Cui and
Dongyuan Song and
Weng Kee Wong and
Jingyi Jessica Li},
title = {Single-cell generalized trend model (scGTM): a flexible and interpretable
model of gene expression trend along cell pseudotime},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {3927--3934},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac423},
doi = {10.1093/BIOINFORMATICS/BTAC423},
timestamp = {Sat, 10 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CuiSWL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CunialDB22,
author = {Fabio Cunial and
Olgert Denas and
Djamal Belazzougui},
title = {Fast and compact matching statistics analytics},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {1838--1845},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac064},
doi = {10.1093/BIOINFORMATICS/BTAC064},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CunialDB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CzechE22,
author = {Lucas Czech and
Moises Exposito{-}Alonso},
title = {grenepipe: a flexible, scalable and reproducible pipeline to automate
variant calling from sequence reads},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4809--4811},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac600},
doi = {10.1093/BIOINFORMATICS/BTAC600},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CzechE22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DabbaghieEM22,
author = {Fawaz Dabbaghie and
Jana Ebler and
Tobias Marschall},
title = {BubbleGun: enumerating bubbles and superbubbles in genome graphs},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4217--4219},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac448},
doi = {10.1093/BIOINFORMATICS/BTAC448},
timestamp = {Thu, 22 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DabbaghieEM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DaeleWRM22,
author = {Dries Van Daele and
Bram Weytjens and
Luc De Raedt and
Kathleen Marchal},
title = {{OMEN:} network-based driver gene identification using mutual exclusivity},
journal = {Bioinform.},
volume = {38},
number = {12},
pages = {3245--3251},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac312},
doi = {10.1093/BIOINFORMATICS/BTAC312},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DaeleWRM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DanailaB22,
author = {Vlad{-}Rares Danaila and
Catalin Buiu},
title = {Prediction of {HIV} sensitivity to monoclonal antibodies using aminoacid
sequences and deep learning},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4278--4285},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac530},
doi = {10.1093/BIOINFORMATICS/BTAC530},
timestamp = {Mon, 24 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DanailaB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DaneshpajouhCSM22,
author = {Habib Daneshpajouh and
Bowen Chen and
Neda Shokraneh and
Shohre Masoumi and
Kay C. Wiese and
Maxwell W. Libbrecht},
title = {Continuous chromatin state feature annotation of the human epigenome},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3029--3036},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac283},
doi = {10.1093/BIOINFORMATICS/BTAC283},
timestamp = {Wed, 27 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DaneshpajouhCSM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DankoSPSS22,
author = {Benedek Dank{\'{o}} and
P{\'{e}}ter Szikora and
Tam{\'{a}}s P{\'{o}}r and
Alexa Szeifert and
Endre Sebesty{\'{e}}n},
title = {SplicingFactory - splicing diversity analysis for transcriptome data},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {384--390},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab648},
doi = {10.1093/BIOINFORMATICS/BTAB648},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DankoSPSS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DarvishSMRR22,
author = {Mitra Darvish and
Enrico Seiler and
Svenja Mehringer and
Ren{\'{e}} Rahn and
Knut Reinert},
title = {Needle: a fast and space-efficient prefilter for estimating the quantification
of very large collections of expression experiments},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4100--4108},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac492},
doi = {10.1093/BIOINFORMATICS/BTAC492},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DarvishSMRR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DavidWHJ22,
author = {Benjamin M. David and
Ryan M. Wyllie and
Ramdane Harouaka and
Paul A. Jensen},
title = {A reinforcement learning framework for pooled oligonucleotide design},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2219--2225},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac073},
doi = {10.1093/BIOINFORMATICS/BTAC073},
timestamp = {Wed, 18 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DavidWHJ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DavidsonWETMPS22,
author = {Russell B. Davidson and
Jess Woods and
T. Chad Effler and
Mathialakan Thavappiragasam and
Julie C. Mitchell and
Jerry M. Parks and
Ada Sedova},
title = {OpenMDlr: parallel, open-source tools for general protein structure
modeling and refinement from pairwise distances},
journal = {Bioinform.},
volume = {38},
number = {12},
pages = {3297--3298},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac307},
doi = {10.1093/BIOINFORMATICS/BTAC307},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DavidsonWETMPS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DengHLL22,
author = {Lei Deng and
Yibiao Huang and
Xuejun Liu and
Hui Liu},
title = {Graph2MDA: a multi-modal variational graph embedding model for predicting
microbe-drug associations},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1118--1125},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab792},
doi = {10.1093/BIOINFORMATICS/BTAB792},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DengHLL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DereeperSM22,
author = {Alexis Dereeper and
Marilyne Summo and
Damien F. Meyer},
title = {PanExplorer: a web-based tool for exploratory analysis and visualization
of bacterial pan-genomes},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4412--4414},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac504},
doi = {10.1093/BIOINFORMATICS/BTAC504},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DereeperSM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DevkotaSWMEAC22,
author = {Kapil Devkota and
Henri Schmidt and
Matthew Werenski and
James M. Murphy and
Mert Erden and
Victor Arsenescu and
Lenore J. Cowen},
title = {{GLIDER:} function prediction from GLIDE-based neighborhoods},
journal = {Bioinform.},
volume = {38},
number = {13},
pages = {3395--3406},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac322},
doi = {10.1093/BIOINFORMATICS/BTAC322},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DevkotaSWMEAC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DeyZD22,
author = {Pritam Dey and
Zhengwu Zhang and
David B. Dunson},
title = {Outlier detection for multi-network data},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {4011--4018},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac431},
doi = {10.1093/BIOINFORMATICS/BTAC431},
timestamp = {Sat, 10 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DeyZD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DheninLDC22,
author = {Jonathan Dhenin and
Diogo B. Lima and
Mathieu Dupr{\'{e}} and
Julia Chamot{-}Rooke},
title = {TDFragMapper: a visualization tool for evaluating experimental parameters
in top-down proteomics},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1136--1138},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab784},
doi = {10.1093/BIOINFORMATICS/BTAB784},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DheninLDC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DiazS22,
author = {L{\'{e}}o P. M. Diaz and
Michael P. H. Stumpf},
title = {HyperGraphs.jl: representing higher-order relationships in Julia},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3660--3661},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac347},
doi = {10.1093/BIOINFORMATICS/BTAC347},
timestamp = {Sun, 22 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DiazS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DiazUriarteH22,
author = {Ram{\'{o}}n D{\'{\i}}az{-}Uriarte and
Pablo Herrera{-}Nieto},
title = {EvAM-Tools: tools for evolutionary accumulation and cancer progression
models},
journal = {Bioinform.},
volume = {38},
number = {24},
pages = {5457--5459},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac710},
doi = {10.1093/BIOINFORMATICS/BTAC710},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DiazUriarteH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DickinsonAOM22,
author = {Quinn Dickinson and
Andreas Aufschnaiter and
Martin Ott and
Jesse G. Meyer},
title = {Multi-omic integration by machine learning (MIMaL)},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4908--4918},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac631},
doi = {10.1093/BIOINFORMATICS/BTAC631},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DickinsonAOM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DimonacoAKCC22,
author = {Nicholas J. Dimonaco and
Wayne Aubrey and
Kim Kenobi and
Amanda Clare and
Christopher J. Creevey},
title = {No one tool to rule them all: prokaryotic gene prediction tool annotations
are highly dependent on the organism of study},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1198--1207},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab827},
doi = {10.1093/BIOINFORMATICS/BTAB827},
timestamp = {Fri, 13 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DimonacoAKCC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DingCLZZS22,
author = {Yi Ding and
Kangwen Cai and
Leiqin Liu and
Zhiqiang Zhang and
Xiaoqi Zheng and
Jiantao Shi},
title = {mHapTk: a comprehensive toolkit for the analysis of {DNA} methylation
haplotypes},
journal = {Bioinform.},
volume = {38},
number = {22},
pages = {5141--5143},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac650},
doi = {10.1093/BIOINFORMATICS/BTAC650},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DingCLZZS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DingJK22,
author = {Yan Ding and
Xiaoqian Jiang and
Yejin Kim},
title = {Relational graph convolutional networks for predicting blood-brain
barrier penetration of drug molecules},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2826--2831},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac211},
doi = {10.1093/BIOINFORMATICS/BTAC211},
timestamp = {Mon, 13 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DingJK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DongB22,
author = {Amy Dong and
Xiaomin Bao},
title = {GPSmatch: an {R} package for comparing Genomic-binding Profile Similarity
among transcriptional regulators using customizable databases},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {853--855},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab728},
doi = {10.1093/BIOINFORMATICS/BTAB728},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DongB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DongKGMWGB22,
author = {Yonghui Dong and
Yana Kazachkova and
Meng Gou and
Liat Morgan and
Tal Wachsman and
Ehud Gazit and
Rune Isak Dupont Birkler},
title = {RawHummus: an {R} Shiny app for automated raw data quality control
in metabolomics},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {2072--2074},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac040},
doi = {10.1093/BIOINFORMATICS/BTAC040},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DongKGMWGB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DongVBL22,
author = {Xiaoxi Dong and
Kovidh Vegesna and
Cory Brouwer and
Weijun Luo},
title = {SBGNview: towards data analysis, integration and visualization on
all pathways},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1473--1476},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab793},
doi = {10.1093/BIOINFORMATICS/BTAB793},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DongVBL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DouglasHLB22,
author = {Gavin M. Douglas and
Molly G. Hayes and
Morgan G. I. Langille and
Elhanan Borenstein},
title = {Integrating phylogenetic and functional data in microbiome studies},
journal = {Bioinform.},
volume = {38},
number = {22},
pages = {5055--5063},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac655},
doi = {10.1093/BIOINFORMATICS/BTAC655},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DouglasHLB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DuGWSZ22,
author = {Yuanqi Du and
Xiaojie Guo and
Yinkai Wang and
Amarda Shehu and
Liang Zhao},
title = {Small molecule generation via disentangled representation learning},
journal = {Bioinform.},
volume = {38},
number = {12},
pages = {3200--3208},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac296},
doi = {10.1093/BIOINFORMATICS/BTAC296},
timestamp = {Mon, 25 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DuGWSZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DuPY22,
author = {Zongyang Du and
Zhenling Peng and
Jianyi Yang},
title = {Toward the assessment of predicted inter-residue distance},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {962--969},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab781},
doi = {10.1093/BIOINFORMATICS/BTAB781},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DuPY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DuS22,
author = {Yuxuan Du and
Fengzhu Sun},
title = {HiFine: integrating Hi-C-based and shotgun-based methods to refine
binning of metagenomic contigs},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {2973--2979},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac295},
doi = {10.1093/BIOINFORMATICS/BTAC295},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DuS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DuanHHLF22,
author = {Daoyu Duan and
Sijia He and
Emina Huang and
Ziyi Li and
Hao Feng},
title = {NeuCA web server: a neural network-based cell annotation tool with
web-app and {GUI}},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2361--2363},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac108},
doi = {10.1093/BIOINFORMATICS/BTAC108},
timestamp = {Wed, 18 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DuanHHLF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DuanmuBLSWTGSKJ22,
author = {Hongyi Duanmu and
Shristi Bhattarai and
Hongxiao Li and
Zhan Shi and
Fusheng Wang and
George Teodoro and
Keerthi Gogineni and
Preeti Subhedar and
Umay Kiraz and
Emiel A. M. Janssen and
Ritu Aneja and
Jun Kong},
title = {A spatial attention guided deep learning system for prediction of
pathological complete response using breast cancer histopathology
images},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4605--4612},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac558},
doi = {10.1093/BIOINFORMATICS/BTAC558},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DuanmuBLSWTGSKJ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DufresneLMPRKMD22,
author = {Yoann Dufresne and
T{\'{e}}o Lemane and
Pierre Marijon and
Pierre Peterlongo and
Amatur Rahman and
Marek Kokot and
Paul Medvedev and
Sebastian Deorowicz and
Rayan Chikhi},
title = {The K-mer File Format: a standardized and compact disk representation
of sets of \emph{k}-mers},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4423--4425},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac528},
doi = {10.1093/BIOINFORMATICS/BTAC528},
timestamp = {Thu, 04 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DufresneLMPRKMD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/EbertEHSSD22,
author = {Vincent Ebert and
Patrick Eiring and
Dominic A. Helmerich and
Rick Seifert and
Markus Sauer and
S{\"{o}}ren Doose},
title = {Convex hull as diagnostic tool in single-molecule localization microscopy},
journal = {Bioinform.},
volume = {38},
number = {24},
pages = {5421--5429},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac700},
doi = {10.1093/BIOINFORMATICS/BTAC700},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/EbertEHSSD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/EbmeyerCBKL22,
author = {Stefan Ebmeyer and
Roelof Dirk Coertze and
Fanny Berglund and
Erik Kristiansson and
D. G. Joakim Larsson},
title = {GEnView: a gene-centric, phylogeny-based comparative genomics pipeline
for bacterial genomes and plasmids},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1727--1728},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab855},
doi = {10.1093/BIOINFORMATICS/BTAB855},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/EbmeyerCBKL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/EguchiHINOY22,
author = {Ryohei Eguchi and
Momoko Hamano and
Michio Iwata and
Toru Nakamura and
Shinya Oki and
Yoshihiro Yamanishi},
title = {{TRANSDIRE:} data-driven direct reprogramming by a pioneer factor-guided
trans-omics approach},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2839--2846},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac209},
doi = {10.1093/BIOINFORMATICS/BTAC209},
timestamp = {Mon, 13 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/EguchiHINOY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/EnjalbertCourrechN22,
author = {Nicolas Enjalbert{-}Courrech and
Pierre Neuvial},
title = {Powerful and interpretable control of false discoveries in two-group
differential expression studies},
journal = {Bioinform.},
volume = {38},
number = {23},
pages = {5214--5221},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac693},
doi = {10.1093/BIOINFORMATICS/BTAC693},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/EnjalbertCourrechN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ErginUCSL22,
author = {Enes K. Ergin and
Anuli C. Uzozie and
Siyuan Chen and
Ye Su and
Philipp F. Lange},
title = {SQuAPP - simple quantitative analysis of proteins and PTMs},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4956--4958},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac628},
doi = {10.1093/BIOINFORMATICS/BTAC628},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ErginUCSL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ErikssonMSBLH22,
author = {Pontus Eriksson and
Nour{-}al{-}dain Marzouka and
Gottfrid Sj{\"{o}}dahl and
Carina Bernardo and
Fredrik Liedberg and
Mattias H{\"{o}}glund},
title = {A comparison of rule-based and centroid single-sample multiclass predictors
for transcriptomic classification},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1022--1029},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab763},
doi = {10.1093/BIOINFORMATICS/BTAB763},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ErikssonMSBLH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ErtenHKB22,
author = {Cesim Erten and
Aissa Houdjedj and
Hilal Kazan and
Ahmed Amine Taleb Bahmed},
title = {PersonaDrive: a method for the identification and prioritization of
personalized cancer drivers},
journal = {Bioinform.},
volume = {38},
number = {13},
pages = {3407--3414},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac329},
doi = {10.1093/BIOINFORMATICS/BTAC329},
timestamp = {Mon, 25 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ErtenHKB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/EscobedoCCGHMPP22,
author = {Nahuel Escobedo and
Ronaldo Romario Tunque Cahui and
Gast{\'{o}}n Caruso and
Emilio Garcia{-}Rios and
Layla Hirsh and
Alexander Miguel Monzon and
Gustavo D. Parisi and
Nicolas Palopoli},
title = {CoDNaS-Q: a database of conformational diversity of the native state
of proteins with quaternary structure},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4959--4961},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac627},
doi = {10.1093/BIOINFORMATICS/BTAC627},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/EscobedoCCGHMPP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/EslamiBEWZUCBMC22,
author = {Mohammed Eslami and
Amin Espah Borujeni and
Hamed Eramian and
Mark Weston and
George Zheng and
Joshua Urrutia and
Carolyn Corbet and
Diveena Becker and
Paul Maschhoff and
Katie Clowers and
Alexander Cristofaro and
Hamid Doost Hosseini and
D. Benjamin Gordon and
Yuval Dorfan and
Jedediah Singer and
Matthew Vaughn and
Niall Gaffney and
John Fonner and
Joe Stubbs and
Christopher A. Voigt and
Enoch Yeung},
title = {Prediction of whole-cell transcriptional response with machine learning},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {404--409},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab676},
doi = {10.1093/BIOINFORMATICS/BTAB676},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/EslamiBEWZUCBMC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FanXZWXQ22,
author = {Yang Fan and
Yingce Xia and
Jinhua Zhu and
Lijun Wu and
Shufang Xie and
Tao Qin},
title = {Back translation for molecule generation},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1244--1251},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab817},
doi = {10.1093/BIOINFORMATICS/BTAB817},
timestamp = {Mon, 26 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/FanXZWXQ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FancelloGFCBSZM22,
author = {Laura Fancello and
Alessandro Guida and
Gianmaria Frige and
Arnaud C{\'{e}}ol and
Gabriele Babini and
Giovanni Luca Scaglione and
Mario Zanfardino and
Tommaso Mazza and
Lorenzo Ferrando and
Pier Giuseppe Pelicci and
Luca Mazzarella},
title = {TMBleR: a bioinformatic tool to optimize {TMB} estimation and predictive
power},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1724--1726},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab836},
doi = {10.1093/BIOINFORMATICS/BTAB836},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/FancelloGFCBSZM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FangP22,
author = {Zhuoqing Fang and
Gary Peltz},
title = {An automated multi-modal graph-based pipeline for mouse genetic discovery},
journal = {Bioinform.},
volume = {38},
number = {13},
pages = {3385--3394},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac356},
doi = {10.1093/BIOINFORMATICS/BTAC356},
timestamp = {Mon, 25 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/FangP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FangRZM22,
author = {Kuangnan Fang and
Rui Ren and
Qingzhao Zhang and
Shuangge Ma},
title = {iSFun: an {R} package for integrative dimension reduction analysis},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3134--3135},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac281},
doi = {10.1093/BIOINFORMATICS/BTAC281},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/FangRZM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FeidakisKHN22,
author = {Christos P. Feidakis and
Radoslav Kriv{\'{a}}k and
David Hoksza and
Marian Novotny},
title = {AHoJ: rapid, tailored search and retrieval of apo and holo protein
structures for user-defined ligands},
journal = {Bioinform.},
volume = {38},
number = {24},
pages = {5452--5453},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac701},
doi = {10.1093/BIOINFORMATICS/BTAC701},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/FeidakisKHN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FemeniasSSAM22,
author = {Martin M. Femenias and
Juan C. Santos and
Jack W. Sites and
Luciano J. Avila and
Mariana Morando},
title = {ExplorATE: a new pipeline to explore active transposable elements
from RNA-seq data},
journal = {Bioinform.},
volume = {38},
number = {13},
pages = {3361--3366},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac354},
doi = {10.1093/BIOINFORMATICS/BTAC354},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/FemeniasSSAM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FengTRTDDSC22,
author = {Qian Feng and
Kathryn E. Tiedje and
Shazia Ruybal{-}Pes{\'{a}}ntez and
Gerry Tonkin{-}Hill and
Michael F. Duffy and
Karen P. Day and
Heejung Shim and
Yao{-}Ban Chan},
title = {An accurate method for identifying recent recombinants from unaligned
sequences},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {1823--1829},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac012},
doi = {10.1093/BIOINFORMATICS/BTAC012},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/FengTRTDDSC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FengXS22,
author = {Shi{-}Hao Feng and
Chun{-}Qiu Xia and
Hong{-}Bin Shen},
title = {CoCoPRED: coiled-coil protein structural feature prediction from amino
acid sequence using deep neural networks},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {720--729},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab744},
doi = {10.1093/BIOINFORMATICS/BTAB744},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/FengXS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FergusonGNGTABD22,
author = {James M. Ferguson and
Hasindu Gamaarachchi and
Thanh Nguyen and
Alyne Gollon and
Stephanie Tong and
Chiara Aquilina{-}Reid and
Rachel Bowen{-}James and
Ira W. Deveson},
title = {InterARTIC: an interactive web application for whole-genome nanopore
sequencing analysis of SARS-CoV-2 and other viruses},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1443--1446},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab846},
doi = {10.1093/BIOINFORMATICS/BTAB846},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/FergusonGNGTABD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Fernandez-Gonzalez22,
author = {Rodrigo Fernandez{-}Gonzalez and
Negar Balaghi and
Kelly Wang and
Ray Hawkins and
Katheryn Rothenberg and
Christopher McFaul and
Clara Schimmer and
Michelle Ly and
Ana Maria do Carmo and
Gordana Scepanovic and
Gonca Erdemci{-}Tandogan and
Veronica Castle},
title = {PyJAMAS: open-source, multimodal segmentation and analysis of microscopy
images},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {594--596},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab589},
doi = {10.1093/BIOINFORMATICS/BTAB589},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Fernandez-Gonzalez22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Fernandez-PozoB22,
author = {No{\'{e}} Fern{\'{a}}ndez{-}Pozo and
Aureliano Bombarely},
title = {EasyGDB: a low-maintenance and highly customizable system to develop
genomics portals},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {4048--4050},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac412},
doi = {10.1093/BIOINFORMATICS/BTAC412},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Fernandez-PozoB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Ferrer-BonsomsJ22,
author = {Juan A. Ferrer{-}Bonsoms and
Laura Jareno and
Angel Rubio},
title = {Rediscover: an {R} package to identify mutually exclusive mutations},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {844--845},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab709},
doi = {10.1093/BIOINFORMATICS/BTAB709},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Ferrer-BonsomsJ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Ferrer-BonsomsM22,
author = {Juan A. Ferrer{-}Bonsoms and
Xabier Morales and
Pegah T. Afshar and
Wing Hung Wong and
Angel Rubio},
title = {On the identifiability of the isoform deconvolution problem: application
to select the proper fragment length in an RNA-seq library},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1491--1496},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab873},
doi = {10.1093/BIOINFORMATICS/BTAB873},
timestamp = {Sun, 08 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Ferrer-BonsomsM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FilimonovCS22,
author = {Maxim Filimonov and
Daphn{\'{e}} Chopard and
Irena Spasic},
title = {Simulation and annotation of global acronyms},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3136--3138},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac298},
doi = {10.1093/BIOINFORMATICS/BTAC298},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/FilimonovCS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FischerG22,
author = {Stephan Fischer and
Jesse A. Gillis},
title = {Defining the extent of gene function using {ROC} curvature},
journal = {Bioinform.},
volume = {38},
number = {24},
pages = {5390--5397},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac692},
doi = {10.1093/BIOINFORMATICS/BTAC692},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/FischerG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FooteARM22,
author = {Alex Foote and
Amina Asif and
Nasir M. Rajpoot and
Fayyaz A. Minhas},
title = {{REET:} robustness evaluation and enhancement toolbox for computational
pathology},
journal = {Bioinform.},
volume = {38},
number = {12},
pages = {3312--3314},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac315},
doi = {10.1093/BIOINFORMATICS/BTAC315},
timestamp = {Mon, 25 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/FooteARM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FormentiABBGGFJ22,
author = {Giulio Formenti and
Linelle Abueg and
Angelo Brajuka and
Nadolina Brajuka and
Crist{\'{o}}bal Gallardo{-}Alba and
Alice Giani and
Olivier Fedrigo and
Erich D. Jarvis},
title = {Gfastats: conversion, evaluation and manipulation of genome sequences
using assembly graphs},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4214--4216},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac460},
doi = {10.1093/BIOINFORMATICS/BTAC460},
timestamp = {Thu, 22 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/FormentiABBGGFJ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FriebelJDH22,
author = {Adrian Friebel and
Tim Johann and
Dirk Drasdo and
Stefan Hoehme},
title = {Guided interactive image segmentation using machine learning and color-based
image set clustering},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4622--4628},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac547},
doi = {10.1093/BIOINFORMATICS/BTAC547},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/FriebelJDH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FryLY22,
author = {Joshua Fry and
Yangyang Li and
Rendong Yang},
title = {ScanExitronLR: characterization and quantification of exitron splicing
events in long-read RNA-seq data},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4966--4968},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac626},
doi = {10.1093/BIOINFORMATICS/BTAC626},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/FryLY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FuHLQZ22,
author = {Haitao Fu and
Feng Huang and
Xuan Liu and
Yang Qiu and
Wen Zhang},
title = {{MVGCN:} data integration through multi-view graph convolutional network
for predicting links in biomedical bipartite networks},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {426--434},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab651},
doi = {10.1093/BIOINFORMATICS/BTAB651},
timestamp = {Wed, 16 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/FuHLQZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FuZGCG22,
author = {Xiaoming Fu and
Xinyi Zhou and
Dongyang Gu and
Zhixing Cao and
Ramon Grima},
title = {DelaySSAToolkit.jl: stochastic simulation of reaction systems with
time delays in Julia},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4243--4245},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac472},
doi = {10.1093/BIOINFORMATICS/BTAC472},
timestamp = {Sun, 22 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/FuZGCG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FukunagaI22,
author = {Tsukasa Fukunaga and
Wataru Iwasaki},
title = {Mirage 2.0: fast and memory-efficient reconstruction of gene-content
evolution considering heterogeneous evolutionary patterns among gene
families},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {4039--4041},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac433},
doi = {10.1093/BIOINFORMATICS/BTAC433},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/FukunagaI22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GaoOSDWHRSBCCMTBG22,
author = {Galen F. Gao and
Coyin Oh and
Gordon Saksena and
Davy Deng and
Lindsay C. Westlake and
Barbara A. Hill and
Michael Reich and
Steven E. Schumacher and
Ashton C. Berger and
Scott L. Carter and
Andrew D. Cherniack and
Matthew Meyerson and
Barbara Tabak and
Rameen Beroukhim and
Gad Getz},
title = {Tangent normalization for somatic copy-number inference in cancer
genome analysis},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4677--4686},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac586},
doi = {10.1093/BIOINFORMATICS/BTAC586},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GaoOSDWHRSBCCMTBG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Garcia-GarciaTP22,
author = {Natalia Garc{\'{\i}}a{-}Garc{\'{\i}}a and
Javier Tamames and
Fernando Puente{-}S{\'{a}}nchez},
title = {M{\&}Ms: a versatile software for building microbial mock communities},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {2057--2059},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab882},
doi = {10.1093/BIOINFORMATICS/BTAB882},
timestamp = {Sun, 22 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Garcia-GarciaTP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Garcia-JimenoTJ22,
author = {Luis Garc{\'{\i}}a{-}Jimeno and
Coral Fustero Torre and
Mar{\'{\i}}a Jos{\'{e}} Jim{\'{e}}nez{-}Santos and
Gonzalo G{\'{o}}mez{-}L{\'{o}}pez and
Tom{\'{a}}s Di Domenico and
F{\'{a}}tima Al{-}Shahrour},
title = {bollito: a flexible pipeline for comprehensive single-cell RNA-seq
analyses},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1155--1156},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab758},
doi = {10.1093/BIOINFORMATICS/BTAB758},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Garcia-JimenoTJ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Garcia-PrietoMV22,
author = {Carlos A. Garcia{-}Prieto and
Francisco Mart{\'{\i}}nez{-}Jim{\'{e}}nez and
Alfonso Valencia and
Eduard Porta{-}Pardo},
title = {Detection of oncogenic and clinically actionable mutations in cancer
genomes critically depends on variant calling tools},
journal = {Bioinform.},
volume = {38},
number = {12},
pages = {3181--3191},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac306},
doi = {10.1093/BIOINFORMATICS/BTAC306},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Garcia-PrietoMV22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GargSMAGR22,
author = {Parth Garg and
Sukriti Sacher and
Mrinal and
Atul and
Prutyay Gautam and
Arjun Ray},
title = {{CICLOP:} a robust and accurate computational framework for protein
inner cavity detection},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2153--2161},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac061},
doi = {10.1093/BIOINFORMATICS/BTAC061},
timestamp = {Wed, 18 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GargSMAGR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GaynorWALLMPL22,
author = {Sheila M. Gaynor and
Kenneth E. Westerman and
Lea L. Ackovic and
Xihao Li and
Zilin Li and
Alisa Manning and
Anthony A. Philippakis and
Xihong Lin},
title = {{STAAR} workflow: a cloud-based workflow for scalable and reproducible
rare variant analysis},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3116--3117},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac272},
doi = {10.1093/BIOINFORMATICS/BTAC272},
timestamp = {Wed, 05 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GaynorWALLMPL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GeerRW22,
author = {Wesley S. van de Geer and
Job van Riet and
Harmen J. G. van de Werken},
title = {ProteoDisco: a flexible {R} approach to generate customized protein
databases for extended search space of novel and variant proteins
in proteogenomic studies},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1437--1439},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab809},
doi = {10.1093/BIOINFORMATICS/BTAB809},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GeerRW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GentiliMSB22,
author = {Michele Gentili and
Leonardo Martini and
Marialuisa Sponziello and
Luca Becchetti},
title = {Biological Random Walks: multi-omics integration for disease gene
prioritization},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4145--4152},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac446},
doi = {10.1093/BIOINFORMATICS/BTAC446},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GentiliMSB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GholamizojM22,
author = {Soroosh Gholamizoj and
Bin Ma},
title = {{SPEQ:} quality assessment of peptide tandem mass spectra with deep
learning},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1568--1574},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab874},
doi = {10.1093/BIOINFORMATICS/BTAB874},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GholamizojM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GitchevZMJ22,
author = {Todor Gitchev and
Gabriel Zala and
Peter Meister and
Daniel Jost},
title = {3DPolyS-LE: an accessible simulation framework to model the interplay
between chromatin and loop extrusion},
journal = {Bioinform.},
volume = {38},
number = {24},
pages = {5454--5456},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac705},
doi = {10.1093/BIOINFORMATICS/BTAC705},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GitchevZMJ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GoelS22,
author = {Manish Goel and
Korbinian Schneeberger},
title = {plotsr: visualizing structural similarities and rearrangements between
multiple genomes},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2922--2926},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac196},
doi = {10.1093/BIOINFORMATICS/BTAC196},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GoelS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GongC22,
author = {Yao Gong and
Yue Chen},
title = {UbE3-APA: a bioinformatic strategy to elucidate ubiquitin {E3} ligase
activities in quantitative proteomics study},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2211--2218},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac069},
doi = {10.1093/BIOINFORMATICS/BTAC069},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GongC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Gonzalez-Reymundez22,
author = {Agustin Gonzalez{-}Reymundez and
Alexander Grueneberg and
Guanqi Lu and
Filipe Couto Alves and
Gonzalo Rincon and
Ana I Vazquez},
title = {{MOSS:} multi-omic integration with sparse value decomposition},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2956--2958},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac179},
doi = {10.1093/BIOINFORMATICS/BTAC179},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Gonzalez-Reymundez22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GonzalezAlemanPRHCLM22,
author = {Roy Gonz{\'{a}}lez{-}Alem{\'{a}}n and
Daniel Platero{-}Rochart and
Alejandro Rodr{\'{\i}}guez{-}Serradet and
Erix Wiliam Hern{\'{a}}ndez{-}Rodr{\'{\i}}guez and
Julio Caballero and
Fabrice Leclerc and
Luis Alberto Montero{-}Cabrera},
title = {{MDSCAN:} RMSD-based {HDBSCAN} clustering of long molecular dynamics},
journal = {Bioinform.},
volume = {38},
number = {23},
pages = {5191--5198},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac666},
doi = {10.1093/BIOINFORMATICS/BTAC666},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GonzalezAlemanPRHCLM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GrafCMCSLSSSDLL22,
author = {John F. Graf and
Sanghee Cho and
Elizabeth McDonough and
Alex Corwin and
Anup Sood and
Andreas Lindner and
Manuela Salvucci and
Xanthi Stachtea and
Sandra Van Schaeybroeck and
Philip D. Dunne and
Pierre Laurent{-}Puig and
Daniel B. Longley and
Jochen H. M. Prehn and
Fiona Ginty},
title = {{FLINO:} a new method for immunofluorescence bioimage normalization},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {520--526},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab686},
doi = {10.1093/BIOINFORMATICS/BTAB686},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GrafCMCSLSSSDLL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Grant-PetersRGC22,
author = {Melissa Grant{-}Peters and
Charlotte Rich{-}Griffin and
Jonathan E. Grant{-}Peters and
Gianfelice Cinque and
Calliope A. Dendrou},
title = {Photizo: an open-source library for cross-sample analysis of {FTIR}
spectroscopy data},
journal = {Bioinform.},
volume = {38},
number = {13},
pages = {3490--3492},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac346},
doi = {10.1093/BIOINFORMATICS/BTAC346},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Grant-PetersRGC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GrassiPT22,
author = {Mario Grassi and
Fernando Palluzzi and
Barbara Tarantino},
title = {SEMgraph: an {R} package for causal network inference of high-throughput
data with structural equation models},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4829--4830},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac567},
doi = {10.1093/BIOINFORMATICS/BTAC567},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GrassiPT22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GromihaOST22,
author = {M. Michael Gromiha and
Christine A. Orengo and
Ramanathan Sowdhamini and
Janet M. Thornton},
title = {Srinivasan {(1962-2021)} in Bioinformatics and beyond},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2377--2379},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac054},
doi = {10.1093/BIOINFORMATICS/BTAC054},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GromihaOST22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GrothDGN22,
author = {Theodore Groth and
Alexander D. Diehl and
Rudiyanto Gunawan and
Sriram Neelamegham},
title = {GlycoEnzOnto: a GlycoEnzyme pathway and molecular function ontology},
journal = {Bioinform.},
volume = {38},
number = {24},
pages = {5413--5420},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac704},
doi = {10.1093/BIOINFORMATICS/BTAC704},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GrothDGN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GrucaHKSWS22,
author = {Aleksandra Gruca and
Joanna Henzel and
Iwona Kostorz and
Tomasz Steclik and
Lukasz Wr{\'{o}}bel and
Marek Sikora},
title = {{MAINE:} a web tool for multi-omics feature selection and rule-based
data exploration},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1773--1775},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab862},
doi = {10.1093/BIOINFORMATICS/BTAB862},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GrucaHKSWS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GrudmanFF22,
author = {Steven Grudman and
J. Eduardo Fajardo and
Andr{\'{a}}s Fiser},
title = {{INTERCAAT:} identifying interface residues between macromolecules},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {554--555},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab596},
doi = {10.1093/BIOINFORMATICS/BTAB596},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GrudmanFF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GuCMLWXM22,
author = {Haocheng Gu and
Hao Cheng and
Anjun Ma and
Yang Li and
Juexin Wang and
Dong Xu and
Qin Ma},
title = {scGNN 2.0: a graph neural network tool for imputation and clustering
of single-cell RNA-Seq data},
journal = {Bioinform.},
volume = {38},
number = {23},
pages = {5322--5325},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac684},
doi = {10.1093/BIOINFORMATICS/BTAC684},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GuCMLWXM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GuH22,
author = {Zuguang Gu and
Daniel H{\"{u}}bschmann},
title = {spiralize: an {R} package for visualizing data on spirals},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1434--1436},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab778},
doi = {10.1093/BIOINFORMATICS/BTAB778},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GuH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GuH22a,
author = {Zuguang Gu and
Daniel H{\"{u}}bschmann},
title = {Make Interactive Complex Heatmaps in {R}},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1460--1462},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab806},
doi = {10.1093/BIOINFORMATICS/BTAB806},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GuH22a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GuH22b,
author = {Zuguang Gu and
Daniel H{\"{u}}bschmann},
title = {\emph{Pkgndep}: a tool for analyzing dependency heaviness of {R} packages},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4248--4251},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac449},
doi = {10.1093/BIOINFORMATICS/BTAC449},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GuH22b.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GuJGM22,
author = {Shawn Gu and
Meng Jiang and
Pietro Hiram Guzzi and
Tijana Milenkovic},
title = {Modeling multi-scale data via a network of networks},
journal = {Bioinform.},
volume = {38},
number = {9},
pages = {2544--2553},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac133},
doi = {10.1093/BIOINFORMATICS/BTAC133},
timestamp = {Wed, 18 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GuJGM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GuarracinoHNPG22,
author = {Andrea Guarracino and
Simon Heumos and
Sven Nahnsen and
Pjotr Prins and
Erik Garrison},
title = {{ODGI:} understanding pangenome graphs},
journal = {Bioinform.},
volume = {38},
number = {13},
pages = {3319--3326},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac308},
doi = {10.1093/BIOINFORMATICS/BTAC308},
timestamp = {Wed, 27 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GuarracinoHNPG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GuiXWWYGDWC22,
author = {Yifan Gui and
Shuangshuang Xie and
Yanan Wang and
Ping Wang and
Renzhi Yao and
Xukai Gao and
Yutian Dong and
Gaoang Wang and
Kuan Yoow Chan},
title = {pcnaDeep: a fast and robust single-cell tracking method using deep-learning
mediated cell cycle profiling},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4846--4847},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac602},
doi = {10.1093/BIOINFORMATICS/BTAC602},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GuiXWWYGDWC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GuoLZZ22,
author = {Sai{-}Sai Guo and
Jun Liu and
Xiao{-}Gen Zhou and
Gui{-}Jun Zhang},
title = {DeepUMQA: ultrafast shape recognition-based protein model quality
assessment using deep learning},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {1895--1903},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac056},
doi = {10.1093/BIOINFORMATICS/BTAC056},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GuoLZZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GuoSJW22,
author = {Zhenxing Guo and
Andrew M. Shafik and
Peng Jin and
Hao Wu},
title = {Differential {RNA} methylation analysis for MeRIP-seq data under general
experimental design},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4705--4712},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac601},
doi = {10.1093/BIOINFORMATICS/BTAC601},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GuoSJW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GuoZJDP22,
author = {Shuxia Guo and
Xuan Zhao and
Shengdian Jiang and
Liya Ding and
Hanchuan Peng},
title = {Image enhancement to leverage the 3D morphological reconstruction
of single-cell neurons},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {503--512},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab638},
doi = {10.1093/BIOINFORMATICS/BTAB638},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GuoZJDP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GustavssonZRGR22,
author = {Emil K. Gustavsson and
David Zhang and
Regina H. Reynolds and
Sonia Garc{\'{\i}}a{-}Ru{\'{\i}}z and
Mina Ryten},
title = {\emph{ggtranscript}: an {R} package for the visualization and interpretation
of transcript isoforms using \emph{ggplot2}},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3844--3846},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac409},
doi = {10.1093/BIOINFORMATICS/BTAC409},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GustavssonZRGR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GutebierBHMMMLPEWLVLPWJ22,
author = {Lea G{\"{u}}tebier and
Tim Bleimehl and
Ron Henkel and
Jamie Munro and
Sebastian M{\"{u}}ller and
Axel Morgner and
Jakob Laenge and
Anke Pachauer and
Alexander Erdl and
Jens Weimar and
Kirsten Walther Langendorf and
Vincent Vialard and
Thorsten Liebig and
Martin Preusse and
Dagmar Waltemath and
Alexander Jarasch},
title = {CovidGraph: a graph to fight {COVID-19}},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4843--4845},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac592},
doi = {10.1093/BIOINFORMATICS/BTAC592},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GutebierBHMMMLPEWLVLPWJ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GuzziPGV22,
author = {Pietro Hiram Guzzi and
Luisa Di Paola and
Alessandro Giuliani and
Pierangelo Veltri},
title = {PCN-Miner: an open-source extensible tool for the analysis of Protein
Contact Networks},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4235--4237},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac450},
doi = {10.1093/BIOINFORMATICS/BTAC450},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GuzziPGV22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HagiwaraEWZ22,
author = {Kohei Hagiwara and
Michael N. Edmonson and
David A. Wheeler and
Jinghui Zhang},
title = {indelPost: harmonizing ambiguities in simple and complex indel alignments},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {549--551},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab601},
doi = {10.1093/BIOINFORMATICS/BTAB601},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HagiwaraEWZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HalilogluHE22,
author = {Turkan Haliloglu and
Aysima Hacisuleyman and
Burak Erman},
title = {Prediction of allosteric communication pathways in proteins},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3590--3599},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac380},
doi = {10.1093/BIOINFORMATICS/BTAC380},
timestamp = {Mon, 08 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HalilogluHE22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HarmelAKTDIGBFG22,
author = {Christoph Harmel and
Samy Sid Ahmed and
Robin Koch and
Jana T{\"{u}}nnermann and
Tania Distler and
Andrea Imle and
Luca Giorgetti and
Emanuel Bahn and
Oliver T. Fackler and
Frederik Graw},
title = {VisuStatR: visualizing motility and morphology statistics on images
in {R}},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2970--2972},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac191},
doi = {10.1093/BIOINFORMATICS/BTAC191},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HarmelAKTDIGBFG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HarrisMRLSLCWV22,
author = {Coleman R. Harris and
Eliot T. McKinley and
Joseph T. Roland and
Qi Liu and
Martha J. Shrubsole and
Ken S. Lau and
Robert J. Coffey and
Julia Wrobel and
Simon N. Vandekar},
title = {Quantifying and correcting slide-to-slide variation in multiplexed
immunofluorescence images},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1700--1707},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab877},
doi = {10.1093/BIOINFORMATICS/BTAB877},
timestamp = {Thu, 19 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HarrisMRLSLCWV22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HarrisonSMB22,
author = {Jonathan U. Harrison and
Onur Sen and
Andrew D. McAinsh and
Nigel J. Burroughs},
title = {Kinetochore tracking in 3D from lattice light-sheet imaging data with
KiT},
journal = {Bioinform.},
volume = {38},
number = {12},
pages = {3315--3317},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac330},
doi = {10.1093/BIOINFORMATICS/BTAC330},
timestamp = {Wed, 27 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HarrisonSMB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HashimotoRothSLBC22,
author = {Emily Hashimoto{-}Roth and
Anuradha Surendra and
Mathieu Lavall{\'{e}}e{-}Adam and
Steffany A. L. Bennett and
Miroslava Cuperlovic{-}Culf},
title = {METAbolomics data Balancing with Over-sampling Algorithms {(META-BOA):}
an online resource for addressing class imbalance},
journal = {Bioinform.},
volume = {38},
number = {23},
pages = {5326--5327},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac649},
doi = {10.1093/BIOINFORMATICS/BTAC649},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HashimotoRothSLBC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HauschildLMFZHB22,
author = {Anne{-}Christin Hauschild and
Marta Lemanczyk and
Julian O. Matschinske and
Tobias Frisch and
Olga I. Zolotareva and
Andreas Holzinger and
Jan Baumbach and
Dominik Heider},
title = {Federated Random Forests can improve local performance of predictive
models for various healthcare applications},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2278--2286},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac065},
doi = {10.1093/BIOINFORMATICS/BTAC065},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HauschildLMFZHB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HayesNIBTMH22,
author = {Matthew Hayes and
Angela Nguyen and
Rahib Islam and
Caryn Butler and
Ethan Tran and
Derrick Mullins and
Chindo Hicks},
title = {HolistIC: leveraging Hi-C and whole genome shotgun sequencing for
double minute chromosome discovery},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1208--1215},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab816},
doi = {10.1093/BIOINFORMATICS/BTAB816},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HayesNIBTMH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HeFWLWL22,
author = {Huan He and
Sunyang Fu and
Liwei Wang and
Sijia Liu and
Andrew Wen and
Hongfang Liu},
title = {MedTator: a serverless annotation tool for corpus development},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1776--1778},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab880},
doi = {10.1093/BIOINFORMATICS/BTAB880},
timestamp = {Fri, 01 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HeFWLWL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HeZZH22,
author = {Bintao He and
Yan Zhang and
Fa Zhang and
Renmin Han},
title = {Correction of image distortion in large-field ssEM stitching by an
unsupervised intermediate-space solving network},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4797--4805},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac566},
doi = {10.1093/BIOINFORMATICS/BTAC566},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HeZZH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HeinkenT22,
author = {Almut Heinken and
Ines Thiele},
title = {Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of
microbiome communities},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2367--2368},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac082},
doi = {10.1093/BIOINFORMATICS/BTAC082},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HeinkenT22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HennegesP22,
author = {Carsten Henneges and
Joseph N. Paulson},
title = {GameRank: {R} package for feature selection and construction},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4840--4842},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac552},
doi = {10.1093/BIOINFORMATICS/BTAC552},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HennegesP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HentgesSCDHT22,
author = {Lance D. Hentges and
Martin J. Sergeant and
Christopher B. Cole and
Damien J. Downes and
Jim R. Hughes and
Stephen Taylor},
title = {LanceOtron: a deep learning peak caller for genome sequencing experiments},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4255--4263},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac525},
doi = {10.1093/BIOINFORMATICS/BTAC525},
timestamp = {Mon, 24 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HentgesSCDHT22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Hernansaiz-Ballesteros22,
author = {Rosa D. Hernansaiz{-}Ballesteros and
Christian H. Holland and
Aur{\'{e}}lien Dugourd and
Julio Saez{-}Rodriguez},
title = {{FUNKI:} interactive functional footprint-based analysis of omics
data},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {2075--2076},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac055},
doi = {10.1093/BIOINFORMATICS/BTAC055},
timestamp = {Fri, 13 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Hernansaiz-Ballesteros22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HeydariDZHS22,
author = {Abbas{-}Ali Heydari and
Oscar A. Davalos and
Lihong Zhao and
Katrina K. Hoyer and
Suzanne S. Sindi},
title = {\emph{ACTIVA}: realistic single-cell RNA-seq generation with automatic
cell-type identification using introspective variational autoencoders},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2194--2201},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac095},
doi = {10.1093/BIOINFORMATICS/BTAC095},
timestamp = {Sat, 26 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HeydariDZHS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HillertonSNS22,
author = {Thomas Hillerton and
Deniz Se{\c{c}}ilmis and
Sven Nelander and
Erik L. L. Sonnhammer},
title = {Fast and accurate gene regulatory network inference by normalized
least squares regression},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2263--2268},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac103},
doi = {10.1093/BIOINFORMATICS/BTAC103},
timestamp = {Thu, 02 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HillertonSNS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HippenCGG22,
author = {Ariel A. Hippen and
Jake Crawford and
Jacob R. Gardner and
Casey S. Greene},
title = {wenda{\_}gpu: fast domain adaptation for genomic data},
journal = {Bioinform.},
volume = {38},
number = {22},
pages = {5129--5130},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac663},
doi = {10.1093/BIOINFORMATICS/BTAC663},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HippenCGG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HohlerPISS22,
author = {Dimitri H{\"{o}}hler and
Wayne Pfeiffer and
Vassilios Ioannidis and
Heinz Stockinger and
Alexandros Stamatakis},
title = {RAxML Grove: an empirical phylogenetic tree database},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1741--1742},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab863},
doi = {10.1093/BIOINFORMATICS/BTAB863},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HohlerPISS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HolbrookJS22,
author = {Andrew J. Holbrook and
Xiang Ji and
Marc A. Suchard},
title = {From viral evolution to spatial contagion: a biologically modulated
Hawkes model},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {1846--1856},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac027},
doi = {10.1093/BIOINFORMATICS/BTAC027},
timestamp = {Wed, 27 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HolbrookJS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HongLJL22,
author = {Yue Hong and
Pengyu Luo and
Shuting Jin and
Xiangrong Liu},
title = {LaGAT: link-aware graph attention network for drug-drug interaction
prediction},
journal = {Bioinform.},
volume = {38},
number = {24},
pages = {5406--5412},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac682},
doi = {10.1093/BIOINFORMATICS/BTAC682},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HongLJL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HongTF22,
author = {Chen Hong and
Robin Thiele and
Lars Feuerbach},
title = {GenomeTornadoPlot: a novel {R} package for {CNV} visualization and
focality analysis},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {2036--2038},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac037},
doi = {10.1093/BIOINFORMATICS/BTAC037},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HongTF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HostalleroLE22,
author = {David Earl Hostallero and
Yihui Li and
Amin Emad},
title = {Looking at the BiG picture: incorporating bipartite graphs in drug
response prediction},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3609--3620},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac383},
doi = {10.1093/BIOINFORMATICS/BTAC383},
timestamp = {Mon, 08 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HostalleroLE22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HouH22,
author = {Ruiyan Hou and
Yuanghua Huang},
title = {Genomic sequences and RNA-binding proteins predict {RNA} splicing
efficiency in various single-cell contexts},
journal = {Bioinform.},
volume = {38},
number = {12},
pages = {3231--3237},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac321},
doi = {10.1093/BIOINFORMATICS/BTAC321},
timestamp = {Mon, 25 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HouH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HouJ22,
author = {Wenpin Hou and
Zhicheng Ji},
title = {Palo: spatially aware color palette optimization for single-cell and
spatial data},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3654--3656},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac368},
doi = {10.1093/BIOINFORMATICS/BTAC368},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HouJ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HouXWXFZQL22,
author = {Yutai Hou and
Yingce Xia and
Lijun Wu and
Shufang Xie and
Yang Fan and
Jinhua Zhu and
Tao Qin and
Tie{-}Yan Liu},
title = {Discovering drug-target interaction knowledge from biomedical literature},
journal = {Bioinform.},
volume = {38},
number = {22},
pages = {5100--5107},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac648},
doi = {10.1093/BIOINFORMATICS/BTAC648},
timestamp = {Mon, 26 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HouXWXFZQL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuFZHC22,
author = {Xiaotian Hu and
Cong Feng and
Yincong Zhou and
Andrew P. Harrison and
Ming Chen},
title = {DeepTrio: a ternary prediction system for protein-protein interaction
using mask multiple parallel convolutional neural networks},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {694--702},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab737},
doi = {10.1093/BIOINFORMATICS/BTAB737},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuFZHC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuLMDST22,
author = {Fengyuan Hu and
Jia Lu and
Louise S. Matheson and
Manuel D. D{\'{\i}}az{-}Mu{\~{n}}oz and
Alexander Saveliev and
Martin Turner},
title = {Correction to: ORFLine: a bioinformatic pipeline to prioritize small
open reading frames identifies candidate secreted small proteins from
lymphocytes},
journal = {Bioinform.},
volume = {38},
number = {9},
pages = {2673},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac162},
doi = {10.1093/BIOINFORMATICS/BTAC162},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuLMDST22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuS22,
author = {Yi{-}Juan Hu and
Glen A. Satten},
title = {A rarefaction-without-resampling extension of {PERMANOVA} for testing
presence-absence associations in the microbiome},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3689--3697},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac399},
doi = {10.1093/BIOINFORMATICS/BTAC399},
timestamp = {Thu, 25 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuYXS22,
author = {Jin{-}Xian Hu and
Yang Yang and
Ying{-}Ying Xu and
Hong{-}Bin Shen},
title = {GraphLoc: a graph neural network model for predicting protein subcellular
localization from immunohistochemistry images},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4941--4948},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac634},
doi = {10.1093/BIOINFORMATICS/BTAC634},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuYXS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuangDCC22,
author = {Pu Huang and
Erin Davis and
Xia Cao and
Hunter J. Cameron},
title = {riboCleaner: a pipeline to identify and quantify rRNA read contamination
from RNA-seq data in plants},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3840--3843},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac402},
doi = {10.1093/BIOINFORMATICS/BTAC402},
timestamp = {Thu, 25 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuangDCC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuangLLLLTY22,
author = {Kaimei Huang and
Binghu Lin and
Jinyang Liu and
Yankun Liu and
Jingwu Li and
Geng Tian and
Jialiang Yang},
title = {Predicting colorectal cancer tumor mutational burden from histopathological
images and clinical information using multi-modal deep learning},
journal = {Bioinform.},
volume = {38},
number = {22},
pages = {5108--5115},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac641},
doi = {10.1093/BIOINFORMATICS/BTAC641},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuangLLLLTY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuangR22,
author = {Yilei Huang and
Harald Ringbauer},
title = {hapCon: estimating contamination of ancient genomes by copying from
reference haplotypes},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3768--3777},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac390},
doi = {10.1093/BIOINFORMATICS/BTAC390},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuangR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuffelSB22,
author = {Kirsten Van Huffel and
Michiel Stock and
Bernard De Baets},
title = {BioCCP.jl: collecting coupons in combinatorial biotechnology},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1144--1145},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab775},
doi = {10.1093/BIOINFORMATICS/BTAB775},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuffelSB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HughesTMLMLTC22,
author = {David A. Hughes and
Kurt Taylor and
Nancy McBride and
Matthew A. Lee and
Dan Mason and
Deborah A. Lawlor and
Nicholas J. Timpson and
Laura J. Corbin},
title = {metaboprep: an {R} package for preanalysis data description and processing},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {1980--1987},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac059},
doi = {10.1093/BIOINFORMATICS/BTAC059},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HughesTMLMLTC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuiN22,
author = {Sandra Hui and
Rasmus Nielsen},
title = {{SCONCE:} a method for profiling copy number alterations in cancer
evolution using single-cell whole genome sequencing},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {1801--1808},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac041},
doi = {10.1093/BIOINFORMATICS/BTAC041},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuiN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuizingPC22,
author = {Geert{-}Jan Huizing and
Gabriel Peyr{\'{e}} and
Laura Cantini},
title = {Optimal transport improves cell-cell similarity inference in single-cell
omics data},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2169--2177},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac084},
doi = {10.1093/BIOINFORMATICS/BTAC084},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuizingPC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuntDKHG22,
author = {Gregory J. Hunt and
Mark A. Dane and
James E. Korkola and
Laura M. Heiser and
Johann Gagnon{-}Bartsch},
title = {Systematic replication enables normalization of high-throughput imaging
assays},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4934--4940},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac606},
doi = {10.1093/BIOINFORMATICS/BTAC606},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuntDKHG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuntSCFI22,
author = {Martin Hunt and
Jeremy Swann and
Bede Constantinides and
Philip Fowler and
Zamin Iqbal},
title = {ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads},
journal = {Bioinform.},
volume = {38},
number = {12},
pages = {3291--3293},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac311},
doi = {10.1093/BIOINFORMATICS/BTAC311},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuntSCFI22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuoLWJV22,
author = {Hongwei Huo and
Pengfei Liu and
Chenhui Wang and
Hongbo Jiang and
Jeffrey Scott Vitter},
title = {CIndex: compressed indexes for fast retrieval of {FASTQ} files},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {335--343},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab655},
doi = {10.1093/BIOINFORMATICS/BTAB655},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuoLWJV22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HwangboLLHKP22,
author = {Suhyun Hwangbo and
Sungyoung Lee and
Seungyeoun Lee and
Heungsun Hwang and
Inyoung Kim and
Taesung Park},
title = {Kernel-based hierarchical structural component models for pathway
analysis},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3078--3086},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac276},
doi = {10.1093/BIOINFORMATICS/BTAC276},
timestamp = {Mon, 08 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HwangboLLHKP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/IeremieEN22,
author = {Ioan Ieremie and
Rob M. Ewing and
Mahesan Niranjan},
title = {TransformerGO: predicting protein-protein interactions by modelling
the attention between sets of gene ontology terms},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2269--2277},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac104},
doi = {10.1093/BIOINFORMATICS/BTAC104},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/IeremieEN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/IidaKWIO22,
author = {Keita Iida and
Jumpei Kondo and
Johannes Nicolaus Wibisana and
Masahiro Inoue and
Mariko Okada},
title = {{ASURAT:} functional annotation-driven unsupervised clustering of
single-cell transcriptomes},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4330--4336},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac541},
doi = {10.1093/BIOINFORMATICS/BTAC541},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/IidaKWIO22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/IkedaOOCNMKYOGK22,
author = {Shuya Ikeda and
Hiromasa Ono and
Tazro Ohta and
Hirokazu Chiba and
Yuki Naito and
Yuki Moriya and
Shuichi Kawashima and
Yasunori Yamamoto and
Shinobu Okamoto and
Susumu Goto and
Toshiaki Katayama},
title = {TogoID: an exploratory {ID} converter to bridge biological datasets},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4194--4199},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac491},
doi = {10.1093/BIOINFORMATICS/BTAC491},
timestamp = {Mon, 24 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/IkedaOOCNMKYOGK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/IrlmeierHBDC22,
author = {Rebecca Irlmeier and
Jacob J. Hughey and
Lisa Bastarache and
Joshua C. Denny and
Qingxia Chen},
title = {Cox regression is robust to inaccurate EHR-extracted event time: an
application to EHR-based {GWAS}},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2297--2306},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac086},
doi = {10.1093/BIOINFORMATICS/BTAC086},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/IrlmeierHBDC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JablonskiPCBB22,
author = {Kim Philipp Jablonski and
Martin Pirkl and
Domagoj Cevid and
Peter B{\"{u}}hlmann and
Niko Beerenwinkel},
title = {Identifying cancer pathway dysregulations using differential causal
effects},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1550--1559},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab847},
doi = {10.1093/BIOINFORMATICS/BTAB847},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/JablonskiPCBB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Jackson22,
author = {Benjamin C. Jackson},
title = {gofasta: command-line utilities for genomic epidemiology research},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {4033--4035},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac424},
doi = {10.1093/BIOINFORMATICS/BTAC424},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Jackson22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JacquemardBGK22,
author = {C{\'{e}}lien Jacquemard and
Guillaume Bret and
Thomas Grutter and
Esther Kellenberger},
title = {Comparing transmembrane protein structures with {ATOLL}},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1743--1744},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab860},
doi = {10.1093/BIOINFORMATICS/BTAB860},
timestamp = {Fri, 01 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/JacquemardBGK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JadhavKRLN22,
author = {Aditya Jadhav and
Tarun Kumar and
Mohit Raghavendra and
Tamizhini Loganathan and
Manikandan Narayanan},
title = {Predicting cross-tissue hormone-gene relations using balanced word
embeddings},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4771--4781},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac578},
doi = {10.1093/BIOINFORMATICS/BTAC578},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/JadhavKRLN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JafariJWLHW22,
author = {Elham Jafari and
Travis S. Johnson and
Yue Wang and
Yunlong Liu and
Kun Huang and
Yijie Wang},
title = {AIscEA: unsupervised integration of single-cell gene expression and
chromatin accessibility via their biological consistency},
journal = {Bioinform.},
volume = {38},
number = {23},
pages = {5236--5244},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac683},
doi = {10.1093/BIOINFORMATICS/BTAC683},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JafariJWLHW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JagtapCPBDM22,
author = {Surabhi Jagtap and
Abdulkadir {\c{C}}elikkanat and
Aur{\'{e}}lie Pirayre and
Fr{\'{e}}d{\'{e}}rique Bidard and
Laurent Duval and
Fragkiskos D. Malliaros},
title = {BraneMF: integration of biological networks for functional analysis
of proteins},
journal = {Bioinform.},
volume = {38},
number = {24},
pages = {5383--5389},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac691},
doi = {10.1093/BIOINFORMATICS/BTAC691},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JagtapCPBDM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JhaZ22,
author = {Kishlay Jha and
Aidong Zhang},
title = {Continual knowledge infusion into pre-trained biomedical language
models},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {494--502},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab671},
doi = {10.1093/BIOINFORMATICS/BTAB671},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JhaZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JiaS22,
author = {Shengji Jia and
Lei Shi},
title = {Efficient change-points detection for genomic sequences via cumulative
segmented regression},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {311--317},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab685},
doi = {10.1093/BIOINFORMATICS/BTAB685},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JiaS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JiangABZTYW22,
author = {Shiyu Jiang and
Hemn Barzan Abdalla and
Chuyun Bi and
Yi Zhu and
Xuechen Tian and
Yixin Yang and
Aloysius Wong},
title = {HNOXPred: a web tool for the prediction of gas-sensing {H-NOX} proteins
from amino acid sequence},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4643--4644},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac571},
doi = {10.1093/BIOINFORMATICS/BTAC571},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/JiangABZTYW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JiangSSCZAADTPG22,
author = {Qibing Jiang and
Praneeth Sudalagunta and
Maria C. Silva and
Rafael R. Canevarolo and
Xiaohong Zhao and
Khandakar Tanvir Ahmed and
Raghunandan Reddy Alugubelli and
Gabriel Deavila and
Alexandre Tungesvik and
Lia Perez and
Robert A. Gatenby and
Robert J. Gillies and
Rachid Baz and
Mark B. Meads and
Kenneth H. Shain and
Ariosto Siqueira Silva and
Wei Zhang},
title = {CancerCellTracker: a brightfield time-lapse microscopy framework for
cancer drug sensitivity estimation},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {4002--4010},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac417},
doi = {10.1093/BIOINFORMATICS/BTAC417},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/JiangSSCZAADTPG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JiangZZMLYN22,
author = {Jing Jiang and
Ruisheng Zhang and
Zhili Zhao and
Jun Ma and
Yunwu Liu and
Yongna Yuan and
Bojuan Niu},
title = {MultiGran-SMILES: multi-granularity {SMILES} learning for molecular
property prediction},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4573--4580},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac550},
doi = {10.1093/BIOINFORMATICS/BTAC550},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/JiangZZMLYN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JiaoISNDLIC22,
author = {Xiaoli Jiao and
Hiromi Imamichi and
Brad T. Sherman and
Rishub Nahar and
Robin L. Dewar and
H. Clifford Lane and
Tomozumi Imamichi and
Weizhong Chang},
title = {QuasiSeq: profiling viral quasispecies via self-tuning spectral clustering
with PacBio long sequencing reads},
journal = {Bioinform.},
volume = {38},
number = {12},
pages = {3192--3199},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac313},
doi = {10.1093/BIOINFORMATICS/BTAC313},
timestamp = {Mon, 25 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/JiaoISNDLIC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JiaoT22,
author = {Feng Jiao and
Moxun Tang},
title = {Quantification of transcription noise's impact on cell fate commitment
with digital resolutions},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3062--3069},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac277},
doi = {10.1093/BIOINFORMATICS/BTAC277},
timestamp = {Fri, 01 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/JiaoT22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JinLYZ22,
author = {Ke Jin and
Bo Li and
Hong Yan and
Xiao{-}Fei Zhang},
title = {Imputing dropouts for single-cell {RNA} sequencing based on multi-objective
optimization},
journal = {Bioinform.},
volume = {38},
number = {12},
pages = {3222--3230},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac300},
doi = {10.1093/BIOINFORMATICS/BTAC300},
timestamp = {Mon, 25 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/JinLYZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JinW22,
author = {Jin Jin and
Yue Wang},
title = {{T2-DAG:} a powerful test for differentially expressed gene pathways
via graph-informed structural equation modeling},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1005--1014},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab770},
doi = {10.1093/BIOINFORMATICS/BTAB770},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JinW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JinXNH22,
author = {Boyang Tom Jin and
Feng Xu and
Raymond T. Ng and
James C. Hogg},
title = {Mian: interactive web-based microbiome data table visualization and
machine learning platform},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1176--1178},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab754},
doi = {10.1093/BIOINFORMATICS/BTAB754},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JinXNH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Johansson-AkheW22,
author = {Isak Johansson{-}{\AA}khe and
Bj{\"{o}}rn Wallner},
title = {InterPepScore: a deep learning score for improving the FlexPepDock
refinement protocol},
journal = {Bioinform.},
volume = {38},
number = {12},
pages = {3209--3215},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac325},
doi = {10.1093/BIOINFORMATICS/BTAC325},
timestamp = {Thu, 25 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Johansson-AkheW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JonkheerWABHBLR22,
author = {Eef M. Jonkheer and
Dirk{-}Jan M. van Workum and
Siavash Sheikhizadeh Anari and
Bal{\'{a}}zs Brankovics and
Jorn R. de Haan and
Lidija Berke and
Theo A. J. van der Lee and
Dick de Ridder and
Sandra Smit},
title = {PanTools v3: functional annotation, classification and phylogenomics},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4403--4405},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac506},
doi = {10.1093/BIOINFORMATICS/BTAC506},
timestamp = {Mon, 05 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JonkheerWABHBLR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JornodJBSTA22,
author = {Florence Jornod and
Thomas Jaylet and
Ludek Bl{\'{a}}ha and
Denis Sarigiannis and
Luc Tamisier and
Karine Audouze},
title = {AOP-helpFinder webserver: a tool for comprehensive analysis of the
literature to support adverse outcome pathways development},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1173--1175},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab750},
doi = {10.1093/BIOINFORMATICS/BTAB750},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/JornodJBSTA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JuZZWSZB22,
author = {Fusong Ju and
Jianwei Zhu and
Qi Zhang and
Guozheng Wei and
Shiwei Sun and
Wei{-}Mou Zheng and
Dongbo Bu},
title = {Seq-SetNet: directly exploiting multiple sequence alignment for protein
secondary structure prediction},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {990--996},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab777},
doi = {10.1093/BIOINFORMATICS/BTAB777},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JuZZWSZB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JungH22,
author = {Youngmok Jung and
Dongsu Han},
title = {{BWA-MEME:} {BWA-MEM} emulated with a machine learning approach},
journal = {Bioinform.},
volume = {38},
number = {9},
pages = {2404--2413},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac137},
doi = {10.1093/BIOINFORMATICS/BTAC137},
timestamp = {Wed, 18 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/JungH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JunkK22,
author = {Philipp Junk and
Christina Kiel},
title = {{HOMELETTE:} a unified interface to homology modelling software},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1749--1751},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab866},
doi = {10.1093/BIOINFORMATICS/BTAB866},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/JunkK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KanDSSJH22,
author = {Mengyuan Kan and
Avantika R. Diwadkar and
Supriya Saxena and
Haoyue Shuai and
Jaehyun Joo and
Blanca E. Himes},
title = {{REALGAR:} a web app of integrated respiratory omics data},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4442--4445},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac524},
doi = {10.1093/BIOINFORMATICS/BTAC524},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KanDSSJH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KaraaslanliSAM22,
author = {Abdullah Karaaslanli and
Satabdi Saha and
Selin Aviyente and
Tapabrata Maiti},
title = {scSGL: kernelized signed graph learning for single-cell gene regulatory
network inference},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3011--3019},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac288},
doi = {10.1093/BIOINFORMATICS/BTAC288},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KaraaslanliSAM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KarasanSTC22,
author = {Oya Ekin Karasan and
Alper Sen and
Banu Tiryaki and
A. Erc{\"{u}}ment {\c{C}}i{\c{c}}ek},
title = {A unifying network modeling approach for codon optimization},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {3935--3941},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac428},
doi = {10.1093/BIOINFORMATICS/BTAC428},
timestamp = {Sat, 10 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KarasanSTC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KarlickiAK22,
author = {Michal Karlicki and
Stanislaw Antonowicz and
Anna Karnkowska},
title = {Tiara: deep learning-based classification system for eukaryotic sequences},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {344--350},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab672},
doi = {10.1093/BIOINFORMATICS/BTAB672},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KarlickiAK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KaushikZ22,
author = {Rahul Kaushik and
Kam Y. J. Zhang},
title = {ProFitFun: a protein tertiary structure fitness function for quantifying
the accuracies of model structures},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {369--376},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab666},
doi = {10.1093/BIOINFORMATICS/BTAB666},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KaushikZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KazemiWNMWB22,
author = {Parham Kazemi and
Johnathan Wong and
Vladimir Nikolic and
Hamid Mohamadi and
Ren{\'{e}} L. Warren and
Inan{\c{c}} Birol},
title = {ntHash2: recursive spaced seed hashing for nucleotide sequences},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4812--4813},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac564},
doi = {10.1093/BIOINFORMATICS/BTAC564},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KazemiWNMWB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KeRQCTYM22,
author = {Hongjie Ke and
Zhao Ren and
Jianfei Qi and
Shuo Chen and
George C. Tseng and
Zhenyao Ye and
Tianzhou Ma},
title = {High-dimension to high-dimension screening for detecting genome-wide
epigenetic and noncoding {RNA} regulators of gene expression},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4078--4087},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac518},
doi = {10.1093/BIOINFORMATICS/BTAC518},
timestamp = {Thu, 22 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KeRQCTYM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KerouantonSHCR22,
author = {Baptiste Kerouanton and
Sebastian Sch{\"{a}}fer and
Lena Ho and
Sonia Chothani and
Owen J. L. Rackham},
title = {CLIPreg: constructing translational regulatory networks from CLIP-,
Ribo- and RNA-seq},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3651--3653},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac363},
doi = {10.1093/BIOINFORMATICS/BTAC363},
timestamp = {Mon, 08 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KerouantonSHCR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KhatiwadaWYRPLH22,
author = {Aastha Khatiwada and
Bethany J. Wolf and
Ayse Selen Yilmaz and
Paula S. Ramos and
Maciej Pietrzak and
Andrew Lawson and
Kelly J. Hunt and
Hang J. Kim and
Dongjun Chung},
title = {GPA-Tree: statistical approach for functional-annotation-tree-guided
prioritization of {GWAS} results},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1067--1074},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab802},
doi = {10.1093/BIOINFORMATICS/BTAB802},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KhatiwadaWYRPLH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KimFCCAM22,
author = {Jeremie S. Kim and
Can Firtina and
Meryem Banu Cavlak and
Damla Senol Cali and
Can Alkan and
Onur Mutlu},
title = {FastRemap: a tool for quickly remapping reads between genome assemblies},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4633--4635},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac554},
doi = {10.1093/BIOINFORMATICS/BTAC554},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KimFCCAM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KimbleACCJKSYB22,
author = {Melissa Kimble and
Steven Allers and
K. Campbell and
Chaofan Chen and
Laura M. Jackson and
Benjamin L. King and
Samantha Silverbrand and
G. York and
Kate Beard},
title = {medna-metadata: an open-source data management system for tracking
environmental {DNA} samples and metadata},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4589--4597},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac556},
doi = {10.1093/BIOINFORMATICS/BTAC556},
timestamp = {Fri, 26 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KimbleACCJKSYB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KirchlerKNMKSL22,
author = {Matthias Kirchler and
Stefan Konigorski and
Matthias Norden and
Christian Meltendorf and
Marius Kloft and
Claudia Schurmann and
Christoph Lippert},
title = {transferGWAS: {GWAS} of images using deep transfer learning},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3621--3628},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac369},
doi = {10.1093/BIOINFORMATICS/BTAC369},
timestamp = {Mon, 08 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KirchlerKNMKSL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KirchoffG22,
author = {Kathryn E. Kirchoff and
Shawn M. Gomez},
title = {{EMBER:} multi-label prediction of kinase-substrate phosphorylation
events through deep learning},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2119--2126},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac083},
doi = {10.1093/BIOINFORMATICS/BTAC083},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KirchoffG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KnappVLC22,
author = {Adam C. Knapp and
Luis Sordo Vieira and
Reinhard C. Laubenbacher and
Julia Chifman},
title = {\emph{SteadyCellPhenotype}: a web-based tool for the modeling of biological
networks with ternary logic},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2369--2370},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac097},
doi = {10.1093/BIOINFORMATICS/BTAC097},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KnappVLC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KoCJH22,
author = {Kuei{-}Yueh Ko and
Cho{-}Yi Chen and
Hsueh{-}Fen Juan and
Hsuan{-}Cheng Huang},
title = {Phylotranscriptomic patterns of network stochasticity and pathway
dynamics during embryogenesis},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {763--769},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab735},
doi = {10.1093/BIOINFORMATICS/BTAB735},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KoCJH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KochenWFS22,
author = {Michael A Kochen and
H. Steven Wiley and
Song Feng and
Herbert M. Sauro},
title = {SBbadger: biochemical reaction networks with definable degree distributions},
journal = {Bioinform.},
volume = {38},
number = {22},
pages = {5064--5072},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac630},
doi = {10.1093/BIOINFORMATICS/BTAC630},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KochenWFS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KomodromosAEFR22,
author = {Michael Komodromos and
Eric O. Aboagye and
Marina Evangelou and
Sarah Filippi and
Kolyan Ray},
title = {Variational Bayes for high-dimensional proportional hazards models
with applications within gene expression},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {3918--3926},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac416},
doi = {10.1093/BIOINFORMATICS/BTAC416},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KomodromosAEFR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KovacsSTNP22,
author = {Szabolcs Cselgo Kov{\'{a}}cs and
Bal{\'{a}}zs Szappanos and
Roland Teng{\"{o}}lics and
Richard A. Notebaart and
Bal{\'{a}}zs Papp},
title = {Underground metabolism as a rich reservoir for pathway engineering},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3070--3077},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac282},
doi = {10.1093/BIOINFORMATICS/BTAC282},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KovacsSTNP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KramerDWDPLP22,
author = {Nicole E. Kramer and
Eric S. Davis and
Craig Wenger and
Erika Deoudes and
Sarah M. Parker and
Michael I. Love and
Douglas H. Phanstiel},
title = {Plotgardener: cultivating precise multi-panel figures in {R}},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {2042--2045},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac057},
doi = {10.1093/BIOINFORMATICS/BTAC057},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KramerDWDPLP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KrannichWNHHK22,
author = {Thomas Krannich and
W. Timothy J. White and
Sebastian Niehus and
Guillaume Holley and
Bjarni V. Halld{\'{o}}rsson and
Birte Kehr},
title = {Population-scale detection of non-reference sequence variants using
colored de Bruijn graphs},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {604--611},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab749},
doi = {10.1093/BIOINFORMATICS/BTAB749},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KrannichWNHHK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KratochvilHWPAN22,
author = {Miroslav Kratochv{\'{\i}}l and
Laurent Heirendt and
St Elmo Wilken and
Taneli Pusa and
Sylvain Arreckx and
Alberto Noronha and
Marvin van Aalst and
Venkata P. Satagopam and
Oliver Ebenh{\"{o}}h and
Reinhard Schneider and
Christophe Trefois and
Wei Gu},
title = {COBREXA.jl: constraint-based reconstruction and exascale analysis},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1171--1172},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab782},
doi = {10.1093/BIOINFORMATICS/BTAB782},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KratochvilHWPAN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KruitboschMOGM22,
author = {Herbert Teun Kruitbosch and
Yasmin Mzayek and
Sara Omlor and
Paolo Guerra and
Andreas Milias{-}Argeitis},
title = {A convolutional neural network for segmentation of yeast cells without
manual training annotations},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1427--1433},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab835},
doi = {10.1093/BIOINFORMATICS/BTAB835},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KruitboschMOGM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KuceraTM22,
author = {Tim Kucera and
Matteo Togninalli and
Laetitia Meng{-}Papaxanthos},
title = {Conditional generative modeling for \emph{de novo} protein design
with hierarchical functions},
journal = {Bioinform.},
volume = {38},
number = {13},
pages = {3454--3461},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac353},
doi = {10.1093/BIOINFORMATICS/BTAC353},
timestamp = {Wed, 27 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KuceraTM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KuipersSB22,
author = {Jack Kuipers and
Jochen Singer and
Niko Beerenwinkel},
title = {Single-cell mutation calling and phylogenetic tree reconstruction
with loss and recurrence},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4713--4719},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac577},
doi = {10.1093/BIOINFORMATICS/BTAC577},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KuipersSB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KumarKDJ22,
author = {Ambuj Kumar and
Pranav M. Khade and
Karin S. Dorman and
Robert L. Jernigan},
title = {Coarse-graining protein structures into their dynamic communities
with DCI, a dynamic community identifier},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2727--2733},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac159},
doi = {10.1093/BIOINFORMATICS/BTAC159},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KumarKDJ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KumarS22,
author = {Sajal Kumar and
Mingzhou Song},
title = {Overcoming biases in causal inference of molecular interactions},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2818--2825},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac206},
doi = {10.1093/BIOINFORMATICS/BTAC206},
timestamp = {Mon, 13 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KumarS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KwongBWVBAK22,
author = {Alan Kwong and
Andrew P. Boughton and
Mukai Wang and
Peter Vandehaar and
Michael Boehnke and
Gon{\c{c}}alo R. Abecasis and
Hyun Min Kang},
title = {FIVEx: an interactive eQTL browser across public datasets},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {559--561},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab614},
doi = {10.1093/BIOINFORMATICS/BTAB614},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KwongBWVBAK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KynastSH22,
author = {Josef Paul Kynast and
Felix Schw{\"{a}}gerl and
Birte H{\"{o}}cker},
title = {{ATLIGATOR:} editing protein interactions with an atlas-based approach},
journal = {Bioinform.},
volume = {38},
number = {23},
pages = {5199--5205},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac685},
doi = {10.1093/BIOINFORMATICS/BTAC685},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KynastSH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LaboryBPYSBEPB22,
author = {Justine Labory and
Gwendal Le Bideau and
David Pratella and
Jean{-}Elis{\'{e}}e Yao and
Samira Ait{-}El{-}Mkadem Saadi and
Sylvie Bannwarth and
Loubna El{-}Hami and
V{\'{e}}ronique Paquis{-}Flucklinger and
Silvia Bottini},
title = {{ABEILLE:} a novel method for ABerrant Expression Identification empLoying
machine LEarning from RNA-sequencing data},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4754--4761},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac603},
doi = {10.1093/BIOINFORMATICS/BTAC603},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LaboryBPYSBEPB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LachmannXM22,
author = {Alexander Lachmann and
Zhuorui Xie and
Avi Ma'ayan},
title = {blitzGSEA: efficient computation of gene set enrichment analysis through
gamma distribution approximation},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2356--2357},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac076},
doi = {10.1093/BIOINFORMATICS/BTAC076},
timestamp = {Wed, 18 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LachmannXM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LaiG22,
author = {Fei{-}Liao Lai and
Feng Gao},
title = {GC-Profile 2.0: an extended web server for the prediction and visualization
of CpG islands},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1738--1740},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab864},
doi = {10.1093/BIOINFORMATICS/BTAB864},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LaiG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LakeZXL22,
author = {Nicole J. Lake and
Lily Zhou and
Jenny Xu and
Monkol Lek},
title = {MitoVisualize: a resource for analysis of variants in human mitochondrial
RNAs and {DNA}},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2967--2969},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac216},
doi = {10.1093/BIOINFORMATICS/BTAC216},
timestamp = {Mon, 13 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LakeZXL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LamuriasSAHN22,
author = {Andre Lamurias and
Mantas Sereika and
Mads Albertsen and
Katja Hose and
Thomas Dyhre Nielsen},
title = {Metagenomic binning with assembly graph embeddings},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4481--4487},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac557},
doi = {10.1093/BIOINFORMATICS/BTAC557},
timestamp = {Tue, 06 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LamuriasSAHN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LangeASK22,
author = {Lukas Lange and
Heike Adel and
Jannik Str{\"{o}}tgen and
Dietrich Klakow},
title = {\emph{CLIN-X}: pre-trained language models and a study on cross-task
transfer for concept extraction in the clinical domain},
journal = {Bioinform.},
volume = {38},
number = {12},
pages = {3267--3274},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac297},
doi = {10.1093/BIOINFORMATICS/BTAC297},
timestamp = {Mon, 25 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LangeASK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LaurentVDSVM22,
author = {Fran{\c{c}}ois Laurent and
Hippolyte Verdier and
Maxime Duval and
Alexander Serov and
Christian L. Vestergaard and
Jean{-}Baptiste Masson},
title = {TRamWAy: mapping physical properties of individual biomolecule random
motion in large-scale single-particle tracking experiments},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3149--3150},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac291},
doi = {10.1093/BIOINFORMATICS/BTAC291},
timestamp = {Tue, 28 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LaurentVDSVM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Lee22,
author = {Daewon Lee},
title = {Nezzle: an interactive and programmable visualization of biological
networks in Python},
journal = {Bioinform.},
volume = {38},
number = {12},
pages = {3310--3311},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac324},
doi = {10.1093/BIOINFORMATICS/BTAC324},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Lee22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LeeBVAP22,
author = {Soohyun Lee and
Clara R. Bakker and
Carl Vitzthum and
Burak Han Alver and
Peter J. Park},
title = {Pairs and Pairix: a file format and a tool for efficient storage and
retrieval for Hi-C read pairs},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1729--1731},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab870},
doi = {10.1093/BIOINFORMATICS/BTAB870},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LeeBVAP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LeeRRKC22,
author = {Myungjin Lee and
Mateo Reveiz and
Reda Rawi and
Peter D. Kwong and
Gwo{-}Yu Chuang},
title = {{GLYCO:} a tool to quantify glycan shielding of glycosylated proteins},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1152--1154},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab791},
doi = {10.1093/BIOINFORMATICS/BTAB791},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LeeRRKC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LeeS22,
author = {Dohyeon Lee and
Giltae Song},
title = {FastqCLS: a {FASTQ} compressor for long-read sequencing via read reordering
using a novel scoring model},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {351--356},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab696},
doi = {10.1093/BIOINFORMATICS/BTAB696},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LeeS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LegonCBM22,
author = {Laurence Legon and
Christophe Corre and
Declan G. Bates and
Ahmad A. Mannan},
title = {gcFront: a tool for determining a Pareto front of growth-coupled cell
factory designs},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3657--3659},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac376},
doi = {10.1093/BIOINFORMATICS/BTAC376},
timestamp = {Mon, 08 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LegonCBM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LelongZAQCTXMYA22,
author = {Sebastien Lelong and
Xinghua Zhou and
Cyrus Afrasiabi and
Zhongchao Qian and
Marco Alvarado Cano and
Ginger Tsueng and
Jiwen Xin and
Julia Mullen and
Yao Yao and
Ricardo Avila and
Greg Taylor and
Andrew I. Su and
Chunlei Wu},
title = {BioThings {SDK:} a toolkit for building high-performance data APIs
in biomedical research},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {2077--2079},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac017},
doi = {10.1093/BIOINFORMATICS/BTAC017},
timestamp = {Wed, 27 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LelongZAQCTXMYA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LemaneCP22,
author = {T{\'{e}}o Lemane and
Rayan Chikhi and
Pierre Peterlongo},
title = {{\textless}tt{\textgreater}k{\textless}/tt{\textgreater} {\textless}tt{\textgreater}mdiff{\textless}/tt{\textgreater},
large-scale and user-friendly differential \emph{k}-mer analyses},
journal = {Bioinform.},
volume = {38},
number = {24},
pages = {5443--5445},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac689},
doi = {10.1093/BIOINFORMATICS/BTAC689},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LemaneCP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LengW22,
author = {Jiacheng Leng and
Ling{-}Yun Wu},
title = {Importance-Penalized Joint Graphical Lasso {(IPJGL):} differential
network inference via GGMs},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {770--777},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab751},
doi = {10.1093/BIOINFORMATICS/BTAB751},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LengW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LeoneGMP22,
author = {Michele Leone and
Eugenia Galeota and
Marco Masseroli and
Mattia Pelizzola},
title = {Identification, semantic annotation and comparison of combinations
of functional elements in multiple biological conditions},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1183--1190},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab815},
doi = {10.1093/BIOINFORMATICS/BTAB815},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LeoneGMP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LeviRES22,
author = {Hagai Levi and
Nima Rahmanian and
Ran Elkon and
Ron Shamir},
title = {The {DOMINO} web-server for active module identification analysis},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2364--2366},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac067},
doi = {10.1093/BIOINFORMATICS/BTAC067},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LeviRES22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LexaCNJTKHK22,
author = {Matej Lexa and
Monika Cechova and
Son Hoang Nguyen and
Pavel Jedlicka and
Viktor Tokan and
Zdenek Kubat and
Roman Hobza and
Eduard Kejnovsk{\'{y}}},
title = {HiC-TE: a computational pipeline for Hi-C data analysis to study the
role of repeat family interactions in the genome 3D organization},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {4030--4032},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac442},
doi = {10.1093/BIOINFORMATICS/BTAC442},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LexaCNJTKHK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiBRZJE22,
author = {Wenhao Li and
Martin P. Boer and
Bart{-}Jan van Rossum and
Chaozhi Zheng and
Ronny V. L. Joosen and
Fred A. van Eeuwijk},
title = {\emph{statgenMPP}: an {R} package implementing an IBD-based mixed
model approach for {QTL} mapping in a wide range of multi-parent populations},
journal = {Bioinform.},
volume = {38},
number = {22},
pages = {5134--5136},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac662},
doi = {10.1093/BIOINFORMATICS/BTAC662},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiBRZJE22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiCLY22,
author = {Jin Li and
Feng Chen and
Hong Liang and
Jingwen Yan},
title = {MoNET: an {R} package for multi-omic network analysis},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1165--1167},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab722},
doi = {10.1093/BIOINFORMATICS/BTAB722},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiCLY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiCRKYG22,
author = {Yu Li and
Siyuan Chen and
Trisevgeni Rapakoulia and
Hiroyuki Kuwahara and
Kevin Y. Yip and
Xin Gao},
title = {Deep learning identifies and quantifies recombination hotspot determinants},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2683--2691},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac234},
doi = {10.1093/BIOINFORMATICS/BTAC234},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiCRKYG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiFL22,
author = {Xiaoguang Li and
Xingdong Feng and
Xu Liu},
title = {Heritability estimation for a linear combination of phenotypes via
ridge regression},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4687--4696},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac587},
doi = {10.1093/BIOINFORMATICS/BTAC587},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiFL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiKOYMCCCLGYN22,
author = {Longjie Li and
Arun Mouli Kolinjivadi and
Kok Haur Ong and
David M. Young and
Gabriel Pik Liang Marini and
Sock Hoai Chan and
Siao Ting Chong and
Ee Ling Chew and
Haoda Lu and
Laurent Gole and
Weimiao Yu and
Joanne Ngeow},
title = {Automatic {DNA} replication tract measurement to assess replication
and repair dynamics at the single-molecule level},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4395--4402},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac533},
doi = {10.1093/BIOINFORMATICS/BTAC533},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiKOYMCCCLGYN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiL22,
author = {Pengpai Li and
Zhi{-}Ping Liu},
title = {{PST-PRNA:} prediction of RNA-binding sites using protein surface
topography and deep learning},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2162--2168},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac078},
doi = {10.1093/BIOINFORMATICS/BTAC078},
timestamp = {Wed, 18 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiL22a,
author = {Mengtian Li and
Lei M. Li},
title = {RegScaf: a regression approach to scaffolding},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2675--2682},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac174},
doi = {10.1093/BIOINFORMATICS/BTAC174},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiL22a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiLH22,
author = {Xinmeng Li and
Li{-}Ping Liu and
Soha Hassoun},
title = {Boost-RS: boosted embeddings for recommender systems and its application
to enzyme-substrate interaction prediction},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2832--2838},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac201},
doi = {10.1093/BIOINFORMATICS/BTAC201},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiLH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiLWL22,
author = {Min Li and
Zhangli Lu and
Yifan Wu and
Yaohang Li},
title = {{BACPI:} a bi-directional attention neural network for compound-protein
interaction and binding affinity prediction},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {1995--2002},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac035},
doi = {10.1093/BIOINFORMATICS/BTAC035},
timestamp = {Wed, 27 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiLWL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiLZ22,
author = {Hong{-}Dong Li and
Cui{-}Xiang Lin and
Jiantao Zheng},
title = {GTFtools: a software package for analyzing various features of gene
models},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4806--4808},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac561},
doi = {10.1093/BIOINFORMATICS/BTAC561},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiLZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiLZG22,
author = {Haoyang Li and
Hanmin Li and
Juexiao Zhou and
Xin Gao},
title = {{SD2:} spatially resolved transcriptomics deconvolution through integration
of dropout and spatial information},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4878--4884},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac605},
doi = {10.1093/BIOINFORMATICS/BTAC605},
timestamp = {Fri, 08 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiLZG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiMLTG22,
author = {Xuejian Li and
Shiqiang Ma and
Jin Liu and
Jijun Tang and
Fei Guo},
title = {Inferring gene regulatory network via fusing gene expression image
and RNA-seq data},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1716--1723},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac008},
doi = {10.1093/BIOINFORMATICS/BTAC008},
timestamp = {Wed, 17 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiMLTG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiQGW22,
author = {Yang Li and
Guanyu Qiao and
Xin Gao and
Guohua Wang},
title = {Supervised graph co-contrastive learning for drug-target interaction
prediction},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2847--2854},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac164},
doi = {10.1093/BIOINFORMATICS/BTAC164},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiQGW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiQZJLWL22,
author = {Yan Li and
Lijun Quan and
Yiting Zhou and
Yelu Jiang and
Kailong Li and
Tingfang Wu and
Qiang Lyu},
title = {Identifying modifications on DNA-bound histones with joint deep learning
of multiple binding sites in {DNA} sequence},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4070--4077},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac489},
doi = {10.1093/BIOINFORMATICS/BTAC489},
timestamp = {Fri, 23 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiQZJLWL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiS22,
author = {Qiufu Li and
Linlin Shen},
title = {Neuron segmentation using 3D wavelet integrated encoder-decoder network},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {809--817},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab716},
doi = {10.1093/BIOINFORMATICS/BTAB716},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiSWL22,
author = {Yanfei Li and
Chang Sun and
Jin{-}Mao Wei and
Jian Liu},
title = {Drug-Protein interaction prediction by correcting the effect of incomplete
information in heterogeneous information},
journal = {Bioinform.},
volume = {38},
number = {22},
pages = {5073--5080},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac629},
doi = {10.1093/BIOINFORMATICS/BTAC629},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiSWL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiWGCD22,
author = {Ziyi Li and
Yizhuo Wang and
Irene Ganan{-}Gomez and
Simona Colla and
Kim{-}Anh Do},
title = {A machine learning-based method for automatically identifying novel
cells in annotating single-cell RNA-seq data},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4885--4892},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac617},
doi = {10.1093/BIOINFORMATICS/BTAC617},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiWGCD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiWLXZPQ22,
author = {Yuanyuan Li and
Jun Wu and
Donghuan Lu and
Chao Xu and
Yefeng Zheng and
Hanchuan Peng and
Lei Qu},
title = {mBrainAligner-Web: a web server for cross-modal coherent registration
of whole mouse brains},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4654--4655},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac549},
doi = {10.1093/BIOINFORMATICS/BTAC549},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiWLXZPQ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiXMW22,
author = {Yang Li and
Shaodong Xu and
Shuangge Ma and
Mengyun Wu},
title = {Network-based cancer heterogeneity analysis incorporating multi-view
of prior information},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2855--2862},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac183},
doi = {10.1093/BIOINFORMATICS/BTAC183},
timestamp = {Mon, 13 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiXMW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiYYOA22,
author = {Jianan Li and
Keisuke Yanagisawa and
Yasushi Yoshikawa and
Masahito Ohue and
Yutaka Akiyama},
title = {Plasma protein binding prediction focusing on residue-level features
and circularity of cyclic peptides by deep learning},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1110--1117},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab726},
doi = {10.1093/BIOINFORMATICS/BTAB726},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiYYOA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiYZCWKKZW22,
author = {Kaiqiao Li and
Sijie Yao and
Zhenyu Zhang and
Biwei Cao and
Christopher M. Wilson and
Denise Kalos and
Pei Fen Kuan and
Ruoqing Zhu and
Xuefeng Wang},
title = {Efficient gradient boosting for prognostic biomarker discovery},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1631--1638},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab869},
doi = {10.1093/BIOINFORMATICS/BTAB869},
timestamp = {Fri, 01 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiYZCWKKZW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiZGZ22,
author = {Fei Li and
Ziqiao Zhang and
Jihong Guan and
Shuigeng Zhou},
title = {Effective drug-target interaction prediction with mutual interaction
neural network},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3582--3589},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac377},
doi = {10.1093/BIOINFORMATICS/BTAC377},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiZGZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiZS22,
author = {Xinjie Li and
Shengli Zhang and
Hongyan Shi},
title = {An improved residual network using deep fusion for identifying {RNA}
5-methylcytosine sites},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4271--4277},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac532},
doi = {10.1093/BIOINFORMATICS/BTAC532},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiZS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiZWYLLHZZ22,
author = {Hongjia Li and
Hui Zhang and
Xiaohua Wan and
Zhidong Yang and
Chengmin Li and
Jintao Li and
Renmin Han and
Ping Zhu and
Fa Zhang},
title = {Noise-Transfer2Clean: denoising cryo-EM images based on noise modeling
and transfer},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {2022--2029},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac052},
doi = {10.1093/BIOINFORMATICS/BTAC052},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiZWYLLHZZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiZYDWWH22,
author = {Zongren Li and
Qin Zhong and
Jing Yang and
Yongjie Duan and
Wenjun Wang and
Chengkun Wu and
Kunlun He},
title = {DeepKG: an end-to-end deep learning-based workflow for biomedical
knowledge graph extraction, optimization and applications},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1477--1479},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab767},
doi = {10.1093/BIOINFORMATICS/BTAB767},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiZYDWWH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiZZC22,
author = {Jun Li and
Sicheng Zhang and
Dong Zhang and
Shi{-}Jie Chen},
title = {Vfold-Pipeline: a web server for {RNA} 3D structure prediction from
sequences},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {4042--4043},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac426},
doi = {10.1093/BIOINFORMATICS/BTAC426},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiZZC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiaoFHCYLC22,
author = {Chun{-}Chieh Liao and
Po{-}Ying Fu and
Chih{-}Wei Huang and
Chia{-}Hsien Chuang and
Yun Yen and
Chung{-}Yen Lin and
Shu{-}Hwa Chen},
title = {MetaSquare: an integrated metadatabase of 16S rRNA gene amplicon for
microbiome taxonomic classification},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2930--2931},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac184},
doi = {10.1093/BIOINFORMATICS/BTAC184},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiaoFHCYLC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LibradoO22,
author = {Pablo Librado and
Ludovic Orlando},
title = {Struct-f4: a Rcpp package for ancestry profile and population structure
inference from \emph{f}4-statistics},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {2070--2071},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac046},
doi = {10.1093/BIOINFORMATICS/BTAC046},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LibradoO22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LimTKNG22,
author = {Hansaim Lim and
Chung{-}Jung Tsai and
Ozlem Keskin and
Ruth Nussinov and
Attila G{\"{u}}rsoy},
title = {{HMI-PRED} 2.0: a biologist-oriented web application for prediction
of host-microbe protein-protein interaction by interface mimicry},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4962--4965},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac633},
doi = {10.1093/BIOINFORMATICS/BTAC633},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LimTKNG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LinCYH22,
author = {Jyun{-}Hong Lin and
Liang{-}Chi Chen and
Shu{-}Chi Yu and
Yao{-}Ting Huang},
title = {LongPhase: an ultra-fast chromosome-scale phasing algorithm for small
and large variants},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {1816--1822},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac058},
doi = {10.1093/BIOINFORMATICS/BTAC058},
timestamp = {Sun, 06 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LinCYH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LinLDEWPW22,
author = {Cui{-}Xiang Lin and
Hong{-}Dong Li and
Chao Deng and
Shannon Erhardt and
Jun Wang and
Xiaoqing Peng and
Jianxin Wang},
title = {AlzCode: a platform for multiview analysis of genes related to Alzheimer's
disease},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {2030--2032},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac033},
doi = {10.1093/BIOINFORMATICS/BTAC033},
timestamp = {Wed, 14 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LinLDEWPW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuAPLL22,
author = {Hongfei Liu and
Zhanerke Akhatayeva and
Chuanying Pan and
Mingzhi Liao and
Xianyong Lan},
title = {Comprehensive comparison of two types of algorithm for circRNA detection
from short-read RNA-Seq},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3037--3043},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac302},
doi = {10.1093/BIOINFORMATICS/BTAC302},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuAPLL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuFWWLCLS22,
author = {Quanzhong Liu and
Honglin Fang and
Xiao Wang and
Miao Wang and
Shuqin Li and
Lachlan J. M. Coin and
Fuyi Li and
Jiangning Song},
title = {DeepGenGrep: a general deep learning-based predictor for multiple
genomic signals and regions},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4053--4061},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac454},
doi = {10.1093/BIOINFORMATICS/BTAC454},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuFWWLCLS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuHLS22,
author = {Qi Liu and
Chih{-}Yuan Hsu and
Jia Li and
Yu Shyr},
title = {Dysregulated ligand-receptor interactions from single-cell transcriptomics},
journal = {Bioinform.},
volume = {38},
number = {12},
pages = {3216--3221},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac294},
doi = {10.1093/BIOINFORMATICS/BTAC294},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuHLS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuJGWWZY22,
author = {Yushuang Liu and
Shuping Jin and
Hongli Gao and
Xue Wang and
Congjing Wang and
Weifeng Zhou and
Bin Yu},
title = {Predicting the multi-label protein subcellular localization through
multi-information fusion and {MLSI} dimensionality reduction based
on {MLFE} classifier},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1223--1230},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab811},
doi = {10.1093/BIOINFORMATICS/BTAB811},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuJGWWZY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuK22,
author = {Huidong Liu and
Tahsin Kurc},
title = {Deep learning for survival analysis in breast cancer with whole slide
image data},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3629--3637},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac381},
doi = {10.1093/BIOINFORMATICS/BTAC381},
timestamp = {Mon, 08 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuMZ22,
author = {Lizhi Liu and
Hiroshi Mamitsuka and
Shanfeng Zhu},
title = {HPODNets: deep graph convolutional networks for predicting human protein-phenotype
associations},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {799--808},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab729},
doi = {10.1093/BIOINFORMATICS/BTAB729},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuMZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuO22,
author = {Xuexue Liu and
Ludovic Orlando},
title = {mapDATAge: a ShinyR package to chart ancient {DNA} data through space
and time},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {3992--3994},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac425},
doi = {10.1093/BIOINFORMATICS/BTAC425},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuO22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuQ22,
author = {Lijuan Liu and
Penghao Qian},
title = {Manifold classification of neuron types from microscopic images},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4987--4989},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac594},
doi = {10.1093/BIOINFORMATICS/BTAC594},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuQ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuSLLZZ22,
author = {Xuan Liu and
Congzhi Song and
Shichao Liu and
Menglu Li and
Xionghui Zhou and
Wen Zhang},
title = {Multi-way relation-enhanced hypergraph representation learning for
anti-cancer drug synergy prediction},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4782--4789},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac579},
doi = {10.1093/BIOINFORMATICS/BTAC579},
timestamp = {Fri, 01 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuSLLZZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuSOA22,
author = {Chunting Liu and
Jiangning Song and
Hiroyuki Ogata and
Tatsuya Akutsu},
title = {MSNet-4mC: learning effective multi-scale representations for identifying
{DNA} N4-methylcytosine sites},
journal = {Bioinform.},
volume = {38},
number = {23},
pages = {5160--5167},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac671},
doi = {10.1093/BIOINFORMATICS/BTAC671},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuSOA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuWAZL22,
author = {Yufeng Liu and
Gaoyu Wang and
Giorgio A. Ascoli and
Jiangning Zhou and
Lijuan Liu},
title = {Neuron tracing from light microscopy images: automation, deep learning
and bench testing},
journal = {Bioinform.},
volume = {38},
number = {24},
pages = {5329--5339},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac712},
doi = {10.1093/BIOINFORMATICS/BTAC712},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuWAZL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuZFZLJZLHL22,
author = {Shun Liu and
Jianchao Zhou and
Ziyan Feng and
Jiawen Zhang and
Shuang Li and
Zilong Jin and
Chenfei Zhang and
Shiliang Li and
Gaoqi He and
Honglin Li},
title = {VRPharmer: bringing virtual reality into pharmacophore-based virtual
screening with interactive exploration and realistic visualization},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4953--4955},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac615},
doi = {10.1093/BIOINFORMATICS/BTAC615},
timestamp = {Tue, 16 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuZFZLJZLHL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuZLCXS22,
author = {Zhentao Liu and
Zhengdong Zhang and
Sheng Liang and
Zhen Chen and
Xiaoyao Xie and
Tie Shen},
title = {CeCaFLUX: the first web server for standardized and visual instationary
13C metabolic flux analysis},
journal = {Bioinform.},
volume = {38},
number = {13},
pages = {3481--3483},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac341},
doi = {10.1093/BIOINFORMATICS/BTAC341},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuZLCXS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiyanageBDEFGHJ22,
author = {Isuru Udara Liyanage and
Tony Burdett and
Bert Droesbeke and
Karoly Erdos and
Rolando Fernandez and
Alasdair J. G. Gray and
Muhammad Haseeb and
Simon Jupp and
Flavia Penim and
Cyril Pommier and
Philippe Rocca{-}Serra and
M{\'{e}}lanie Courtot and
Frederik Coppens},
title = {{ELIXIR} biovalidator for semantic validation of life science metadata},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3141--3142},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac195},
doi = {10.1093/BIOINFORMATICS/BTAC195},
timestamp = {Wed, 27 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiyanageBDEFGHJ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LlambrichCGBC22,
author = {Maria Llambrich and
Eudald Correig and
Josep Gum{\`{a}} and
Jes{\'{u}}s Brezmes and
Raquel Cumeras},
title = {Amanida: an {R} package for meta-analysis of metabolomics non-integral
data},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {583--585},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab591},
doi = {10.1093/BIOINFORMATICS/BTAB591},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LlambrichCGBC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LoSCDFGHLJXC22,
author = {Chien{-}Chi Lo and
Migun Shakya and
Ryan Connor and
Karen Davenport and
Mark Flynn and
Ad{\'{a}}n Myers y Guti{\'{e}}rrez and
Bin Hu and
Po{-}E Li and
Elais Player Jackson and
Yan Xu and
Patrick S. G. Chain},
title = {{EDGE} {COVID-19:} a web platform to generate submission-ready genomes
from SARS-CoV-2 sequencing efforts},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2700--2704},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac176},
doi = {10.1093/BIOINFORMATICS/BTAC176},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LoSCDFGHLJXC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LongWLFKCLL22,
author = {Yahui Long and
Min Wu and
Yong Liu and
Yuan Fang and
Chee Keong Kwoh and
Jinmiao Chen and
Jiawei Luo and
Xiaoli Li},
title = {Pre-training graph neural networks for link prediction in biomedical
networks},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2254--2262},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac100},
doi = {10.1093/BIOINFORMATICS/BTAC100},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LongWLFKCLL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LoodRSVLN22,
author = {C{\'{e}}dric Lood and
Alejandro Correa Rojo and
Deniz Sinar and
Emma Verkinderen and
Rob Lavigne and
Vera van Noort},
title = {SASpector: analysis of missing genomic regions in draft genomes of
prokaryotes},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2920--2921},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac208},
doi = {10.1093/BIOINFORMATICS/BTAC208},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LoodRSVLN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Lopez-Cortegano22,
author = {Eugenio L{\'{o}}pez{-}Cortegano},
title = {purgeR: inbreeding and purging in pedigreed populations},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {564--565},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab599},
doi = {10.1093/BIOINFORMATICS/BTAB599},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Lopez-Cortegano22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LuCYLLWL22,
author = {Chih{-}Hao Lu and
Chih{-}Chieh Chen and
Chin{-}Sheng Yu and
Yen{-}Yi Liu and
Jia{-}Jun Liu and
Sung{-}Tai Wei and
Yu{-}Feng Lin},
title = {{MIB2:} metal ion-binding site prediction and modeling server},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4428--4429},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac534},
doi = {10.1093/BIOINFORMATICS/BTAC534},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LuCYLLWL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LuFZW22,
author = {Yurun Lu and
Zhan{-}Ying Feng and
Songmao Zhang and
Yong Wang},
title = {Annotating regulatory elements by heterogeneous network embedding},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2899--2911},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac185},
doi = {10.1093/BIOINFORMATICS/BTAC185},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LuFZW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LuW22,
author = {Lu Lu and
Joshua D. Welch},
title = {PyLiger: scalable single-cell multi-omic data integration in Python},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2946--2948},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac190},
doi = {10.1093/BIOINFORMATICS/BTAC190},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LuW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LuYWMWL22,
author = {Yifu Lu and
Zhuohan Yu and
Yunhe Wang and
Zhiqiang Ma and
Ka{-}Chun Wong and
Xiangtao Li},
title = {{GMHCC:} high-throughput analysis of biomolecular data using graph-based
multiple hierarchical consensus clustering},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3020--3028},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac290},
doi = {10.1093/BIOINFORMATICS/BTAC290},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LuYWMWL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LuZMWJAOHLXGYX22,
author = {Haoda Lu and
Min Zang and
Gabriel Pik Liang Marini and
Xiangxue Wang and
Yiping Jiao and
Nianfei Ao and
Kok Haur Ong and
Xinmi Huo and
Longjie Li and
Eugene Yujun Xu and
Wilson Wen Bin Goh and
Weimiao Yu and
Jun Xu},
title = {A novel pipeline for computerized mouse spermatogenesis staging},
journal = {Bioinform.},
volume = {38},
number = {23},
pages = {5307--5314},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac677},
doi = {10.1093/BIOINFORMATICS/BTAC677},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LuZMWJAOHLXGYX22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LubbockL22,
author = {Alexander L. R. Lubbock and
Carlos F. Lopez},
title = {\emph{Microbench:} automated metadata management for systems biology
benchmarking and reproducibility in Python},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4823--4825},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac580},
doi = {10.1093/BIOINFORMATICS/BTAC580},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LubbockL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LutteroppSKMS22,
author = {Sarah Lutteropp and
C{\'{e}}line Scornavacca and
Alexey M. Kozlov and
Benoit Morel and
Alexandros Stamatakis},
title = {NetRAX: accurate and fast maximum likelihood phylogenetic network
inference},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3725--3733},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac396},
doi = {10.1093/BIOINFORMATICS/BTAC396},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LutteroppSKMS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LuuFLMSW22,
author = {Gordon T. Luu and
Michael A. Freitas and
Itzel Lizama{-}Chamu and
Catherine S. McCaughey and
Laura M. Sanchez and
Mingxun Wang},
title = {{TIMSCONVERT:} a workflow to convert trapped ion mobility data to
open data formats},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {4046--4047},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac419},
doi = {10.1093/BIOINFORMATICS/BTAC419},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LuuFLMSW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LyuHLCLTWHL22,
author = {Chen Lyu and
Manyan Huang and
Nianjun Liu and
Zhongxue Chen and
Philip J. Lupo and
Benjamin Tycko and
John S. Witte and
Charlotte A. Hobbs and
Ming Li},
title = {Random field modeling of multi-trait multi-locus association for detecting
methylation quantitative trait loci},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {3853--3862},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac443},
doi = {10.1093/BIOINFORMATICS/BTAC443},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LyuHLCLTWHL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LyuLWLLY22,
author = {Hongqiang Lyu and
Erhu Liu and
Zhifang Wu and
Yao Li and
Yuan Liu and
Xiaoran Yin},
title = {scHiCPTR: unsupervised pseudotime inference through dual graph refinement
for single-cell Hi-C data},
journal = {Bioinform.},
volume = {38},
number = {23},
pages = {5151--5159},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac670},
doi = {10.1093/BIOINFORMATICS/BTAC670},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LyuLWLLY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MaBRHXXYH22,
author = {Hehuan Ma and
Yatao Bian and
Yu Rong and
Wenbing Huang and
Tingyang Xu and
Weiyang Xie and
Geyan Ye and
Junzhou Huang},
title = {Cross-dependent graph neural networks for molecular property prediction},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {2003--2009},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac039},
doi = {10.1093/BIOINFORMATICS/BTAC039},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MaBRHXXYH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MaM22,
author = {Yingjun Ma and
Yuanyuan Ma},
title = {Hypergraph-based logistic matrix factorization for metabolite-disease
interaction prediction},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {435--443},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab652},
doi = {10.1093/BIOINFORMATICS/BTAB652},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MaM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MaWZ22,
author = {Jinfa Ma and
Jane Y. Wu and
Li Zhu},
title = {Detection of orthologous exons and isoforms using {EGIO}},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4474--4480},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac548},
doi = {10.1093/BIOINFORMATICS/BTAC548},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MaWZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MaYCH22,
author = {Baoshan Ma and
Ge Yan and
Bingjie Chai and
Xiaoyu Hou},
title = {{XGBLC:} an improved survival prediction model based on XGBoost},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {410--418},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab675},
doi = {10.1093/BIOINFORMATICS/BTAB675},
timestamp = {Mon, 04 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MaYCH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MaccarthyZZK22,
author = {Elijah A. MacCarthy and
Chengxin Zhang and
Yang Zhang and
Dukka B. KC},
title = {{GPU-I-TASSER:} a {GPU} accelerated {I-TASSER} protein structure prediction
tool},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1754--1755},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab871},
doi = {10.1093/BIOINFORMATICS/BTAB871},
timestamp = {Wed, 27 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MaccarthyZZK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MadadiSCWY22,
author = {Yeganeh Madadi and
Jian Sun and
Hao Chen and
Robert W. Williams and
Siamak Yousefi},
title = {Detecting retinal neural and stromal cell classes and ganglion cell
subtypes based on transcriptome data with deep transfer learning},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4321--4329},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac514},
doi = {10.1093/BIOINFORMATICS/BTAC514},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MadadiSCWY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MaddouriQY22,
author = {Omar Maddouri and
Xiaoning Qian and
Byung{-}Jun Yoon},
title = {Deep graph representations embed network information for robust disease
marker identification},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1075--1086},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab772},
doi = {10.1093/BIOINFORMATICS/BTAB772},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MaddouriQY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MahbubSBP22,
author = {Maria Mahbub and
Sudarshan Srinivasan and
Edmon Begoli and
Gregory D. Peterson},
title = {BioADAPT-MRC: adversarial learning-based domain adaptation improves
biomedical machine reading comprehension task},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4369--4379},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac508},
doi = {10.1093/BIOINFORMATICS/BTAC508},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MahbubSBP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MaiM22,
author = {Uyen Mai and
Siavash Mirarab},
title = {Completing gene trees without species trees in sub-quadratic time},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1532--1541},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab875},
doi = {10.1093/BIOINFORMATICS/BTAB875},
timestamp = {Fri, 01 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MaiM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MaityP22,
author = {Dibyajyoti Maity and
Debnath Pal},
title = {{MD} DaVis: interactive data visualization of protein molecular dynamics},
journal = {Bioinform.},
volume = {38},
number = {12},
pages = {3299--3301},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac314},
doi = {10.1093/BIOINFORMATICS/BTAC314},
timestamp = {Mon, 25 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MaityP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MalinkaZPSN22,
author = {Frantisek Malinka and
Ashkan Zareie and
Jan Proch{\'{a}}zka and
Radislav Sedlacek and
Vendula Novosadova},
title = {Batch alignment via retention orders for preprocessing large-scale
multi-batch {LC-MS} experiments},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3759--3767},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac407},
doi = {10.1093/BIOINFORMATICS/BTAC407},
timestamp = {Thu, 25 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MalinkaZPSN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MalletOBHW22,
author = {Vincent Mallet and
Carlos G. Oliver and
Jonathan Broadbent and
William L. Hamilton and
J{\'{e}}r{\^{o}}me Waldisp{\"{u}}hl},
title = {RNAglib: a python package for {RNA} 2.5 {D} graphs},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1458--1459},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab844},
doi = {10.1093/BIOINFORMATICS/BTAB844},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MalletOBHW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MalletRMNDBS22,
author = {Vincent Mallet and
Luis Checa Ruano and
Alexandra Moine{-}Franel and
Michael Nilges and
Karen Druart and
Guillaume Bouvier and
Olivier Sperandio},
title = {InDeep: 3D fully convolutional neural networks to assist in silico
drug design on protein-protein interactions},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1261--1268},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab849},
doi = {10.1093/BIOINFORMATICS/BTAB849},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MalletRMNDBS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MalloryN22,
author = {Xian F. Mallory and
Luay Nakhleh},
title = {SimSCSnTree: a simulator of single-cell {DNA} sequencing data},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2912--2914},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac169},
doi = {10.1093/BIOINFORMATICS/BTAC169},
timestamp = {Mon, 13 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MalloryN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ManfrediSMC22,
author = {Matteo Manfredi and
Castrense Savojardo and
Pier Luigi Martelli and
Rita Casadio},
title = {E-SNPs{\&}GO: embedding of protein sequence and function improves
the annotation of human pathogenic variants},
journal = {Bioinform.},
volume = {38},
number = {23},
pages = {5168--5174},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac678},
doi = {10.1093/BIOINFORMATICS/BTAC678},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ManfrediSMC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MaoPKC22,
author = {Weiguang Mao and
Maziyar Baran Pouyan and
Dennis Kostka and
Maria Chikina},
title = {Non-negative Independent Factor Analysis disentangles discrete and
continuous sources of variation in scRNA-seq data},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2749--2756},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac136},
doi = {10.1093/BIOINFORMATICS/BTAC136},
timestamp = {Mon, 13 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MaoPKC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MaoZLFDQY22,
author = {Jiawei Mao and
He Zhu and
Luyao Liu and
Zheng Fang and
Mingming Dong and
Hongqiang Qin and
Mingliang Ye},
title = {MS-Decipher: a user-friendly proteome database search software with
an emphasis on deciphering the spectra of O-linked glycopeptides},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {1911--1919},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac014},
doi = {10.1093/BIOINFORMATICS/BTAC014},
timestamp = {Wed, 27 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MaoZLFDQY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MaoZSK22,
author = {Shunfu Mao and
Yue Zhang and
Georg Seelig and
Sreeram Kannan},
title = {CellMeSH: probabilistic cell-type identification using indexed literature},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1393--1402},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab834},
doi = {10.1093/BIOINFORMATICS/BTAB834},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MaoZSK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MariappanJSR22,
author = {Ragunathan Mariappan and
Aishwarya Jayagopal and
Ho Zong Sien and
Vaibhav Rajan},
title = {Neural Collective Matrix Factorization for integrated analysis of
heterogeneous biomedical data},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4554--4561},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac543},
doi = {10.1093/BIOINFORMATICS/BTAC543},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MariappanJSR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MarinVHJEDSSIAV22,
author = {Maximillian G. Marin and
Roger Vargas and
Michael Harris and
Brendan Jeffrey and
L. Elaine Epperson and
David Durbin and
Michael Strong and
Max Salfinger and
Zamin Iqbal and
Irada Akhundova and
Sergo Vashakidze and
Valeriu Crudu and
Alex Rosenthal and
Maha R. Farhat},
title = {Benchmarking the empirical accuracy of short-read sequencing across
the \emph{M. tuberculosis} genome},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {1781--1787},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac023},
doi = {10.1093/BIOINFORMATICS/BTAC023},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MarinVHJEDSSIAV22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MariniMRPSM22,
author = {Simone Marini and
Carla Mavian and
Alberto Riva and
Mattia Prosperi and
Marco Salemi and
Brittany Rife Magalis},
title = {Optimizing viral genome subsampling by genetic diversity and temporal
distribution (TARDiS) for phylogenetics},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {856--860},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab725},
doi = {10.1093/BIOINFORMATICS/BTAB725},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MariniMRPSM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MarinisSCP22,
author = {Ilaria De Marinis and
Prisca Lo Surdo and
Gianni Cesareni and
Livia Perfetto},
title = {SIGNORApp: a Cytoscape 3 application to access {SIGNOR} data},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1764--1766},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab865},
doi = {10.1093/BIOINFORMATICS/BTAB865},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MarinisSCP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MarkinWAE22,
author = {Alexey Markin and
Sanket Wagle and
Tavis K. Anderson and
Oliver Eulenstein},
title = {RF-Net 2: fast inference of virus reassortment and hybridization networks},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2144--2152},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac075},
doi = {10.1093/BIOINFORMATICS/BTAC075},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MarkinWAE22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MartinelliR22,
author = {Adriano Luca Martinelli and
Maria Anna Rapsomaniki},
title = {{ATHENA:} analysis of tumor heterogeneity from spatial omics measurements},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3151--3153},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac303},
doi = {10.1093/BIOINFORMATICS/BTAC303},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MartinelliR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MasoumiLW22,
author = {Shohre Masoumi and
Maxwell W. Libbrecht and
Kay C. Wiese},
title = {SigTools: exploratory visualization for genomic signals},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1126--1128},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab742},
doi = {10.1093/BIOINFORMATICS/BTAB742},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MasoumiLW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MatsuiAUM22,
author = {Yusuke Matsui and
Yuichi Abe and
Kohei Uno and
Satoru Miyano},
title = {RoDiCE: robust differential protein co-expression analysis for cancer
complexome},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1269--1276},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab612},
doi = {10.1093/BIOINFORMATICS/BTAB612},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MatsuiAUM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MayKFHGKBH22,
author = {Vinzenz May and
Leonard Koch and
Bj{\"{o}}rn Fischer{-}Zirnsak and
Denise Horn and
Petra Gehle and
Uwe Kornak and
Dieter Beule and
Manuel Holtgrewe},
title = {ClearCNV: {CNV} calling from {NGS} panel data in the presence of ambiguity
and noise},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {3871--3876},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac418},
doi = {10.1093/BIOINFORMATICS/BTAC418},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MayKFHGKBH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MayersTSLQS22,
author = {Michael Mayers and
Roger Tu and
Dylan Steinecke and
Tong Shu Li and
N{\'{u}}ria Queralt{-}Rosinach and
Andrew I. Su},
title = {Design and application of a knowledge network for automatic prioritization
of drug mechanisms},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2880--2891},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac205},
doi = {10.1093/BIOINFORMATICS/BTAC205},
timestamp = {Mon, 13 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MayersTSLQS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/McFarlandKMTHH22,
author = {Alexander G. McFarland and
Nolan W. Kennedy and
Carolyn E. Mills and
Danielle Tullman{-}Ercek and
Curtis Huttenhower and
Erica M. Hartmann},
title = {Density-based binning of gene clusters to infer function or evolutionary
history using GeneGrouper},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {612--620},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab752},
doi = {10.1093/BIOINFORMATICS/BTAB752},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/McFarlandKMTHH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/McHaleQ22,
author = {Peter McHale and
Aaron R. Quinlan},
title = {trfermikit: a tool to discover VNTR-associated deletions},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1231--1234},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab805},
doi = {10.1093/BIOINFORMATICS/BTAB805},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/McHaleQ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MedeirosCSDAMA22,
author = {Jessie J. F. Medeiros and
Jose{-}Mario Capo{-}Chichi and
Liran I Shlush and
John E. Dick and
Andrea Arruda and
Mark D. Minden and
Sagi Abelson},
title = {SmMIP-tools: a computational toolset for processing and analysis of
single-molecule molecular inversion probes-derived data},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2088--2095},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac081},
doi = {10.1093/BIOINFORMATICS/BTAC081},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MedeirosCSDAMA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MedvedevPG22,
author = {Kirill E. Medvedev and
Jimin Pei and
Nick V. Grishin},
title = {DisEnrich: database of enriched regions in human dark proteome},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {1870--1876},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac051},
doi = {10.1093/BIOINFORMATICS/BTAC051},
timestamp = {Wed, 27 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MedvedevPG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MelkonianJDRB22,
author = {Marc Melkonian and
Camille Juign{\'{e}} and
Olivier Dameron and
Gwena{\"{e}}l Rabut and
Emmanuelle Becker},
title = {Towards a reproducible interactome: semantic-based detection of redundancies
to unify protein-protein interaction databases},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1685--1691},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac013},
doi = {10.1093/BIOINFORMATICS/BTAC013},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MelkonianJDRB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MengOPSPFGZKBC22,
author = {Zaiqiao Meng and
Anya Okhmatovskaia and
Maxime Polleri and
Yannan Shen and
Guido Powell and
Zihao Fu and
Iris Ganser and
Meiru Zhang and
Nicholas B. King and
David L. Buckeridge and
Nigel Collier},
title = {BioCaster in 2021: automatic disease outbreaks detection from global
news media},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4446--4448},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac497},
doi = {10.1093/BIOINFORMATICS/BTAC497},
timestamp = {Mon, 24 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MengOPSPFGZKBC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MerinoSMSM22,
author = {Gabriela Alejandra Merino and
Rabie Saidi and
Diego H. Milone and
Georgina Stegmayer and
Maria Jesus Martin},
title = {Hierarchical deep learning for predicting {GO} annotations by integrating
protein knowledge},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4488--4496},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac536},
doi = {10.1093/BIOINFORMATICS/BTAC536},
timestamp = {Mon, 24 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MerinoSMSM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MertschS22,
author = {Darvin Mertsch and
Mario Stanke},
title = {End-to-end learning of evolutionary models to find coding regions
in genome alignments},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {1857--1862},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac028},
doi = {10.1093/BIOINFORMATICS/BTAC028},
timestamp = {Wed, 27 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MertschS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MetwallyZWKZCTS22,
author = {Ahmed A. Metwally and
Tom Zhang and
Si Wu and
Ryan Kellogg and
Wenyu Zhou and
K{\'{e}}vin Contrepois and
Hua Tang and
Michael Snyder},
title = {Robust identification of temporal biomarkers in longitudinal omics
studies},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3802--3811},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac403},
doi = {10.1093/BIOINFORMATICS/BTAC403},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MetwallyZWKZCTS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MiaoLHL22,
author = {Yan Miao and
Fu Liu and
Tao Hou and
Yun Liu},
title = {Virtifier: a deep learning-based identifier for viral sequences from
metagenomes},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1216--1222},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab845},
doi = {10.1093/BIOINFORMATICS/BTAB845},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MiaoLHL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MiaoXLLYG22,
author = {Ya{-}Ru Miao and
Meng{-}Xuan Xia and
Mei Luo and
Tao Luo and
Mei Yang and
An{-}Yuan Guo},
title = {ImmuCellAI-mouse: a tool for comprehensive prediction of mouse immune
cell abundance and immune microenvironment depiction},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {785--791},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab711},
doi = {10.1093/BIOINFORMATICS/BTAB711},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MiaoXLLYG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MidlikVHCBV22,
author = {Adam Midlik and
Ivana Hutarov{\'{a}} Varekov{\'{a}} and
Jan Hutar and
Aliaksei Chareshneu and
Karel Berka and
Radka Svobodov{\'{a}} Varekov{\'{a}}},
title = {OverProt: secondary structure consensus for protein families},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3648--3650},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac384},
doi = {10.1093/BIOINFORMATICS/BTAC384},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MidlikVHCBV22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MierECBA22,
author = {Pablo Mier and
Carlos A. Elena{-}Real and
Juan Cort{\'{e}}s and
Pau Bernad{\'{o}} and
Miguel A. Andrade{-}Navarro},
title = {The sequence context in poly-alanine regions: structure, function
and conservation},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4851--4858},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac610},
doi = {10.1093/BIOINFORMATICS/BTAC610},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MierECBA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MildauHFWAKZB22,
author = {Kevin Mildau and
Justin J. J. van der Hooft and
Mira Flasch and
Benedikt Warth and
Yasin El Abiead and
Gunda Koellensperger and
J{\"{u}}rgen Zanghellini and
Christoph Bueschl},
title = {Homologue series detection and management in {LC-MS} data with \emph{homologueDiscoverer}},
journal = {Bioinform.},
volume = {38},
number = {22},
pages = {5139--5140},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac647},
doi = {10.1093/BIOINFORMATICS/BTAC647},
timestamp = {Sat, 11 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MildauHFWAKZB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MinLY22,
author = {Seonwoo Min and
Byunghan Lee and
Sungroh Yoon},
title = {TargetNet: functional microRNA target prediction with deep neural
networks},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {671--677},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab733},
doi = {10.1093/BIOINFORMATICS/BTAB733},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MinLY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MiottoARRMT22,
author = {Mattia Miotto and
Alexandros Armaos and
Lorenzo Di Rienzo and
Giancarlo Ruocco and
Edoardo Milanetti and
Gian Gaetano Tartaglia},
title = {Thermometer: a webserver to predict protein thermal stability},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {2060--2061},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab868},
doi = {10.1093/BIOINFORMATICS/BTAB868},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MiottoARRMT22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Monfort-LanzasG22,
author = {Pablo Monfort{-}Lanzas and
Raphael Gronauer and
Leonie Madersbacher and
Christoph Schatz and
Dietmar Rieder and
Hubert Hackl},
title = {{MIO:} microRNA target analysis system for immuno-oncology},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3665--3667},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac366},
doi = {10.1093/BIOINFORMATICS/BTAC366},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Monfort-LanzasG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MoniotGVB22,
author = {Antoine Moniot and
Yann Guermeur and
Sjoerd Jacob de Vries and
Isaure Chauvot de Beauch{\^{e}}ne},
title = {ProtNAff: protein-bound Nucleic Acid filters and fragment libraries},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {3911--3917},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac430},
doi = {10.1093/BIOINFORMATICS/BTAC430},
timestamp = {Sat, 10 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MoniotGVB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MoodyKCACSH22,
author = {Jonathan Moody and
Tsukasa Kouno and
Jen{-}Chien Chang and
Yoshinari Ando and
Piero Carninci and
Jay W. Shin and
Chung{-}Chau Hon},
title = {{SCAFE:} a software suite for analysis of transcribed cis-regulatory
elements in single cells},
journal = {Bioinform.},
volume = {38},
number = {22},
pages = {5126--5128},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac644},
doi = {10.1093/BIOINFORMATICS/BTAC644},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MoodyKCACSH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MoonL22,
author = {Sehwan Moon and
Hyunju Lee},
title = {{MOMA:} a multi-task attention learning algorithm for multi-omics
data interpretation and classification},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2287--2296},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac080},
doi = {10.1093/BIOINFORMATICS/BTAC080},
timestamp = {Wed, 18 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MoonL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MooreBGPEM22,
author = {J. Harry Moore and
Matthias R. Bauer and
Jeff Guo and
Atanas Patronov and
Ola Engkvist and
Christian Margreitter},
title = {Icolos: a workflow manager for structure-based post-processing of
\emph{de novo} generated small molecules},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4951--4952},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac614},
doi = {10.1093/BIOINFORMATICS/BTAC614},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MooreBGPEM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MotamediPMFG22,
author = {Fahimeh Motamedi and
Horacio P{\'{e}}rez S{\'{a}}nchez and
Alireza Mehridehnavi and
Afshin Fassihi and
Fahimeh Ghasemi},
title = {Accelerating Big Data Analysis through LASSO-Random Forest Algorithm
in {QSAR} Studies},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {469--475},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab659},
doi = {10.1093/BIOINFORMATICS/BTAB659},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MotamediPMFG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MuSSCPL22,
author = {Wancen Mu and
Hirak Sarkar and
Avi Srivastava and
Kwangbom Choi and
Rob Patro and
Michael I. Love},
title = {Airpart: interpretable statistical models for analyzing allelic imbalance
in single-cell datasets},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2773--2780},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac212},
doi = {10.1093/BIOINFORMATICS/BTAC212},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MuSSCPL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MuhlichCYRSS22,
author = {Jeremy Muhlich and
Yu{-}An Chen and
Clarence Han{-}Wei Yapp and
Douglas Russell and
Sandro Santagata and
Peter K. Sorger},
title = {Stitching and registering highly multiplexed whole-slide images of
tissues and tumors using {ASHLAR}},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4613--4621},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac544},
doi = {10.1093/BIOINFORMATICS/BTAC544},
timestamp = {Mon, 24 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MuhlichCYRSS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MunroSPFOHL22,
author = {Rory Munro and
Roberto Santos and
Alexander Payne and
Teri Forey and
Solomon Osei and
Nadine Holmes and
Matthew Loose},
title = {minoTour, real-time monitoring and analysis for nanopore sequencers},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1133--1135},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab780},
doi = {10.1093/BIOINFORMATICS/BTAB780},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MunroSPFOHL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Murillo-RecioSD22,
author = {Marina Murillo{-}Recio and
Ignacio Miguel Mart{\'{\i}}nez de Lejarza Samper and
Cristina Tu{\~{n}}{\'{\i}} i Dom{\'{\i}}nguez and
Llu{\'{\i}}s Ribas de Pouplana and
Adrian Gabriel Torres},
title = {tRNAstudio: facilitating the study of human mature tRNAs from deep
sequencing datasets},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2934--2936},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac198},
doi = {10.1093/BIOINFORMATICS/BTAC198},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Murillo-RecioSD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MusselIWWMSK22,
author = {Christoph M{\"{u}}ssel and
Nensi Ikonomi and
Silke D. Werle and
Felix M. Weidner and
Markus Maucher and
Julian D. Schwab and
Hans A. Kestler},
title = {\emph{CANTATA - }prediction of missing links in Boolean networks using
genetic programming},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4893--4900},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac623},
doi = {10.1093/BIOINFORMATICS/BTAC623},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MusselIWWMSK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MyungPA22,
author = {Yoochan Myung and
Douglas E. V. Pires and
David B. Ascher},
title = {{CSM-AB:} graph-based antibody-antigen binding affinity prediction
and docking scoring function},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1141--1143},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab762},
doi = {10.1093/BIOINFORMATICS/BTAB762},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MyungPA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NaCP22,
author = {Seungjin Na and
Hyunjin Choi and
Eunok Paek},
title = {Deephos: predicted spectral database search for TMT-labeled phosphopeptides
and its false discovery rate estimation},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {2980--2987},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac280},
doi = {10.1093/BIOINFORMATICS/BTAC280},
timestamp = {Tue, 28 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/NaCP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NaakeH22,
author = {Thomas Naake and
Wolfgang Huber},
title = {MatrixQCvis: shiny-based interactive data quality exploration for
omics data},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1181--1182},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab748},
doi = {10.1093/BIOINFORMATICS/BTAB748},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/NaakeH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NamLPLPKP22,
author = {Seungyoon Nam and
Sungyoung Lee and
Sungjin Park and
Jinhyuk Lee and
Aron Park and
Yon Hui Kim and
Taesung Park},
title = {PATHOME-Drug: a subpathway-based polypharmacology drug-repositioning
method},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {444--452},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab566},
doi = {10.1093/BIOINFORMATICS/BTAB566},
timestamp = {Mon, 08 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/NamLPLPKP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NamasivayamSSPW22,
author = {Vigneshwaran Namasivayam and
Katja Stefan and
Katja Silbermann and
Jens Pahnke and
Michael Wiese and
Sven Marcel Stefan},
title = {Structural feature-driven pattern analysis for multitarget modulator
landscapes},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1385--1392},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab832},
doi = {10.1093/BIOINFORMATICS/BTAB832},
timestamp = {Fri, 13 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/NamasivayamSSPW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NarcisoPDMM22,
author = {Diogo A. C. Narciso and
Ana Pereira and
Nuno O. Dias and
Luis F. Melo and
Fernando Gomes Martins},
title = {Characterization of biofilm structure and properties via processing
of 2D optical coherence tomography images in {BISCAP}},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1708--1715},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac002},
doi = {10.1093/BIOINFORMATICS/BTAC002},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/NarcisoPDMM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NeumannLMMCDCHP22,
author = {Jacob Neumann and
Yen Ting Lin and
Abhishek Mallela and
Ely F. Miller and
Joshua Colvin and
Abell T. Duprat and
Ye Chen and
William S. Hlavacek and
Richard G. Posner},
title = {Implementation of a practical Markov chain Monte Carlo sampling algorithm
in PyBioNetFit},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1770--1772},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac004},
doi = {10.1093/BIOINFORMATICS/BTAC004},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/NeumannLMMCDCHP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NiarakisTBMHBCCD22,
author = {Anna Niarakis and
Juilee Thakar and
Matteo Barberis and
Mar{\'{\i}}a Rodr{\'{\i}}guez Mart{\'{\i}}nez and
Tom{\'{a}}s Helikar and
Marc R. Birtwistle and
Claudine Chaouiya and
Laurence Calzone and
Andreas Dr{\"{a}}ger},
title = {Computational modelling in health and disease: highlights of the 6th
annual SysMod meeting},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4990--4993},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac609},
doi = {10.1093/BIOINFORMATICS/BTAC609},
timestamp = {Sat, 11 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/NiarakisTBMHBCCD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NicheperovichAD22,
author = {Alina Nicheperovich and
Adrian M. Altenhoff and
Christophe Dessimoz and
Sina Majidian},
title = {{OMAMO:} orthology-based alternative model organism selection},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2965--2966},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac163},
doi = {10.1093/BIOINFORMATICS/BTAC163},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/NicheperovichAD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NieQWHL22,
author = {Liangpeng Nie and
Lijun Quan and
Tingfang Wu and
Ruji He and
Qiang Lyu},
title = {TransPPMP: predicting pathogenicity of frameshift and non-sense mutations
by a Transformer based on protein features},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2705--2711},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac188},
doi = {10.1093/BIOINFORMATICS/BTAC188},
timestamp = {Wed, 15 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/NieQWHL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NiuRDH22,
author = {Yi Nian Niu and
Eric G. Roberts and
Danielle Denisko and
Michael M. Hoffman},
title = {Assessing and assuring interoperability of a genomics file format},
journal = {Bioinform.},
volume = {38},
number = {13},
pages = {3327--3336},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac327},
doi = {10.1093/BIOINFORMATICS/BTAC327},
timestamp = {Wed, 27 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/NiuRDH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NiuZW22,
author = {Mengting Niu and
Quan Zou and
Chunyu Wang},
title = {{GMNN2CD:} identification of circRNA-disease associations based on
variational inference and graph Markov neural networks},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2246--2253},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac079},
doi = {10.1093/BIOINFORMATICS/BTAC079},
timestamp = {Wed, 18 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/NiuZW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NodzenskiSKWLLU22,
author = {Michael Nodzenski and
Min Shi and
Juno M. Krahn and
Alison S. Wise and
Yuanyuan Li and
Leping Li and
David M. Umbach and
Clarice R. Weinberg},
title = {Erratum to: {GADGETS:} a genetic algorithm for detecting epistasis
using nuclear families},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {881},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab833},
doi = {10.1093/BIOINFORMATICS/BTAB833},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/NodzenskiSKWLLU22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NodzenskiSKWLLU22a,
author = {Michael Nodzenski and
Min Shi and
Juno M. Krahn and
Alison S. Wise and
Yuanyuan Li and
Leping Li and
David M. Umbach and
Clarice R. Weinberg},
title = {{GADGETS:} a genetic algorithm for detecting epistasis using nuclear
families},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1052--1058},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab766},
doi = {10.1093/BIOINFORMATICS/BTAB766},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/NodzenskiSKWLLU22a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NoeckerEMB22,
author = {Cecilia Noecker and
Alexander Eng and
Efrat Muller and
Elhanan Borenstein},
title = {{MIMOSA2:} a metabolic network-based tool for inferring mechanism-supported
relationships in microbiome-metabolome data},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1615--1623},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac003},
doi = {10.1093/BIOINFORMATICS/BTAC003},
timestamp = {Fri, 01 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/NoeckerEMB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NowakowskaK22,
author = {Alicja W. Nowakowska and
Malgorzata Kotulska},
title = {Topological analysis as a tool for detection of abnormalities in protein-protein
interaction data},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {3968--3975},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac440},
doi = {10.1093/BIOINFORMATICS/BTAC440},
timestamp = {Thu, 05 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/NowakowskaK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NustadSOCKBGL22,
author = {Haakon E. Nustad and
Ingelin Steinsland and
Miina Ollikainen and
Emma Cazaly and
Jaakko Kaprio and
Yuval Benjamini and
Kristina Gervin and
Robert Lyle},
title = {Modeling dependency structures in 450k {DNA} methylation data},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {885--891},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab774},
doi = {10.1093/BIOINFORMATICS/BTAB774},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/NustadSOCKBGL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/OestreichHADKJBU22,
author = {Marie Oestreich and
Lisa Holsten and
Shobhit Agrawal and
Kilian Dahm and
Philipp Koch and
Han Jin and
Matthias Becker and
Thomas Ulas},
title = {hCoCena: horizontal integration and analysis of transcriptomics datasets},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4727--4734},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac589},
doi = {10.1093/BIOINFORMATICS/BTAC589},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/OestreichHADKJBU22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/OliverMPHW22,
author = {Carlos G. Oliver and
Vincent Mallet and
Pericles Philippopoulos and
William L. Hamilton and
J{\'{e}}r{\^{o}}me Waldisp{\"{u}}hl},
title = {Vernal: a tool for mining fuzzy network motifs in {RNA}},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {970--976},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab768},
doi = {10.1093/BIOINFORMATICS/BTAB768},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/OliverMPHW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/OluwayioseWGBSP22,
author = {Oladele A. Oluwayiose and
Haotian Wu and
Feng Gao and
Andrea A. Baccarelli and
Tamar Sofer and
J. Richard Pilsner},
title = {Aclust2.0: a revamped unsupervised {R} tool for Infinium methylation
beadchips data analyses},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4820--4822},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac583},
doi = {10.1093/BIOINFORMATICS/BTAC583},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/OluwayioseWGBSP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/OnogiA22,
author = {Akio Onogi and
Aisaku Arakawa},
title = {An {R} package VIGoR for joint estimation of multiple linear learners
with variational Bayesian inference},
journal = {Bioinform.},
volume = {38},
number = {12},
pages = {3306--3309},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac328},
doi = {10.1093/BIOINFORMATICS/BTAC328},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/OnogiA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/OsmalaEL22,
author = {Maria Osmala and
G{\"{o}}kcen Eraslan and
Harri L{\"{a}}hdesm{\"{a}}ki},
title = {ChromDMM: a Dirichlet-multinomial mixture model for clustering heterogeneous
epigenetic data},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {3863--3870},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac444},
doi = {10.1093/BIOINFORMATICS/BTAC444},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/OsmalaEL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/OsorioKC22,
author = {Daniel Os{\'{o}}rio and
Marieke L. Kuijjer and
James J. Cai},
title = {rPanglaoDB: an {R} package to download and merge labeled single-cell
RNA-seq data from the PanglaoDB database},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {580--582},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab549},
doi = {10.1093/BIOINFORMATICS/BTAB549},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/OsorioKC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/OsuntokiHDBZ22,
author = {Itunu G. Osuntoki and
Andrew Harrison and
Hongsheng Dai and
Yanchun Bao and
Nicolae Radu Zabet},
title = {ZipHiC: a novel Bayesian framework to identify enriched interactions
and experimental biases in Hi-C data},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3523--3531},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac387},
doi = {10.1093/BIOINFORMATICS/BTAC387},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/OsuntokiHDBZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/OttBS22,
author = {Simon Ott and
Adriano Barbosa{-}Silva and
Matthias Samwald},
title = {LinkExplorer: predicting, explaining and exploring links in large
biomedical knowledge graphs},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2371--2373},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac068},
doi = {10.1093/BIOINFORMATICS/BTAC068},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/OttBS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/OuteiralND22,
author = {Carlos Outeiral and
Daniel A. Nissley and
Charlotte M. Deane},
title = {Current structure predictors are not learning the physics of protein
folding},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {1881--1887},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab881},
doi = {10.1093/BIOINFORMATICS/BTAB881},
timestamp = {Fri, 13 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/OuteiralND22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/OvekTATKTNKG22,
author = {Damla Ovek and
Ameer Taweel and
Zeynep Abali and
Ece Tezsezen and
Yunus Emre Koroglu and
Chung{-}Jung Tsai and
Ruth Nussinov and
Ozlem Keskin and
Attila G{\"{u}}rsoy},
title = {SARS-CoV-2 Interactome 3D: {A} Web interface for 3D visualization
and analysis of SARS-CoV-2-human mimicry and interactions},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1455--1457},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab799},
doi = {10.1093/BIOINFORMATICS/BTAB799},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/OvekTATKTNKG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/OzcanLWCSFJS22,
author = {Zuhal Ozcan and
Francis A. San Lucas and
Justin W. Wong and
Kyle Chang and
Konrad H. Stopsack and
Jerry Fowler and
Yasminka A. Jakubek and
Paul Scheet},
title = {Chromosomal imbalances detected via RNA-sequencing in 28 cancers},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1483--1490},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab861},
doi = {10.1093/BIOINFORMATICS/BTAB861},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/OzcanLWCSFJS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/OzsariRADMCA22,
author = {G{\"{o}}khan {\"{O}}zsari and
Ahmet S{\"{u}}reyya Rifaioglu and
Ahmet Atakan and
Tunca Dogan and
Maria Jesus Martin and
Reng{\"{u}}l {\c{C}}etin{-}Atalay and
Volkan Atalay},
title = {SLPred: a multi-view subcellular localization prediction tool for
multi-location human proteins},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4226--4229},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac458},
doi = {10.1093/BIOINFORMATICS/BTAC458},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/OzsariRADMCA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PaciF22,
author = {Paola Paci and
Giulia Fiscon},
title = {SWIMmeR: an R-based software to unveiling crucial nodes in complex
biological networks},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {586--588},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab657},
doi = {10.1093/BIOINFORMATICS/BTAB657},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PaciF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PaciniL22,
author = {Lorenza Pacini and
Claire Lesieur},
title = {A computational methodology to diagnose sequence-variant dynamic perturbations
by comparing atomic protein structures},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {703--709},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab736},
doi = {10.1093/BIOINFORMATICS/BTAB736},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PaciniL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PakI22,
author = {Marina A. Pak and
Dmitry N. Ivankov},
title = {Best templates outperform homology models in predicting the impact
of mutations on protein stability},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4312--4320},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac515},
doi = {10.1093/BIOINFORMATICS/BTAC515},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PakI22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PalshikarHZT22,
author = {Mukta G. Palshikar and
Shannon P. Hilchey and
Martin S. Zand and
Juilee Thakar},
title = {WikiNetworks: translating manually created biological pathways for
topological analysis},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {869--871},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab699},
doi = {10.1093/BIOINFORMATICS/BTAB699},
timestamp = {Wed, 16 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PalshikarHZT22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PanDPV22,
author = {Lu Pan and
Huy Q. Dinh and
Yudi Pawitan and
Trung{-}Nghia Vu},
title = {Isoform-level quantification for single-cell {RNA} sequencing},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1287--1294},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab807},
doi = {10.1093/BIOINFORMATICS/BTAB807},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PanDPV22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PanchiwalaSPZKD22,
author = {Hemil Panchiwala and
Shalin Shah and
Hannes Planatscher and
Mykola Zakharchuk and
Matthias K{\"{o}}nig and
Andreas Dr{\"{a}}ger},
title = {The systems biology simulation core library},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {864--865},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab669},
doi = {10.1093/BIOINFORMATICS/BTAB669},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PanchiwalaSPZKD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PandeyAR22,
author = {Palash Pandey and
Sanjeevani Arora and
Gail L. Rosen},
title = {MetaMutationalSigs: comparison of mutational signature refitting results
made easy},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2344--2347},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac091},
doi = {10.1093/BIOINFORMATICS/BTAC091},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PandeyAR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PaneiTMGB22,
author = {Francesco P. Panei and
Rachel Torchet and
Herv{\'{e}} M{\'{e}}nager and
Paraskevi Gkeka and
Massimiliano Bonomi},
title = {{HARIBOSS:} a curated database of RNA-small molecules structures to
aid rational drug design},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4185--4193},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac483},
doi = {10.1093/BIOINFORMATICS/BTAC483},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PaneiTMGB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PangYXWL22,
author = {Yuxuan Pang and
Lantian Yao and
Jingyi Xu and
Zhuo Wang and
Tzong{-}Yi Lee},
title = {Integrating transformer and imbalanced multi-label learning to identify
antimicrobial peptides and their functional activities},
journal = {Bioinform.},
volume = {38},
number = {24},
pages = {5368--5374},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac711},
doi = {10.1093/BIOINFORMATICS/BTAC711},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PangYXWL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ParkJKSLLKLN22,
author = {Aron Park and
Minjae Joo and
Kyungdoc Kim and
Won{-}Joon Son and
Gyutae Lim and
Jinhyuk Lee and
Jung Ho Kim and
Dae Ho Lee and
Seungyoon Nam},
title = {A comprehensive evaluation of regression-based drug responsiveness
prediction models, using cell viability inhibitory concentrations
{(IC50} values)},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2810--2817},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac177},
doi = {10.1093/BIOINFORMATICS/BTAC177},
timestamp = {Mon, 13 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ParkJKSLLKLN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PassemiersMR22,
author = {Antoine Passemiers and
Yves Moreau and
Daniele Raimondi},
title = {Fast and accurate inference of gene regulatory networks through robust
precision matrix estimation},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2802--2809},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac178},
doi = {10.1093/BIOINFORMATICS/BTAC178},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PassemiersMR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PeacockHRC22,
author = {Thomas Peacock and
James M. Heather and
Tahel Ronel and
Benny Chain},
title = {Corrigendum to: Decombinator {V4:} an improved {AIRR-C} compliant
software package for T-cell receptor sequence annotation},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {883},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab550},
doi = {10.1093/BIOINFORMATICS/BTAB550},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PeacockHRC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PedrolaFLEDBC22,
author = {Anna Pedrola and
Sebasti{\`{a}} Franch{-}Exp{\'{o}}sito and
Sara Lahoz and
Roger Esteban{-}Fabr{\'{o}} and
Rodrigo Dienstmann and
Laia Bassaganyas and
Jordi Camps},
title = {{PCIG:} a web-based application to explore immune-genomics interactions
across cancer types},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2374--2376},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac111},
doi = {10.1093/BIOINFORMATICS/BTAC111},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PedrolaFLEDBC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PeiZC22,
author = {Jimin Pei and
Jing Zhang and
Qian Cong},
title = {Human mitochondrial protein complexes revealed by large-scale coevolution
analysis and deep learning-based structure modeling},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4301--4311},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac527},
doi = {10.1093/BIOINFORMATICS/BTAC527},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PeiZC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PellegrinoGABUP22,
author = {Roberto Maria Pellegrino and
Matteo Giulietti and
Husam B. R. Alabed and
Sandra Buratta and
Lorena Urbanelli and
Francesco Piva and
Carla Emiliani},
title = {LipidOne: user-friendly lipidomic data analysis tool for a deeper
interpretation in a systems biology scenario},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1767--1769},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab867},
doi = {10.1093/BIOINFORMATICS/BTAB867},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PellegrinoGABUP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PenelMTDT22,
author = {Simon Penel and
Hugo Menet and
Th{\'{e}}o Tricou and
Vincent Daubin and
Eric Tannier},
title = {Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2350--2352},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac062},
doi = {10.1093/BIOINFORMATICS/BTAC062},
timestamp = {Thu, 02 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PenelMTDT22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PengLDYW22,
author = {Wei Peng and
Hancheng Liu and
Wei Dai and
Ning Yu and
Jianxin Wang},
title = {Predicting cancer drug response using parallel heterogeneous graph
convolutional networks with neighborhood interactions},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4546--4553},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac574},
doi = {10.1093/BIOINFORMATICS/BTAC574},
timestamp = {Fri, 02 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PengLDYW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PengSK22,
author = {Jing Peng and
David L. Swofford and
Laura Salter Kubatko},
title = {Estimation of speciation times under the multispecies coalescent},
journal = {Bioinform.},
volume = {38},
number = {23},
pages = {5182--5190},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac679},
doi = {10.1093/BIOINFORMATICS/BTAC679},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PengSK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PengZXLHZ22,
author = {Chunxiang Peng and
Xiao{-}Gen Zhou and
Yuhao Xia and
Jun Liu and
Minghua Hou and
Gui{-}Jun Zhang},
title = {Structural analogue-based protein structure domain assembly assisted
by deep learning},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4513--4521},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac553},
doi = {10.1093/BIOINFORMATICS/BTAC553},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PengZXLHZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PerssonS22,
author = {Emma Persson and
Erik L. L. Sonnhammer},
title = {InParanoid-DIAMOND: faster orthology analysis with the InParanoid
algorithm},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2918--2919},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac194},
doi = {10.1093/BIOINFORMATICS/BTAC194},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PerssonS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PesaranghaderMS22,
author = {Ahmad Pesaranghader and
Stan Matwin and
Marina Sokolova and
Jean{-}Christophe Grenier and
Robert G. Beiko and
Julie Hussin},
title = {deepSimDEF: deep neural embeddings of gene products and gene ontology
terms for functional analysis of genes},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3051--3061},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac304},
doi = {10.1093/BIOINFORMATICS/BTAC304},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PesaranghaderMS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PhipsonSPHPO22,
author = {Belinda Phipson and
Choon Boon Sim and
Enzo R. Porrello and
Alex W. Hewitt and
Joseph E. Powell and
Alicia Oshlack},
title = {\emph{propeller:} testing for differences in cell type proportions
in single cell data},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4720--4726},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac582},
doi = {10.1093/BIOINFORMATICS/BTAC582},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PhipsonSPHPO22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PiernikBSPMGSBW22,
author = {Maciej Piernik and
Dariusz Brzezinski and
Pawel Sztromwasser and
Klaudia Pacewicz and
Weronika Majer{-}Burman and
Michal Gniot and
Dawid Sielski and
Oleksii Bryzghalov and
Alicja Wozna and
Pawel Zawadzki},
title = {{DBFE:} distribution-based feature extraction from structural variants
in whole-genome data},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4466--4473},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac513},
doi = {10.1093/BIOINFORMATICS/BTAC513},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PiernikBSPMGSBW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Pierre-JeanMDF22,
author = {Morgane Pierre{-}Jean and
Florence Mauger and
Jean{-}Francois Deleuze and
Edith Le Floch},
title = {PIntMF: Penalized Integrative Matrix Factorization method for multi-omics
data},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {900--907},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab786},
doi = {10.1093/BIOINFORMATICS/BTAB786},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Pierre-JeanMDF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PikalyovaOLTMHP22,
author = {Karina Pikalyova and
Alexey Orlov and
Arkadii I. Lin and
Olga A. Tarasova and
Gilles Marcou and
Dragos Horvath and
Vladimir Poroikov and
Alexandre Varnek},
title = {{HIV-1} drug resistance profiling using amino acid sequence space
cartography},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2307--2314},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac090},
doi = {10.1093/BIOINFORMATICS/BTAC090},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PikalyovaOLTMHP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PilehvarBSC22,
author = {Mohammad Taher Pilehvar and
Adam Bernard and
Damian Smedley and
Nigel Collier},
title = {PheneBank: a literature-based database of phenotypes},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1179--1180},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab740},
doi = {10.1093/BIOINFORMATICS/BTAB740},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PilehvarBSC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PioMMZCA22,
author = {Gianvito Pio and
Paolo Mignone and
Giuseppe Magazz{\`{u}} and
Guido Zampieri and
Michelangelo Ceci and
Claudio Angione},
title = {Integrating genome-scale metabolic modelling and transfer learning
for human gene regulatory network reconstruction},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {487--493},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab647},
doi = {10.1093/BIOINFORMATICS/BTAB647},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PioMMZCA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PipesN22,
author = {Lenore Pipes and
Rasmus Nielsen},
title = {AncestralClust: clustering of divergent nucleotide sequences by ancestral
sequence reconstruction using phylogenetic trees},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {663--670},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab723},
doi = {10.1093/BIOINFORMATICS/BTAB723},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PipesN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Platero-Rochart22,
author = {Daniel Platero{-}Rochart and
Roy Gonz{\'{a}}lez{-}Alem{\'{a}}n and
Erix Wiliam Hern{\'{a}}ndez{-}Rodr{\'{\i}}guez and
Fabrice Leclerc and
Julio Caballero and
Luis Alberto Montero{-}Cabrera},
title = {RCDPeaks: memory-efficient density peaks clustering of long molecular
dynamics},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {1863--1869},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac021},
doi = {10.1093/BIOINFORMATICS/BTAC021},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Platero-Rochart22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PockrandtSS22,
author = {Christopher Pockrandt and
Martin Steinegger and
Steven L. Salzberg},
title = {PhyloCSF++: a fast and user-friendly implementation of PhyloCSF with
annotation tools},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1440--1442},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab756},
doi = {10.1093/BIOINFORMATICS/BTAB756},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PockrandtSS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PomiesBDMCGTKML22,
author = {Lise Pomi{\`{e}}s and
C{\'{e}}line Brouard and
Harold Durufl{\'{e}} and
{\'{E}}lise Maign{\'{e}} and
Cl{\'{e}}ment Carr{\'{e}} and
Louise Gody and
Fulya Tr{\"{o}}sser and
George Katsirelos and
Brigitte Mangin and
Nicolas B. Langlade and
Simon de Givry},
title = {Gene regulatory network inference methodology for genomic and transcriptomic
data acquired in genetically related heterozygote individuals},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4127--4134},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac445},
doi = {10.1093/BIOINFORMATICS/BTAC445},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PomiesBDMCGTKML22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PozzatiZBLKE22,
author = {Gabriele Pozzati and
Wensi Zhu and
Claudio Bassot and
John Lamb and
Petras Kundrotas and
Arne Elofsson},
title = {Limits and potential of combined folding and docking},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {954--961},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab760},
doi = {10.1093/BIOINFORMATICS/BTAB760},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PozzatiZBLKE22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PradelliMT22,
author = {Franco Pradelli and
Giovanni Minervini and
Silvio C. E. Tosatto},
title = {Mocafe: a comprehensive Python library for simulating cancer development
with Phase Field Models},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4440--4441},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac521},
doi = {10.1093/BIOINFORMATICS/BTAC521},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PradelliMT22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PreteCRGFNA22,
author = {Eugenio Del Prete and
Ana Margarida Campos and
Fabio Della Rocca and
Carmela Gallo and
Angelo Fontana and
Genoveffa Nuzzo and
Claudia Angelini},
title = {ADViSELipidomics: a workflow for analyzing lipidomics data},
journal = {Bioinform.},
volume = {38},
number = {24},
pages = {5460--5462},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac706},
doi = {10.1093/BIOINFORMATICS/BTAC706},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PreteCRGFNA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PriceTHSSSPBEFP22,
author = {Stephen Price and
St{\'{e}}phane Tombeur and
Alexander Hudson and
Nanda Kumar Sathiyamoorthy and
Paul Smyth and
Anjana Singh and
Mara Peccianti and
Elisa Baroncelli and
Ahmed Essaghir and
Ilaria Ferlenghi and
Sanjay Kumar Phogat and
Gurpreet Singh},
title = {TMQuery: a database of precomputed template modeling scores for assessment
of protein structural similarity},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {2062--2063},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac044},
doi = {10.1093/BIOINFORMATICS/BTAC044},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PriceTHSSSPBEFP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PrigentVLSK22,
author = {Sylvain Prigent and
Cesar Augusto Valades{-}Cruz and
Ludovic Leconte and
Jean Salamero and
Charles Kervrann},
title = {STracking: a free and open-source Python library for particle tracking
and analysis},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3671--3673},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac365},
doi = {10.1093/BIOINFORMATICS/BTAC365},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PrigentVLSK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Prive22,
author = {Florian Priv{\'{e}}},
title = {Using the {UK} Biobank as a global reference of worldwide populations:
application to measuring ancestry diversity from {GWAS} summary statistics},
journal = {Bioinform.},
volume = {38},
number = {13},
pages = {3477--3480},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac348},
doi = {10.1093/BIOINFORMATICS/BTAC348},
timestamp = {Wed, 27 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Prive22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PutriAPPZ22,
author = {Givanna H. Putri and
Simon Anders and
Paul Theodor Pyl and
John E. Pimanda and
Fabio Zanini},
title = {Analysing high-throughput sequencing data in Python with HTSeq 2.0},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2943--2945},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac166},
doi = {10.1093/BIOINFORMATICS/BTAC166},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PutriAPPZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/QaseemG22,
author = {Ammar Qaseem and
Stefan G{\"{u}}nther},
title = {CPRiL: compound-protein relationships in literature},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4452--4453},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac539},
doi = {10.1093/BIOINFORMATICS/BTAC539},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/QaseemG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/QiaoZG22,
author = {Yanhua Qiao and
Xiaolei Zhu and
Haipeng Gong},
title = {BERT-Kcr: prediction of lysine crotonylation sites by a transfer learning
method with pre-trained {BERT} models},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {648--654},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab712},
doi = {10.1093/BIOINFORMATICS/BTAB712},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/QiaoZG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/QinBZHLZL22,
author = {Dongya Qin and
Weichen Bo and
Xin Zheng and
Youjin Hao and
Bo Li and
Jie Zheng and
Guizhao Liang},
title = {{DFBP:} a comprehensive database of food-derived bioactive peptides
for peptidomics research},
journal = {Bioinform.},
volume = {38},
number = {12},
pages = {3275--3280},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac323},
doi = {10.1093/BIOINFORMATICS/BTAC323},
timestamp = {Mon, 25 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/QinBZHLZL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/QinLXC22,
author = {Fei Qin and
Xizhi Luo and
Feifei Xiao and
Guoshuai Cai},
title = {{SCRIP:} an accurate simulator for single-cell {RNA} sequencing data},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1304--1311},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab824},
doi = {10.1093/BIOINFORMATICS/BTAB824},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/QinLXC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/QiuYLDG22,
author = {Sichao Qiu and
Guoxian Yu and
Xudong Lu and
Carlotta Domeniconi and
Maozu Guo},
title = {Isoform function prediction by Gene Ontology embedding},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4581--4588},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac576},
doi = {10.1093/BIOINFORMATICS/BTAC576},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/QiuYLDG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/QuC22,
author = {Jialin Qu and
Yuehua Cui},
title = {Gene set analysis with graph-embedded kernel association test},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1560--1567},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab851},
doi = {10.1093/BIOINFORMATICS/BTAB851},
timestamp = {Fri, 01 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/QuC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RaadBMS22,
author = {Jonathan Raad and
Leandro A Bugnon and
Diego H. Milone and
Georgina Stegmayer},
title = {miRe2e: a full end-to-end deep model based on transformers for prediction
of pre-miRNAs},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1191--1197},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab823},
doi = {10.1093/BIOINFORMATICS/BTAB823},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RaadBMS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RaduskyS22,
author = {Leandro G. Radusky and
Luis Serrano},
title = {pyFoldX: enabling biomolecular analysis and engineering along structural
ensembles},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2353--2355},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac072},
doi = {10.1093/BIOINFORMATICS/BTAC072},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RaduskyS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RamananMS22,
author = {Vivek Ramanan and
Shanti Mechery and
Indra Neil Sarkar},
title = {GenBank as a source to monitor and analyze Host-Microbiome data},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4172--4177},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac487},
doi = {10.1093/BIOINFORMATICS/BTAC487},
timestamp = {Thu, 22 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RamananMS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RanjanBED22,
author = {Piyush Ranjan and
Christopher A. Brown and
John R. Erb{-}Downward and
Robert P. Dickson},
title = {{SNIKT:} sequence-independent adapter identification and removal in
long-read shotgun sequencing data},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3830--3832},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac389},
doi = {10.1093/BIOINFORMATICS/BTAC389},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RanjanBED22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RaoJHYZ22,
author = {Liang Rao and
Ning{-}Xin Jia and
Jun Hu and
Dong{-}Jun Yu and
Gui{-}Jun Zhang},
title = {ATPdock: a template-based method for ATP-specific protein-ligand docking},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {556--558},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab667},
doi = {10.1093/BIOINFORMATICS/BTAB667},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RaoJHYZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RawatSPRMJG22,
author = {Puneet Rawat and
Divya Sharma and
R. Prabakaran and
Fathima Ridha and
Mugdha Mohkhedkar and
Vani Janakiraman and
M. Michael Gromiha},
title = {Ab-CoV: a curated database for binding affinity and neutralization
profiles of coronavirus-related antibodies},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {4051--4052},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac439},
doi = {10.1093/BIOINFORMATICS/BTAC439},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RawatSPRMJG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RehfeldtKBSR22,
author = {Tobias Greisager Rehfeldt and
Konrad Krawczyk and
Mathias B{\o}gebjerg and
Veit Schw{\"{a}}mmle and
Richard R{\"{o}}ttger},
title = {{MS2AI:} automated repurposing of public peptide {LC-MS} data for
machine learning applications},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {875--877},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab701},
doi = {10.1093/BIOINFORMATICS/BTAB701},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RehfeldtKBSR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RehmanTZC22,
author = {Mobeen Ur Rehman and
Hilal Tayara and
Quan Zou and
Kil To Chong},
title = {i6mA-Caps: a CapsuleNet-based framework for identifying {DNA} N6-methyladenine
sites},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {3885--3891},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac434},
doi = {10.1093/BIOINFORMATICS/BTAC434},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RehmanTZC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ReisfeldCGBGGS22,
author = {Brad Reisfeld and
Aline de Conti and
Fatiha El Ghissassi and
Lamia Benbrahim{-}Tallaa and
William Gwinn and
Yann Grosse and
Mary Schubauer{-}Berigan},
title = {kc-hits: a tool to aid in the evaluation and classification of chemical
carcinogens},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2961--2962},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac189},
doi = {10.1093/BIOINFORMATICS/BTAC189},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ReisfeldCGBGGS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RenCDFFGHSH22,
author = {Yunxiao Ren and
Trinad Chakraborty and
Swapnil Doijad and
Linda Falgenhauer and
Jane Falgenhauer and
Alexander Goesmann and
Anne{-}Christin Hauschild and
Oliver Schwengers and
Dominik Heider},
title = {Prediction of antimicrobial resistance based on whole-genome sequencing
and machine learning},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {325--334},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab681},
doi = {10.1093/BIOINFORMATICS/BTAB681},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RenCDFFGHSH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RenJCS22,
author = {Shumin Ren and
Yanwen Jin and
Yalan Chen and
Bairong Shen},
title = {{CRPMKB:} a knowledge base of cancer risk prediction models for systematic
comparison and personalized applications},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1669--1676},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab850},
doi = {10.1093/BIOINFORMATICS/BTAB850},
timestamp = {Fri, 01 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RenJCS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RenYG22,
author = {Shujie Ren and
Liang Yu and
Lin Gao},
title = {Multidrug representation learning based on pretraining model and molecular
graph for drug interaction and combination prediction},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4387--4394},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac538},
doi = {10.1093/BIOINFORMATICS/BTAC538},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RenYG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RezwaniPN22,
author = {Moosa Rezwani and
Ali Akbar Pourfathollah and
Farshid Noorbakhsh},
title = {rbioapi: user-friendly {R} interface to biologic web services' {API}},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2952--2953},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac172},
doi = {10.1093/BIOINFORMATICS/BTAC172},
timestamp = {Mon, 13 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RezwaniPN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RiederFAGPTF22,
author = {Dietmar Rieder and
Georgios Fotakis and
Markus Ausserhofer and
Rene Geyeregger and
Wolfgang Paster and
Zlatko Trajanoski and
Francesca Finotello},
title = {nextNEOpi: a comprehensive pipeline for computational neoantigen prediction},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1131--1132},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab759},
doi = {10.1093/BIOINFORMATICS/BTAB759},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RiederFAGPTF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RighelliWCPCGLH22,
author = {Dario Righelli and
Lukas M. Weber and
Helena L. Crowell and
Brenda Pardo and
Leonardo Collado{-}Torres and
Shila Ghazanfar and
Aaron T. L. Lun and
Stephanie C. Hicks and
Davide Risso},
title = {SpatialExperiment: infrastructure for spatially-resolved transcriptomics
data in {R} using Bioconductor},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3128--3131},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac299},
doi = {10.1093/BIOINFORMATICS/BTAC299},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RighelliWCPCGLH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RobertSZS22,
author = {Nicolas Serge Matthieu Robert and
Fatih Sarigol and
Elisabeth Zieger and
Oleg Simakov},
title = {{SYNPHONI:} scale-free and phylogeny-aware reconstruction of synteny
conservation and transformation across animal genomes},
journal = {Bioinform.},
volume = {38},
number = {24},
pages = {5434--5436},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac695},
doi = {10.1093/BIOINFORMATICS/BTAC695},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RobertSZS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Rocha22,
author = {Luis M. Rocha},
title = {On the feasibility of dynamical analysis of network models of biochemical
regulation},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3674--3675},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac360},
doi = {10.1093/BIOINFORMATICS/BTAC360},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Rocha22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Rodriguez-Cerro22,
author = {{\'{A}}ngel Rodr{\'{\i}}guez{-}Cerro and
Sergio Sancho and
Miriam Rodr{\'{\i}}guez and
Miguel A. Gam{\'{o}}n and
L{\'{e}}na Guitou and
Rafael J. Mart{\'{\i}}nez and
Javier Buceta},
title = {\emph{ANISE}: an application to design mechanobiology simulations
of planar epithelia},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4246--4247},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac511},
doi = {10.1093/BIOINFORMATICS/BTAC511},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Rodriguez-Cerro22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RognesSGS22,
author = {Torbj{\o}rn Rognes and
Lonneke Scheffer and
Victor Greiff and
Geir Kjetil Sandve},
title = {CompAIRR: ultra-fast comparison of adaptive immune receptor repertoires
by exact and approximate sequence matching},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4230--4232},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac505},
doi = {10.1093/BIOINFORMATICS/BTAC505},
timestamp = {Mon, 24 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RognesSGS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RomanoLCGGCRHFM22,
author = {Joseph D. Romano and
Trang T. Le and
William G. La Cava and
John T. Gregg and
Daniel J. Goldberg and
Praneel Chakraborty and
Natasha L. Ray and
Daniel S. Himmelstein and
Weixuan Fu and
Jason H. Moore},
title = {{PMLB} v1.0: an open-source dataset collection for benchmarking machine
learning methods},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {878--880},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab727},
doi = {10.1093/BIOINFORMATICS/BTAB727},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RomanoLCGGCRHFM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RoquencourtGT22,
author = {Camille Roquencourt and
Stanislas Grassin{-}Delyle and
Etienne A. Th{\'{e}}venot},
title = {ptairMS: real-time processing and analysis of {PTR-TOF-MS} data for
biomarker discovery in exhaled breath},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {1930--1937},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac031},
doi = {10.1093/BIOINFORMATICS/BTAC031},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RoquencourtGT22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RoseMPCSM22,
author = {Bailey S. Rose and
Jody C. May and
Jaqueline A. Picache and
Simona G. Codreanu and
Stacy D. Sherrod and
John A. McLean},
title = {Improving confidence in lipidomic annotations by incorporating empirical
ion mobility regression analysis and chemical class prediction},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2872--2879},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac197},
doi = {10.1093/BIOINFORMATICS/BTAC197},
timestamp = {Mon, 13 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RoseMPCSM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RosignoliP22,
author = {Serena Rosignoli and
Alessandro Paiardini},
title = {DockingPie: a consensus docking plugin for PyMOL},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4233--4234},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac452},
doi = {10.1093/BIOINFORMATICS/BTAC452},
timestamp = {Thu, 22 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RosignoliP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RossiCIP22,
author = {Nicol{\`{o}} Rossi and
Andrea Colautti and
L. Iacumin and
Carla Piazza},
title = {{WGA-LP:} a pipeline for whole genome assembly of contaminated reads},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {846--848},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab719},
doi = {10.1093/BIOINFORMATICS/BTAB719},
timestamp = {Sat, 11 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RossiCIP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RossumCPATSB22,
author = {Thea Van Rossum and
Paul I. Costea and
Lucas Paoli and
Renato Alves and
Roman Thielemann and
Shinichi Sunagawa and
Peer Bork},
title = {metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1162--1164},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab789},
doi = {10.1093/BIOINFORMATICS/BTAB789},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RossumCPATSB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RoyB22,
author = {Parthajit Roy and
Dhananjay Bhattacharyya},
title = {MetBP: a software tool for detection of interaction between metal
ion-RNA base pairs},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3833--3834},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac392},
doi = {10.1093/BIOINFORMATICS/BTAC392},
timestamp = {Thu, 25 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RoyB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RoyGVH22,
author = {Gourab Ghosh Roy and
Nicholas Geard and
Karin Verspoor and
Shan He},
title = {{MPVNN:} Mutated Pathway Visible Neural Network architecture for interpretable
prediction of cancer-specific survival risk},
journal = {Bioinform.},
volume = {38},
number = {22},
pages = {5026--5032},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac636},
doi = {10.1093/BIOINFORMATICS/BTAC636},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RoyGVH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RoyQSC22,
author = {Raj S. Roy and
Farhan Quadir and
Elham Soltanikazemi and
Jianlin Cheng},
title = {A deep dilated convolutional residual network for predicting interchain
contacts of protein homodimers},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {1904--1910},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac063},
doi = {10.1093/BIOINFORMATICS/BTAC063},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RoyQSC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RozhonovaDSRKL22,
author = {Hana Rozhonov{\'{a}} and
Daniel Danciu and
Stefan Stark and
Gunnar R{\"{a}}tsch and
Andr{\'{e}} Kahles and
Kjong{-}Van Lehmann},
title = {{SECEDO:} SNV-based subclone detection using ultra-low coverage single-cell
{DNA} sequencing},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4293--4300},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac510},
doi = {10.1093/BIOINFORMATICS/BTAC510},
timestamp = {Mon, 05 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RozhonovaDSRKL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RozumDPZA22,
author = {Jordan C. Rozum and
D{\'{a}}vid Deritei and
Kyu Hyong Park and
Jorge G{\'{o}}mez Tejeda Za{\~{n}}udo and
R{\'{e}}ka Albert},
title = {pystablemotifs: Python library for attractor identification and control
in Boolean networks},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1465--1466},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab825},
doi = {10.1093/BIOINFORMATICS/BTAB825},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RozumDPZA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RuYSZ22,
author = {Xiaoqing Ru and
Xiucai Ye and
Tetsuya Sakurai and
Quan Zou},
title = {NerLTR-DTA: drug-target binding affinity prediction based on neighbor
relationship and learning to rank},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {1964--1971},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac048},
doi = {10.1093/BIOINFORMATICS/BTAC048},
timestamp = {Wed, 27 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RuYSZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RuanNMSMFHWCPJH22,
author = {Eric Ruan and
Erika Nemeth and
Richard A. Moffitt and
Lorena Sandoval and
Mitchell J. Machiela and
Neal D. Freedman and
Wen{-}Yi Huang and
Wendy Wong and
Kai{-}Ling Chen and
Brian Park and
Kevin Jiang and
Belynda Hicks and
Jia Liu and
Daniel E. Russ and
Lori M. Minasian and
Paul F. Pinsky and
Stephen J. Chanock and
Montserrat Garcia{-}Closas and
Jonas S. Almeida},
title = {PLCOjs, a {FAIR} {GWAS} web {SDK} for the {NCI} Prostate, Lung, Colorectal
and Ovarian Cancer Genetic Atlas project},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4434--4436},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac531},
doi = {10.1093/BIOINFORMATICS/BTAC531},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RuanNMSMFHWCPJH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RubinsteinBZSHS22,
author = {Rebecca L. Rubinstein and
Mikayla A. Borton and
Haiyan Zhou and
Michael Shaffer and
David W. Hoyt and
James Stegen and
Christopher S. Henry and
Kelly C. Wrighton and
Roelof Versteeg},
title = {{ORT:} a workflow linking genome-scale metabolic models with reactive
transport codes},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {778--784},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab753},
doi = {10.1093/BIOINFORMATICS/BTAB753},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RubinsteinBZSHS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RuddenMBD22,
author = {Lucas S. P. Rudden and
Samuel C. Musson and
Justin L. P. Benesch and
Matteo T. Degiacomi},
title = {Biobox: a toolbox for biomolecular modelling},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1149--1151},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab785},
doi = {10.1093/BIOINFORMATICS/BTAB785},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RuddenMBD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RuedaAMR22,
author = {Manuel Rueda and
Roberto Ariosa and
Mauricio Moldes and
Jordi Rambla},
title = {Beacon v2 Reference Implementation: a toolkit to enable federated
sharing of genomic and phenotypic data},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4656--4657},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac568},
doi = {10.1093/BIOINFORMATICS/BTAC568},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RuedaAMR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RuhlemannWEF22,
author = {Malte R{\"{u}}hlemann and
Eike Matthias Wacker and
David Ellinghaus and
Andre Franke},
title = {{\textless}tt{\textgreater}MAGScoT{\textless}/tt{\textgreater}: a
fast, lightweight and accurate bin-refinement tool},
journal = {Bioinform.},
volume = {38},
number = {24},
pages = {5430--5433},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac694},
doi = {10.1093/BIOINFORMATICS/BTAC694},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RuhlemannWEF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RyuLLSAO22,
author = {Jae Yong Ryu and
Jeong Hyun Lee and
Byung Ho Lee and
Jin Sook Song and
Sunjoo Ahn and
Kwang{-}Seok Oh},
title = {PredMS: a random forest model for predicting metabolic stability of
drug candidates in human liver microsomes},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {364--368},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab547},
doi = {10.1093/BIOINFORMATICS/BTAB547},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RyuLLSAO22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SadeghiLN22,
author = {Seyedeh Shaghayegh Sadeghi and
Jianguo Lu and
Alioune Ngom},
title = {A network-based drug repurposing method via non-negative matrix factorization},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1369--1377},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab826},
doi = {10.1093/BIOINFORMATICS/BTAB826},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SadeghiLN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SakhtemanGF22,
author = {Amirhossein Sakhteman and
Arindam Ghosh and
Vittorio Fortino},
title = {EDTox: an {R} Shiny application to predict the endocrine disruption
potential of compounds},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {2066--2069},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac045},
doi = {10.1093/BIOINFORMATICS/BTAC045},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SakhtemanGF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SaldanoEMZDRGMN22,
author = {Tadeo E. Salda{\~{n}}o and
Nahuel Escobedo and
Julia Marchetti and
Diego Javier Zea and
Juan Mac Donagh and
Ana Julia Velez Rueda and
Eduardo Gonik and
Agustina Garc{\'{\i}}a Melani and
Julieta Novomisky Nechcoff and
Mart{\'{\i}}n N. Salas and
Tom{\'{a}}s Peters and
Nicol{\'{a}}s Demitroff and
Sebastian Fernandez Alberti and
Nicolas Palopoli and
Mar{\'{\i}}a Silvina Fornasari and
Gustavo D. Parisi},
title = {Impact of protein conformational diversity on AlphaFold predictions},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2742--2748},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac202},
doi = {10.1093/BIOINFORMATICS/BTAC202},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SaldanoEMZDRGMN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SalzerWS22,
author = {Liesa Salzer and
Michael Witting and
Philippe Schmitt{-}Kopplin},
title = {MobilityTransformR: an {R} package for effective mobility transformation
of {CE-MS} data},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {4044--4045},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac441},
doi = {10.1093/BIOINFORMATICS/BTAC441},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SalzerWS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SamsonLM22,
author = {St{\'{e}}phane Samson and
Etienne Lord and
Vladimir Makarenkov},
title = {SimPlot++: a Python application for representing sequence similarity
and detecting recombination},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3118--3120},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac287},
doi = {10.1093/BIOINFORMATICS/BTAC287},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SamsonLM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SanchezAMCO22,
author = {Daniel Jim{\'{e}}nez S{\'{a}}nchez and
Mikel Ariz and
Jos{\'{e}} M{\'{a}}rio Morgado and
Iv{\'{a}}n Cort{\'{e}}s{-}Dom{\'{\i}}nguez and
Carlos Ortiz{-}de{-}Sol{\'{o}}rzano},
title = {Corrigendum to: {NMF-RI:} blind spectral unmixing of highly mixed
multispectral flow and image cytometry data},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1779},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab796},
doi = {10.1093/BIOINFORMATICS/BTAB796},
timestamp = {Tue, 22 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SanchezAMCO22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SanchezBGS22,
author = {Christopher D. Sanchez and
J. Benjamin Brown and
Omree Gal{-}Oz and
Esther Singer},
title = {EcoPLOT: dynamic analysis of biogeochemical data},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1480--1482},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab842},
doi = {10.1093/BIOINFORMATICS/BTAB842},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SanchezBGS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SandveG22,
author = {Geir Kjetil Sandve and
Victor Greiff},
title = {Access to ground truth at unconstrained size makes simulated data
as indispensable as experimental data for bioinformatics methods development
and benchmarking},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4994--4996},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac612},
doi = {10.1093/BIOINFORMATICS/BTAC612},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SandveG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SantoroPCV22,
author = {Diego Santoro and
Leonardo Pellegrina and
Matteo Comin and
Fabio Vandin},
title = {{SPRISS:} approximating frequent \emph{k}-mers by sampling reads,
and applications},
journal = {Bioinform.},
volume = {38},
number = {13},
pages = {3343--3350},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac180},
doi = {10.1093/BIOINFORMATICS/BTAC180},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SantoroPCV22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SarkarSBMP22,
author = {Arkadeep Sarkar and
Jacopo Santoro and
Luigi Di Biasi and
Francesco Marrafino and
Stefano Piotto},
title = {{YAMACS:} a graphical interface for {GROMACS}},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4645--4646},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac573},
doi = {10.1093/BIOINFORMATICS/BTAC573},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SarkarSBMP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SatoTYO22,
author = {Noriaki Sato and
Yoshinori Tamada and
Guangchuang Yu and
Yasushi Okuno},
title = {\emph{CBNplot}: Bayesian network plots for enrichment analysis},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2959--2960},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac175},
doi = {10.1093/BIOINFORMATICS/BTAC175},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SatoTYO22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SchererTSVSAJL22,
author = {Paul Scherer and
Maja Trebacz and
Nikola Simidjievski and
Ram{\'{o}}n Vi{\~{n}}as and
Zohreh Shams and
Helena Andr{\'{e}}s{-}Terr{\'{e}} and
Mateja Jamnik and
Pietro Li{\`{o}}},
title = {Unsupervised construction of computational graphs for gene expression
data with explicit structural inductive biases},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1320--1327},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab830},
doi = {10.1093/BIOINFORMATICS/BTAB830},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SchererTSVSAJL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SchieboutF22,
author = {Courtney Schiebout and
H. Robert Frost},
title = {{CAMML} with the Integration of Marker Proteins (ChIMP)},
journal = {Bioinform.},
volume = {38},
number = {23},
pages = {5206--5213},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac674},
doi = {10.1093/BIOINFORMATICS/BTAC674},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SchieboutF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SchilderHR22,
author = {Brian M. Schilder and
Jack Humphrey and
Towfique Raj},
title = {echolocatoR: an automated end-to-end statistical and functional genomic
fine-mapping pipeline},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {536--539},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab658},
doi = {10.1093/BIOINFORMATICS/BTAB658},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SchilderHR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SchneiderBKK22,
author = {Philipp Schneider and
Pavlos Stephanos Bekiaris and
Axel von Kamp and
Steffen Klamt},
title = {StrainDesign: a comprehensive Python package for computational design
of metabolic networks},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4981--4983},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac632},
doi = {10.1093/BIOINFORMATICS/BTAC632},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SchneiderBKK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SchneiderBTD22,
author = {Constantin Schneider and
Andrew Buchanan and
Bruck Taddese and
Charlotte M. Deane},
title = {{DLAB:} deep learning methods for structure-based virtual screening
of antibodies},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {377--383},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab660},
doi = {10.1093/BIOINFORMATICS/BTAB660},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SchneiderBTD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SchreiberNBK22,
author = {Jacob M. Schreiber and
Surag Nair and
Akshay Balsubramani and
Anshul Kundaje},
title = {Accelerating \emph{in silico} saturation mutagenesis using compressed
sensing},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3557--3564},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac385},
doi = {10.1093/BIOINFORMATICS/BTAC385},
timestamp = {Thu, 17 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SchreiberNBK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SchwabeF22,
author = {Daniel Schwabe and
Martin Falcke},
title = {On the relation between input and output distributions of scRNA-seq
experiments},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1336--1343},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab841},
doi = {10.1093/BIOINFORMATICS/BTAB841},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SchwabeF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SealG22,
author = {Souvik Seal and
Debashis Ghosh},
title = {{MIAMI:} mutual information-based analysis of multiplex imaging data},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3818--3826},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac414},
doi = {10.1093/BIOINFORMATICS/BTAC414},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SealG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SealeTG22,
author = {Colm Seale and
Yasin Tepeli and
Joana P. Gon{\c{c}}alves},
title = {Overcoming selection bias in synthetic lethality prediction},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4360--4368},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac523},
doi = {10.1093/BIOINFORMATICS/BTAC523},
timestamp = {Mon, 24 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SealeTG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SeguraRBBD22,
author = {Joan Segura and
Yana Rose and
Sebastian Bittrich and
Stephen K. Burley and
Jose M. Duarte},
title = {{RCSB} Protein Data Bank 1D3D module: displaying positional features
on macromolecular assemblies},
journal = {Bioinform.},
volume = {38},
number = {12},
pages = {3304--3305},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac317},
doi = {10.1093/BIOINFORMATICS/BTAC317},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SeguraRBBD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SensalariML22,
author = {Cecilia Sensalari and
Steven Maere and
Rolf Lohaus},
title = {ksrates: positioning whole-genome duplications relative to speciation
events in {KS} distributions},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {530--532},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab602},
doi = {10.1093/BIOINFORMATICS/BTAB602},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SensalariML22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SeversonKM22,
author = {Alissa L. Severson and
Thorfinn Sand Korneliussen and
Ida Moltke},
title = {LocalNgsRelate: a software tool for inferring {IBD} sharing along
the genome between pairs of individuals from low-depth {NGS} data},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1159--1161},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab732},
doi = {10.1093/BIOINFORMATICS/BTAB732},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SeversonKM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShanLGLJYGRZH22,
author = {Nayang Shan and
Yao Lu and
Hao Guo and
Dongyu Li and
Jitong Jiang and
Linlin Yan and
Jiudong Gao and
Yong Ren and
Xing{-}Ming Zhao and
Lin Hou},
title = {CITEdb: a manually curated database of cell-cell interactions in human},
journal = {Bioinform.},
volume = {38},
number = {22},
pages = {5144--5148},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac654},
doi = {10.1093/BIOINFORMATICS/BTAC654},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShanLGLJYGRZH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShanbhagPZSWWTB22,
author = {Sameer Shanbhag and
Riddhi Patil and
Noor Zahara and
Chirag Shetty and
Rachel Weidenhammer and
Sneha Watharkar and
Pranav Tambvekar and
Philip P. Badzuh and
Chester Dias and
Narendra Vankayala and
Prutha Kulkarni and
Charan Vallapureddy and
Shamika Kulkarni and
Pooja Nikhare and
Nowlan H. Freese and
Ann E. Loraine},
title = {Integrated Genome Browser App Store},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2348--2349},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac109},
doi = {10.1093/BIOINFORMATICS/BTAC109},
timestamp = {Wed, 18 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShanbhagPZSWWTB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SharmaARE22,
author = {Ankush Sharma and
Akshay Akshay and
Marie Rogne and
Ragnhild Eskeland},
title = {ShinyArchR.UiO: user-friendly, integrative and open-source tool for
visualization of single-cell ATAC-seq data using ArchR},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {834--836},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab680},
doi = {10.1093/BIOINFORMATICS/BTAB680},
timestamp = {Tue, 12 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SharmaARE22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SharonVALZHL22,
author = {Moran Sharon and
Ekaterina Vinogradov and
Chanan M. Argov and
Or Lazarescu and
Yazeed Zoabi and
Idan Hekselman and
Esti Yeger Lotem},
title = {The differential activity of biological processes in tissues and cell
subsets can illuminate disease-related processes and cell-type identities},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1584--1592},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab883},
doi = {10.1093/BIOINFORMATICS/BTAB883},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SharonVALZHL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SharpnackJCHCHH22,
author = {Michael F. Sharpnack and
Travis S. Johnson and
Robert Chalkley and
Zhi Han and
David Carbone and
Kun Huang and
Kai He},
title = {TSAFinder: exhaustive tumor-specific antigen detection with RNAseq},
journal = {Bioinform.},
volume = {38},
number = {9},
pages = {2422--2427},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac116},
doi = {10.1093/BIOINFORMATICS/BTAC116},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SharpnackJCHCHH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShatoffB22,
author = {Elan Shatoff and
Ralf Bundschuh},
title = {dsRBPBind: modeling the effect of {RNA} secondary structure on double-stranded
RNA-protein binding},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {687--693},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab724},
doi = {10.1093/BIOINFORMATICS/BTAB724},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShatoffB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShawY22,
author = {Jim Shaw and
Yun William Yu},
title = {Theory of local k-mer selection with applications to long-read alignment},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4659--4669},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab790},
doi = {10.1093/BIOINFORMATICS/BTAB790},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShawY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SheffieldBDFJ22,
author = {Thomas Sheffield and
Jason Brown and
Sarah Davidson and
Katie Paul Friedman and
Richard S. Judson},
title = {tcplfit2: an R-language general purpose concentration-response modeling
package},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1157--1158},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab779},
doi = {10.1093/BIOINFORMATICS/BTAB779},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SheffieldBDFJ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShegaySVSP22,
author = {Maksim V. Shegay and
Vytas K. Svedas and
Vladimir V. Voevodin and
Dmitry A. Suplatov and
Nina N. Popova},
title = {Guide tree optimization with genetic algorithm to improve multiple
protein 3D-structure alignment},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {985--989},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab798},
doi = {10.1093/BIOINFORMATICS/BTAB798},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShegaySVSP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShehwanaKMRWJSLBWMA22,
author = {Huma Shehwana and
Shwetha V. Kumar and
James M. Melott and
Mary A. Rohrdanz and
Chris Wakefield and
Zhenlin Ju and
Doris R. Siwak and
Yiling Lu and
Bradley M. Broom and
John N. Weinstein and
Gordon B. Mills and
Rehan Akbani},
title = {{RPPA} {SPACE:} an {R} package for normalization and quantitation
of Reverse-Phase Protein Array data},
journal = {Bioinform.},
volume = {38},
number = {22},
pages = {5131--5133},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac665},
doi = {10.1093/BIOINFORMATICS/BTAC665},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShehwanaKMRWJSLBWMA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShenWLCCZS22,
author = {Xiaotao Shen and
Si Wu and
Liang Liang and
Songjie Chen and
K{\'{e}}vin Contrepois and
Zheng{-}Jiang Zhu and
Michael P. Snyder},
title = {metID: an {R} package for automatable compound annotation for LC-MS-based
data},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {568--569},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab583},
doi = {10.1093/BIOINFORMATICS/BTAB583},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShenWLCCZS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShenWS22,
author = {Xiaotao Shen and
Chuchu Wang and
Michael P. Snyder},
title = {massDatabase: utilities for the operation of the public compound and
pathway database},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4650--4651},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac546},
doi = {10.1093/BIOINFORMATICS/BTAC546},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShenWS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShenZK22,
author = {Siqi Shen and
Ye Zheng and
S{\"{u}}nd{\"{u}}z Keles},
title = {scGAD: single-cell gene associating domain scores for exploratory
analysis of scHi-C data},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3642--3644},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac372},
doi = {10.1093/BIOINFORMATICS/BTAC372},
timestamp = {Thu, 25 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShenZK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShenZW22,
author = {Chengze Shen and
Paul Zaharias and
Tandy J. Warnow},
title = {MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary
sequences},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {918--924},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab788},
doi = {10.1093/BIOINFORMATICS/BTAB788},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShenZW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShiLKL22,
author = {Quan Shi and
Shiping Liu and
Karsten Kristiansen and
Longqi Liu},
title = {The {FASTQ+} format and {PISA}},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4639--4642},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac562},
doi = {10.1093/BIOINFORMATICS/BTAC562},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShiLKL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShihLMZDLC22,
author = {David J. H. Shih and
Ruoxing Li and
Peter M{\"{u}}ller and
W. Jim Zheng and
Kim{-}Anh Do and
Shiaw{-}Yih Lin and
Scott L. Carter},
title = {{CNGPLD:} case-control copy-number analysis using Gaussian process
latent difference},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2096--2101},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac096},
doi = {10.1093/BIOINFORMATICS/BTAC096},
timestamp = {Wed, 18 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShihLMZDLC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShinCLPPKHOHKY22,
author = {Hyun Kil Shin and
Hang{-}Suk Chun and
Sangwoo Lee and
Se{-}Myo Park and
Daeui Park and
Myung{-}Gyun Kang and
Sungbo Hwang and
Jung{-}Hwa Oh and
Hyoung{-}Yun Han and
Woo{-}Keun Kim and
Seokjoo Yoon},
title = {ToxSTAR: drug-induced liver injury prediction tool for the web environment},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4426--4427},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac490},
doi = {10.1093/BIOINFORMATICS/BTAC490},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShinCLPPKHOHKY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShineZP22,
author = {Morgan Shine and
Chengxin Zhang and
Anna Marie Pyle},
title = {{AMIGOS} {III:} pseudo-torsion angle visualization and motif-based
structure comparison of nucleic acids},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2937--2939},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac207},
doi = {10.1093/BIOINFORMATICS/BTAC207},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShineZP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShinkaiIKO22,
author = {Soya Shinkai and
Hiroya Itoga and
Koji Kyoda and
Shuichi Onami},
title = {PHi-C2: interpreting Hi-C data as the dynamic 3D genome state},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4984--4986},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac613},
doi = {10.1093/BIOINFORMATICS/BTAC613},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShinkaiIKO22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShresthaA22,
author = {Bikash Shrestha and
Badri Adhikari},
title = {Scoring protein sequence alignments using deep learning},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {2988--2995},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac210},
doi = {10.1093/BIOINFORMATICS/BTAC210},
timestamp = {Tue, 28 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShresthaA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShtarRSKBB22,
author = {Guy Shtar and
Lior Rokach and
Bracha Shapira and
Elkana Kohn and
Matitiahu Berkovitch and
Maya Berlin},
title = {Explainable multimodal machine learning model for classifying pregnancy
drug safety},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1102--1109},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab769},
doi = {10.1093/BIOINFORMATICS/BTAB769},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShtarRSKBB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SinghLSPZ22,
author = {Jaspreet Singh and
Thomas Litfin and
Jaswinder Singh and
Kuldip K. Paliwal and
Yaoqi Zhou},
title = {SPOT-Contact-LM: improving single-sequence-based prediction of protein
contact map using a transformer language model},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {1888--1894},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac053},
doi = {10.1093/BIOINFORMATICS/BTAC053},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SinghLSPZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SinghMASBZ22,
author = {Vinod Kumar Singh and
Rohan Misra and
Steven C. Almo and
Ulrich G. Steidl and
Hannes E. B{\"{u}}low and
Deyou Zheng},
title = {HSMotifDiscover: identification of motifs in sequences composed of
non-single-letter elements},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {4036--4038},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac437},
doi = {10.1093/BIOINFORMATICS/BTAC437},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SinghMASBZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SinghPLSZ22,
author = {Jaswinder Singh and
Kuldip K. Paliwal and
Thomas Litfin and
Jaspreet Singh and
Yaoqi Zhou},
title = {Predicting {RNA} distance-based contact maps by integrated deep learning
on physics-inferred secondary structure and evolutionary-derived mutational
coupling},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {3900--3910},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac421},
doi = {10.1093/BIOINFORMATICS/BTAC421},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SinghPLSZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SinghRASSM22,
author = {Nisha Singh and
Hukam C. Rawal and
Ulavappa B. Angadi and
Tilak Raj Sharma and
Nagendra Kumar Singh and
Tapan Kumar Mondal},
title = {A first-generation haplotype map (HapMap-1) of tea (Camellia sinensis
L. O. Kuntz)},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {318--324},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab690},
doi = {10.1093/BIOINFORMATICS/BTAB690},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SinghRASSM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SirenP22,
author = {Jouni Sir{\'{e}}n and
Benedict Paten},
title = {{GBZ} file format for pangenome graphs},
journal = {Bioinform.},
volume = {38},
number = {22},
pages = {5012--5018},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac656},
doi = {10.1093/BIOINFORMATICS/BTAC656},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SirenP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SlenkerKM22,
author = {Marek Slenker and
Petr Kouteck{\'{y}} and
Karol Marhold},
title = {MorphoTools2: an {R} package for multivariate morphometric analysis},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2954--2955},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac173},
doi = {10.1093/BIOINFORMATICS/BTAC173},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SlenkerKM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SmolanderJVE22,
author = {Johannes Smolander and
Sini Junttila and
Mikko S. Ven{\"{a}}l{\"{a}}inen and
Laura L. Elo},
title = {scShaper: an ensemble method for fast and accurate linear trajectory
inference from single-cell RNA-seq data},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1328--1335},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab831},
doi = {10.1093/BIOINFORMATICS/BTAB831},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SmolanderJVE22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SolariYMF22,
author = {Sean M. Solari and
Remy B. Young and
Vanessa R. Marcelino and
Samuel C. Forster},
title = {expam - high-resolution analysis of metagenomes using distance trees},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4814--4816},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac591},
doi = {10.1093/BIOINFORMATICS/BTAC591},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SolariYMF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SonabendBV22,
author = {Raphael Sonabend and
Andreas Bender and
Sebastian J. Vollmer},
title = {Avoiding C-hacking when evaluating survival distribution predictions
with discrimination measures},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4178--4184},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac451},
doi = {10.1093/BIOINFORMATICS/BTAC451},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SonabendBV22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SongHL22,
author = {Shuang Song and
Lin Hou and
Jun S. Liu},
title = {A data-adaptive Bayesian regression approach for polygenic risk prediction},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {1938--1946},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac024},
doi = {10.1093/BIOINFORMATICS/BTAC024},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SongHL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SongHL22a,
author = {Shuang Song and
Lin Hou and
Jun S. Liu},
title = {Erratum to: {A} data-adaptive Bayesian regression approach for polygenic
risk prediction},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {2080},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac092},
doi = {10.1093/BIOINFORMATICS/BTAC092},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SongHL22a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SongMLMGK22,
author = {Tianci Song and
Kathleen K. Markham and
Zhuliu Li and
Kristen E. Muller and
Kathleen Greenham and
Rui Kuang},
title = {Detecting spatially co-expressed gene clusters with functional coherence
by graph-regularized convolutional neural network},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1344--1352},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab812},
doi = {10.1093/BIOINFORMATICS/BTAB812},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SongMLMGK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SongXLW22,
author = {Dongyuan Song and
Nan Miles Xi and
Jingyi Jessica Li and
Lin Wang},
title = {scSampler: fast diversity-preserving subsampling of large-scale single-cell
transcriptomic data},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3126--3127},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac271},
doi = {10.1093/BIOINFORMATICS/BTAC271},
timestamp = {Tue, 28 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SongXLW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SongY22,
author = {Jian Song and
Changbin Yu},
title = {Alpha-Tri: a deep neural network for scoring the similarity between
predicted and measured spectra improves peptide identification of
{DIA} data},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1525--1531},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab878},
doi = {10.1093/BIOINFORMATICS/BTAB878},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SongY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SongZT22,
author = {Wei{-}Zhi Song and
Shan Zhang and
Torsten Thomas},
title = {MarkerMAG: linking metagenome-assembled genomes (MAGs) with 16S rRNA
marker genes using paired-end short reads},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3684--3688},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac398},
doi = {10.1093/BIOINFORMATICS/BTAC398},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SongZT22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SouzaDMCSMBB22,
author = {Eduardo Vieira de Souza and
Pedro Ferrari Dalberto and
Vinicius Pellisoli Machado and
Adriana Canedo and
Alan Saghatelian and
Pablo Machado and
Luiz Augusto Basso and
Cristiano Valim Bizarro},
title = {{\(\mathrm{\mu}\)}ProteInS - a proteogenomics pipeline for finding
novel bacterial microproteins encoded by small ORFs},
journal = {Bioinform.},
volume = {38},
number = {9},
pages = {2612--2614},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac115},
doi = {10.1093/BIOINFORMATICS/BTAC115},
timestamp = {Wed, 18 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SouzaDMCSMBB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Spouge22,
author = {John L. Spouge},
title = {A closed formula relevant to 'Theory of local k-mer selection with
applications to long-read alignment' by Jim Shaw and Yun William Yu},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4848--4849},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac604},
doi = {10.1093/BIOINFORMATICS/BTAC604},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Spouge22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/StammlerKSSTKHL22,
author = {Sebastian Stammler and
Tobias Kussel and
Phillipp Schoppmann and
Florian Stampe and
Galina Tremper and
Stefan Katzenbeisser and
Kay Hamacher and
Martin Lablans},
title = {Mainzelliste SecureEpiLinker (MainSEL): privacy-preserving record
linkage using secure multi-party computation},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1657--1668},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btaa764},
doi = {10.1093/BIOINFORMATICS/BTAA764},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/StammlerKSSTKHL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/StantonVH22,
author = {Richard A. Stanton and
Nicholas Vlachos and
Alison Laufer Halpin},
title = {{GAMMA:} a tool for the rapid identification, classification and annotation
of translated gene matches from sequencing data},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {546--548},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab607},
doi = {10.1093/BIOINFORMATICS/BTAB607},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/StantonVH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SteinJPT22,
author = {Alexander N. Stein and
Anoushka Joglekar and
Chi{-}Lam Poon and
Hagen U. Tilgner},
title = {ScisorWiz: visualizing differential isoform expression in single-cell
long-read data},
journal = {Bioinform.},
volume = {38},
number = {13},
pages = {3474--3476},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac340},
doi = {10.1093/BIOINFORMATICS/BTAC340},
timestamp = {Wed, 27 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SteinJPT22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/StephensFBIK22,
author = {Zachary Stephens and
Alejandro Ferrer and
Lisa Boardman and
Ravishankar K. Iyer and
Jean{-}Pierre A. Kocher},
title = {Telogator: a method for reporting chromosome-specific telomere lengths
from long reads},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {1788--1793},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac005},
doi = {10.1093/BIOINFORMATICS/BTAC005},
timestamp = {Wed, 27 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/StephensFBIK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/StilianoudakisM22,
author = {Spiro C. Stilianoudakis and
Maggie A. Marshall and
Mikhail G. Dozmorov},
title = {preciseTAD: a transfer learning framework for 3D domain boundary prediction
at base-pair resolution},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {621--630},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab743},
doi = {10.1093/BIOINFORMATICS/BTAB743},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/StilianoudakisM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/StockerAMWHS22,
author = {Tyll St{\"{o}}cker and
Lena Altrogge and
Caroline Marcon and
Yan Naing Win and
Frank Hochholdinger and
Heiko Schoof},
title = {MuWU: Mutant-seq library analysis and annotation},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {837--838},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab679},
doi = {10.1093/BIOINFORMATICS/BTAB679},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/StockerAMWHS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/StringerFAHFH22,
author = {Bas Stringer and
Hans de Ferrante and
Sanne Abeln and
Jaap Heringa and
K. Anton Feenstra and
Reza Haydarlou},
title = {{PIPENN:} protein interface prediction from sequence with an ensemble
of neural nets},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2111--2118},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac071},
doi = {10.1093/BIOINFORMATICS/BTAC071},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/StringerFAHFH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/StrutzSBT22,
author = {Jonathan Strutz and
Kevin M. Shebek and
Linda J. Broadbelt and
Keith E. J. Tyo},
title = {{MINE} 2.0: enhanced biochemical coverage for peak identification
in untargeted metabolomics},
journal = {Bioinform.},
volume = {38},
number = {13},
pages = {3484--3487},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac331},
doi = {10.1093/BIOINFORMATICS/BTAC331},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/StrutzSBT22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SuWZLWL22,
author = {Yanchi Su and
Fuzhou Wang and
Shixiong Zhang and
Yanchun Liang and
Ka{-}Chun Wong and
Xiangtao Li},
title = {scWMC: weighted matrix completion-based imputation of scRNA-seq data
via prior subspace information},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4537--4545},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac570},
doi = {10.1093/BIOINFORMATICS/BTAC570},
timestamp = {Mon, 21 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SuWZLWL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SugitaMDKI22,
author = {Itsuki Sugita and
Shohei Matsuyama and
Hiroki Dobashi and
Daisuke Komura and
Shumpei Ishikawa},
title = {Viola: a structural variant signature extractor with user-defined
classifications},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {540--542},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab662},
doi = {10.1093/BIOINFORMATICS/BTAB662},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SugitaMDKI22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SunDCZHH22,
author = {Dandan Sun and
Shaozhen Ding and
Pengli Cai and
Dachuan Zhang and
Mengying Han and
Qian{-}Nan Hu},
title = {BioBulkFoundary: a customized webserver for exploring biosynthetic
potentials of bulk chemicals},
journal = {Bioinform.},
volume = {38},
number = {22},
pages = {5137--5138},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac640},
doi = {10.1093/BIOINFORMATICS/BTAC640},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SunDCZHH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SunFAJM22,
author = {Huangqingbo Sun and
Xuecong Fu and
Serena Abraham and
Shen Jin and
Robert F. Murphy},
title = {Improving and evaluating deep learning models of cellular organization},
journal = {Bioinform.},
volume = {38},
number = {23},
pages = {5299--5306},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac688},
doi = {10.1093/BIOINFORMATICS/BTAC688},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SunFAJM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SunLYLXSJC22,
author = {Tao Sun and
Mengci Li and
Xiangtian Yu and
Dandan Liang and
Guoxiang Xie and
Chao Sang and
Wei Jia and
Tianlu Chen},
title = {3MCor: an integrative web server for metabolome-microbiome-metadata
correlation analysis},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1378--1384},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab818},
doi = {10.1093/BIOINFORMATICS/BTAB818},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SunLYLXSJC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SunWWRYKZZL22,
author = {Jinyu Sun and
Ming Wen and
Huabei Wang and
Yuezhe Ruan and
Qiong Yang and
Xiao Kang and
Hailiang Zhang and
Zhimin Zhang and
Hongmei Lu},
title = {Prediction of drug-likeness using graph convolutional attention network},
journal = {Bioinform.},
volume = {38},
number = {23},
pages = {5262--5269},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac676},
doi = {10.1093/BIOINFORMATICS/BTAC676},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SunWWRYKZZL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SungJCKLK22,
author = {Mujeen Sung and
Minbyul Jeong and
Yonghwa Choi and
Donghyeon Kim and
Jinhyuk Lee and
Jaewoo Kang},
title = {{BERN2:} an advanced neural biomedical named entity recognition and
normalization tool},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4837--4839},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac598},
doi = {10.1093/BIOINFORMATICS/BTAC598},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SungJCKLK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SzawulakRF22,
author = {Bartlomiej Szawulak and
Marcin Radom and
Piotr Formanowicz},
title = {Comparing Petri net-based models of biological systems using Holmes},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4652--4653},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac540},
doi = {10.1093/BIOINFORMATICS/BTAC540},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SzawulakRF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SzikszaiWDWM22,
author = {Marcell Szikszai and
Michael J. Wise and
Amitava Datta and
Max Ward and
David H. Mathews},
title = {Deep learning models for {RNA} secondary structure prediction (probably)
do not generalize across families},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {3892--3899},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac415},
doi = {10.1093/BIOINFORMATICS/BTAC415},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SzikszaiWDWM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SzymborskiE22,
author = {Joseph Szymborski and
Amin Emad},
title = {{RAPPPID:} towards generalizable protein interaction prediction with
{AWD-LSTM} twin networks},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {3958--3967},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac429},
doi = {10.1093/BIOINFORMATICS/BTAC429},
timestamp = {Sat, 10 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SzymborskiE22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TadmorP22,
author = {Arbel D. Tadmor and
Rob Phillips},
title = {{MCRL:} using a reference library to compress a metagenome into a
non-redundant list of sequences, considering viruses as a case study},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {631--647},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab703},
doi = {10.1093/BIOINFORMATICS/BTAB703},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TadmorP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TagashiraA22,
author = {Masaki Tagashira and
Kiyoshi Asai},
title = {ConsAlifold: considering {RNA} structural alignments improves prediction
accuracy of {RNA} consensus secondary structures},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {710--719},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab738},
doi = {10.1093/BIOINFORMATICS/BTAB738},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TagashiraA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TahiriFM22,
author = {Nadia Tahiri and
Bernard Fichet and
Vladimir Makarenkov},
title = {Building alternative consensus trees and supertrees using \emph{k}-means
and Robinson and Foulds distance},
journal = {Bioinform.},
volume = {38},
number = {13},
pages = {3367--3376},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac326},
doi = {10.1093/BIOINFORMATICS/BTAC326},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TahiriFM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TakisVTDLLM22,
author = {Panteleimon G. Takis and
Ivan Vuckovic and
Tricia Tan and
Aleksandar Denic and
John C. Lieske and
Matthew R. Lewis and
Slobodan Macura},
title = {\emph{NMRpQuant}: an automated software for large scale urinary total
protein quantification by one-dimensional 1H {NMR} profiles},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4437--4439},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac502},
doi = {10.1093/BIOINFORMATICS/BTAC502},
timestamp = {Mon, 24 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/TakisVTDLLM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TanFWGJZ22,
author = {Jie Tan and
Zhencheng Fang and
Shufang Wu and
Qian Guo and
Xiaoqing Jiang and
Huaiqiu Zhu},
title = {HoPhage: an ab initio tool for identifying hosts of phage fragments
from metaviromes},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {543--545},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab585},
doi = {10.1093/BIOINFORMATICS/BTAB585},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/TanFWGJZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TangLTFTLZDZ22,
author = {Deyou Tang and
Yucheng Li and
Daqiang Tan and
Juan Fu and
Yelei Tang and
Jiabin Lin and
Rong Zhao and
Hongli Du and
Zhongming Zhao},
title = {{KCOSS:} an ultra-fast k-mer counter for assembled genome analysis},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {933--940},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab797},
doi = {10.1093/BIOINFORMATICS/BTAB797},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TangLTFTLZDZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TangPL22,
author = {Yi{-}Jun Tang and
Yihe Pang and
Bin Liu},
title = {DeepIDP-2L: protein intrinsically disordered region prediction by
combining convolutional attention network and hierarchical attention
network},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1252--1260},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab810},
doi = {10.1093/BIOINFORMATICS/BTAB810},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TangPL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TaoZZLH22,
author = {Huanyu Tao and
Xuejun Zhao and
Keqiong Zhang and
Peicong Lin and
Sheng{-}You Huang},
title = {Docking cyclic peptides formed by a disulfide bond through a hierarchical
strategy},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4109--4116},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac486},
doi = {10.1093/BIOINFORMATICS/BTAC486},
timestamp = {Thu, 22 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/TaoZZLH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TarafderISR22,
author = {Sumit Tarafder and
Mazharul Islam and
Swakkhar Shatabda and
Atif Rahman},
title = {Figbird: a probabilistic method for filling gaps in genome assemblies},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3717--3724},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac404},
doi = {10.1093/BIOINFORMATICS/BTAC404},
timestamp = {Thu, 25 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/TarafderISR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TavakolianFBSL22,
author = {Nik Tavakolian and
Jo{\~{a}}o Guilherme Fraz{\~{a}}o and
Devin Bendixsen and
Rike Stelkens and
Chun{-}Biu Li},
title = {Shepherd: accurate clustering for correcting {DNA} barcode errors},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3710--3716},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac395},
doi = {10.1093/BIOINFORMATICS/BTAC395},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/TavakolianFBSL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TengYB22,
author = {Haotian Teng and
Ye Yuan and
Ziv Bar{-}Joseph},
title = {Clustering spatial transcriptomics data},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {997--1004},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab704},
doi = {10.1093/BIOINFORMATICS/BTAB704},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TengYB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TheorellJNS22,
author = {Axel Theorell and
Johann F. Jadebeck and
Katharina N{\"{o}}h and
J{\"{o}}rg Stelling},
title = {PolyRound: polytope rounding for random sampling in metabolic networks},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {566--567},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab552},
doi = {10.1093/BIOINFORMATICS/BTAB552},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/TheorellJNS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ThieleGF22,
author = {Ines Thiele and
German A. Preciat Gonzalez and
Ronan M. T. Fleming},
title = {MetaboAnnotator: an efficient toolbox to annotate metabolites in genome-scale
metabolic reconstructions},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4831--4832},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac596},
doi = {10.1093/BIOINFORMATICS/BTAC596},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ThieleGF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ThieleKBSK22,
author = {Sven Thiele and
Axel von Kamp and
Pavlos Stephanos Bekiaris and
Philipp Schneider and
Steffen Klamt},
title = {CNApy: a CellNetAnalyzer {GUI} in Python for analyzing and designing
metabolic networks},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1467--1469},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab828},
doi = {10.1093/BIOINFORMATICS/BTAB828},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ThieleKBSK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ThumuluriMASNJ22,
author = {Vineet Thumuluri and
Hannah{-}Marie Martiny and
Jos{\'{e}} Juan Almagro Armenteros and
Jesper Salomon and
Henrik Nielsen and
Alexander Rosenberg Johansen},
title = {NetSolP: predicting protein solubility in Escherichia coli using language
models},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {941--946},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab801},
doi = {10.1093/BIOINFORMATICS/BTAB801},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ThumuluriMASNJ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TianLMZTWKLY22,
author = {Leqi Tian and
Zhenjiang Li and
Guoxuan Ma and
Xiaoyue Zhang and
Ziyin Tang and
Siheng Wang and
Jian Kang and
Donghai Liang and
Tianwei Yu},
title = {Metapone: a Bioconductor package for joint pathway testing for untargeted
metabolomics data},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3662--3664},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac364},
doi = {10.1093/BIOINFORMATICS/BTAC364},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TianLMZTWKLY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TianYHL22,
author = {Peixin Tian and
Minhao Yao and
Tao Huang and
Zhonghua Liu},
title = {CoxMKF: a knockoff filter for high-dimensional mediation analysis
with a survival outcome in epigenetic studies},
journal = {Bioinform.},
volume = {38},
number = {23},
pages = {5229--5235},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac687},
doi = {10.1093/BIOINFORMATICS/BTAC687},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TianYHL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TiwaryMG22,
author = {Priya Tiwary and
Akshayraj Madhubalan and
Amit Gautam},
title = {No means 'No': a non-improper modeling approach, with embedded speculative
context},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4790--4796},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac593},
doi = {10.1093/BIOINFORMATICS/BTAC593},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/TiwaryMG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TokarPARJ22,
author = {Tom{\'{a}}s Tok{\'{a}}r and
Chiara Pastrello and
Mark Abovsky and
Sara Rahmati and
Igor Jurisica},
title = {miRAnno - network-based functional microRNA annotation},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {592--593},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab527},
doi = {10.1093/BIOINFORMATICS/BTAB527},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/TokarPARJ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TongZZFZWZN22,
author = {Yiqi Tong and
Fuzhen Zhuang and
Huajie Zhang and
Chuyu Fang and
Yu Zhao and
Deqing Wang and
Hengshu Zhu and
Bin Ni},
title = {Improving biomedical named entity recognition by dynamic caching inter-sentence
information},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {3976--3983},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac422},
doi = {10.1093/BIOINFORMATICS/BTAC422},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/TongZZFZWZN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TrieuMA22,
author = {Hai{-}Long Trieu and
Makoto Miwa and
Sophia Ananiadou},
title = {BioVAE: a pre-trained latent variable language model for biomedical
text mining},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {872--874},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab702},
doi = {10.1093/BIOINFORMATICS/BTAB702},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/TrieuMA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TsiamisS22,
author = {Vasileios Tsiamis and
Veit Schw{\"{a}}mmle},
title = {VIQoR: a web service for visually supervised protein inference and
protein quantification},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2757--2764},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac182},
doi = {10.1093/BIOINFORMATICS/BTAC182},
timestamp = {Mon, 13 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/TsiamisS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TsuchiyaHO22,
author = {Takaho Tsuchiya and
Hiroki Hori and
Haruka Ozaki},
title = {{CCPLS} reveals cell-type-specific spatial dependence of transcriptomes
in single cells},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4868--4877},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac599},
doi = {10.1093/BIOINFORMATICS/BTAC599},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TsuchiyaHO22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/UgidosNPFCT22,
author = {Manuel Ugidos and
Mar{\'{\i}}a Jos{\'{e}} Nueda and
Jos{\'{e}} Manuel Prats{-}Montalb{\'{a}}n and
Alberto Ferrer and
Ana Conesa and
Sonia Tarazona},
title = {MultiBaC: an {R} package to remove batch effects in multi-omic experiments},
journal = {Bioinform.},
volume = {38},
number = {9},
pages = {2657--2658},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac132},
doi = {10.1093/BIOINFORMATICS/BTAC132},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/UgidosNPFCT22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/UhlREB22,
author = {Michael Uhl and
Dominik Rabsch and
Florian Eggenhofer and
Rolf Backofen},
title = {Peakhood: individual site context extraction for CLIP-seq peak regions},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1139--1140},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab755},
doi = {10.1093/BIOINFORMATICS/BTAB755},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/UhlREB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/UhlmannPDUSF22,
author = {Virginie Uhlmann and
Zsuzsanna P{\"{u}}sp{\"{o}}ki and
Adrien Depeursinge and
Michael Unser and
Daniel Sage and
Julien Fageot},
title = {Steer'n'Detect: fast 2D template detection with accurate orientation
estimation},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3146--3148},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac270},
doi = {10.1093/BIOINFORMATICS/BTAC270},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/UhlmannPDUSF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/UllahHSY22,
author = {Matee Ullah and
Fazal Hadi and
Jiangning Song and
Dong{-}Jun Yu},
title = {PScL-DDCFPred: an ensemble deep learning-based approach for characterizing
multiclass subcellular localization of human proteins from bioimage
data},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {4019--4026},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac432},
doi = {10.1093/BIOINFORMATICS/BTAC432},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/UllahHSY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/UllanatKV22,
author = {Varun Ullanat and
Nikhil Kasukurthi and
Shruthi Viswanath},
title = {PrISM: precision for integrative structural models},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3837--3839},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac400},
doi = {10.1093/BIOINFORMATICS/BTAC400},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/UllanatKV22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/UmerAZPSLBP22,
author = {Husen M. Umer and
Enrique Audain and
Yafeng Zhu and
Julianus Pfeuffer and
Timo Sachsenberg and
Janne Lehti{\"{o}} and
Rui Mamede Branca and
Yasset P{\'{e}}rez{-}Riverol},
title = {Generation of ENSEMBL-based proteogenomics databases boosts the identification
of non-canonical peptides},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1470--1472},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab838},
doi = {10.1093/BIOINFORMATICS/BTAB838},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/UmerAZPSLBP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/UrbanMB22,
author = {Gregor Urban and
Christophe N. Magnan and
Pierre Baldi},
title = {SSpro/ACCpro 6: almost perfect prediction of protein secondary structure
and relative solvent accessibility using profiles, deep learning and
structural similarity},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {2064--2065},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac019},
doi = {10.1093/BIOINFORMATICS/BTAC019},
timestamp = {Wed, 27 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/UrbanMB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Vainberg-Slutskin22,
author = {Ilya Vainberg{-}Slutskin and
Noga Kowalsman and
Yael Silberberg and
Tal Cohen and
Jenia Gold and
Edith Kario and
Iddo Weiner and
Inbar Gahali{-}Sass and
Sharon Kredo{-}Russo and
Naomi B. Zak and
Merav Bassan},
title = {Exodus: sequencing-based pipeline for quantification of pooled variants},
journal = {Bioinform.},
volume = {38},
number = {12},
pages = {3288--3290},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac319},
doi = {10.1093/BIOINFORMATICS/BTAC319},
timestamp = {Wed, 27 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Vainberg-Slutskin22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ValierisDDDRS22,
author = {Renan Valieris and
Rodrigo D. Drummond and
Alexandre Defelicibus and
Emmanuel Dias{-}Neto and
Rafael Rosales and
Israel T. da Silva},
title = {A mixture model for determining SARS-Cov-2 variant composition in
pooled samples},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {1809--1815},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac047},
doi = {10.1093/BIOINFORMATICS/BTAC047},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ValierisDDDRS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VazquezSNKR22,
author = {Pavel Vazquez and
Kayoko Shoji and
Steffen Novik and
Stefan Krauss and
Simon Rayner},
title = {Globally Accessible Distributed Data Sharing {(GADDS):} a decentralized
{FAIR} platform to facilitate data sharing in the life sciences},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3812--3817},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac362},
doi = {10.1093/BIOINFORMATICS/BTAC362},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/VazquezSNKR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VerschaffeltCBM22,
author = {Pieter Verschaffelt and
James H. Collier and
Alexander Botzki and
Lennart Martens and
Peter Dawyndt and
Bart Mesuere},
title = {Unipept Visualizations: an interactive visualization library for biological
data},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {562--563},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab590},
doi = {10.1093/BIOINFORMATICS/BTAB590},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/VerschaffeltCBM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VinasALB22,
author = {Ram{\'{o}}n Vi{\~{n}}as and
Helena Andr{\'{e}}s{-}Terr{\'{e}} and
Pietro Li{\`{o}} and
Kevin Bryson},
title = {Adversarial generation of gene expression data},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {730--737},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab035},
doi = {10.1093/BIOINFORMATICS/BTAB035},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/VinasALB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VirgoulayRL22,
author = {Thimoth{\'{e}}e Virgoulay and
Fran{\c{c}}ois Rousset and
Rapha{\"{e}}l Leblois},
title = {Correction to: GSpace: an exact coalescence simulator of recombining
genomes under isolation by distance},
journal = {Bioinform.},
volume = {38},
number = {9},
pages = {2674},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac193},
doi = {10.1093/BIOINFORMATICS/BTAC193},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/VirgoulayRL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VogtSW22,
author = {Frank Vogt and
Gautam Shirsekar and
Detlef Weigel},
title = {vcf2gwas: Python {API} for comprehensive {GWAS} analysis using {GEMMA}},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {839--840},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab710},
doi = {10.1093/BIOINFORMATICS/BTAB710},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/VogtSW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VollgerKPE22,
author = {Mitchell R. Vollger and
Peter Kerpedjiev and
Adam M. Phillippy and
Evan E. Eichler},
title = {StainedGlass: interactive visualization of massive tandem repeat structures
with identity heatmaps},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {2049--2051},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac018},
doi = {10.1093/BIOINFORMATICS/BTAC018},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/VollgerKPE22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VoytikBWHBSM22,
author = {Eugenia Voytik and
Isabell Bludau and
Sander Willems and
Fynn M. Hansen and
Andreas{-}David Brunner and
Maximilian T. Strauss and
Matthias Mann},
title = {AlphaMap: an open-source Python package for the visual annotation
of proteomics data with sequence-specific knowledge},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {849--852},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab674},
doi = {10.1093/BIOINFORMATICS/BTAB674},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/VoytikBWHBSM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VulliardHKFSLND22,
author = {Loan Vulliard and
Joel Hancock and
Anton Kamnev and
Christopher W. Fell and
Joana Ferreira da Silva and
Joanna I Loizou and
Vanja Nagy and
Lo{\"{\i}}c Dupr{\'{e}} and
J{\"{o}}rg Menche},
title = {BioProfiling.jl: profiling biological perturbations with high-content
imaging in single cells and heterogeneous populations},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1692--1699},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab853},
doi = {10.1093/BIOINFORMATICS/BTAB853},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/VulliardHKFSLND22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WacquetL22,
author = {Guillaume Wacquet and
Alain Lefebvre},
title = {EcoTransLearn: an R-package to easily use transfer learning for ecological
studies - a plankton case study},
journal = {Bioinform.},
volume = {38},
number = {24},
pages = {5469--5471},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac703},
doi = {10.1093/BIOINFORMATICS/BTAC703},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WacquetL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WaeleCMW22,
author = {Gaetan De Waele and
Jim Clauwaert and
Gerben Menschaert and
Willem Waegeman},
title = {CpG Transformer for imputation of single-cell methylomes},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {597--603},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab746},
doi = {10.1093/BIOINFORMATICS/BTAB746},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WaeleCMW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WagholikarAZCMKBMCOGASM22,
author = {Kavishwar B. Wagholikar and
Layne Ainsworth and
David Zelle and
Kira Chaney and
Michael Mendis and
Jeffrey G. Klann and
Alexander J. Blood and
Angela Miller and
Rupendra Chulyadyo and
Michael Oates and
William J. Gordon and
Samuel J. Aronson and
Benjamin M. Scirica and
Shawn N. Murphy},
title = {I2b2-etl: Python application for importing electronic health data
into the informatics for integrating biology and the bedside platform},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4833--4836},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac595},
doi = {10.1093/BIOINFORMATICS/BTAC595},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WagholikarAZCMKBMCOGASM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WagnerAGZTP22,
author = {Naama Wagner and
Oren Avram and
Dafna Gold{-}Binshtok and
Ben Zerah and
Doron Teper and
Tal Pupko},
title = {Effectidor: an automated machine-learning-based web server for the
prediction of type-III secretion system effectors},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2341--2343},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac087},
doi = {10.1093/BIOINFORMATICS/BTAC087},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WagnerAGZTP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WagnerCOR22,
author = {Vincent Wagner and
Benjamin Castellaz and
Marco Oesting and
Nicole Radde},
title = {Quasi-Entropy Closure: a fast and reliable approach to close the moment
equations of the Chemical Master Equation},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4352--4359},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac501},
doi = {10.1093/BIOINFORMATICS/BTAC501},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WagnerCOR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WaldropCBPCHKBW22,
author = {Alexander M. Waldrop and
John B. Cheadle and
Kira Bradford and
Alexander Preiss and
Robert F. Chew and
Jonathan R. Holt and
Yaphet Kebede and
Nathan Braswell and
Matthew Watson and
Virginia Hench and
Andrew Crerar and
Chris M. Ball and
Carl Schreep and
P. J. Linebaugh and
Hannah Hiles and
Rebecca R. Boyles and
Chris Bizon and
Ashok Kumar Krishnamurthy and
Steven Cox},
title = {Dug: a semantic search engine leveraging peer-reviewed knowledge to
query biomedical data repositories},
journal = {Bioinform.},
volume = {38},
number = {12},
pages = {3252--3258},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac284},
doi = {10.1093/BIOINFORMATICS/BTAC284},
timestamp = {Sun, 11 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WaldropCBPCHKBW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WalterCZGHH22,
author = {Vonn Walter and
Hyo Young Choi and
Xiaobei Zhao and
Yan Gao and
Jeremiah Holt and
D. Neil Hayes},
title = {DiNAMIC.Duo: detecting somatic {DNA} copy number differences without
a normal reference},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4415--4417},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac542},
doi = {10.1093/BIOINFORMATICS/BTAC542},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WalterCZGHH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WanCD22,
author = {Hui Wan and
Liang Chen and
Minghua Deng},
title = {scNAME: neighborhood contrastive clustering with ancillary mask estimation
for scRNA-seq data},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1575--1583},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac011},
doi = {10.1093/BIOINFORMATICS/BTAC011},
timestamp = {Fri, 01 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WanCD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangA22,
author = {Yen{-}Wen Wang and
C{\'{e}}cile An{\'{e}}},
title = {{KIMGENS:} a novel method to estimate kinship in organisms with mixed
haploid diploid genetic systems robust to population structure},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3044--3050},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac293},
doi = {10.1093/BIOINFORMATICS/BTAC293},
timestamp = {Mon, 25 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangC22,
author = {Ye Wang and
Li Chen},
title = {DeepPerVar: a multi-modal deep learning framework for functional interpretation
of genetic variants in personal genome},
journal = {Bioinform.},
volume = {38},
number = {24},
pages = {5340--5351},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac696},
doi = {10.1093/BIOINFORMATICS/BTAC696},
timestamp = {Wed, 11 Sep 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangFLH22,
author = {Yizhuo Wang and
Christopher R. Flowers and
Ziyi Li and
Xuelin Huang},
title = {CondiS web app: imputation of censored lifetimes for machine learning-based
survival analysis},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4252--4254},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac461},
doi = {10.1093/BIOINFORMATICS/BTAC461},
timestamp = {Thu, 22 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangFLH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangGGAZMS22,
author = {Yucheng Wang and
Tyler J. Gorrie{-}Stone and
Olivia A. Grant and
Alexandria D. Andrayas and
Xiaojun Zhai and
Klaus D. McDonald{-}Maier and
Leonard C. Schalkwyk},
title = {InterpolatedXY: a two-step strategy to normalize {DNA} methylation
microarray data avoiding sex bias},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {3950--3957},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac436},
doi = {10.1093/BIOINFORMATICS/BTAC436},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangGGAZMS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangHHSR22,
author = {Wenxiu Wang and
Hamidreza Heydarian and
Teun A. P. M. Huijben and
Sjoerd Stallinga and
Bernd Rieger},
title = {Joint registration of multiple point clouds for fast particle fusion
in localization microscopy},
journal = {Bioinform.},
volume = {38},
number = {12},
pages = {3281--3287},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac320},
doi = {10.1093/BIOINFORMATICS/BTAC320},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangHHSR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangHKBXGWBSDS22,
author = {Yanan Wang and
Changyuan Hu and
Terry Kwok and
Christopher A. Bain and
Xiangyang Xue and
Robin B. Gasser and
Geoffrey I. Webb and
Alex Boussioutas and
Xian Shen and
Roger J. Daly and
Jiangning Song},
title = {DEMoS: a deep learning-based ensemble approach for predicting the
molecular subtypes of gastric adenocarcinomas from histopathological
images},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4206--4213},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac456},
doi = {10.1093/BIOINFORMATICS/BTAC456},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangHKBXGWBSDS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangHSXYLC22,
author = {Junjie Wang and
Jie Hu and
Huiting Sun and
Mengdie Xu and
Yun Yu and
Yun Liu and
Liang Cheng},
title = {{MGPLI:} exploring multigranular representations for protein-ligand
interaction prediction},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4859--4867},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac597},
doi = {10.1093/BIOINFORMATICS/BTAC597},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangHSXYLC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangJZNW22,
author = {Ruheng Wang and
Junru Jin and
Quan Zou and
Kenta Nakai and
Leyi Wei},
title = {Predicting protein-peptide binding residues via interpretable deep
learning},
journal = {Bioinform.},
volume = {38},
number = {13},
pages = {3351--3360},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac352},
doi = {10.1093/BIOINFORMATICS/BTAC352},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangJZNW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangLLCYSTGM22,
author = {Shaojing Wang and
Guoqiang Li and
Zitong Liao and
Yunke Cao and
Yuan Yun and
Zhaoying Su and
Xuefeng Tian and
Ziyu Gui and
Ting Ma},
title = {CnnPOGTP: a novel CNN-based predictor for identifying the optimal
growth temperatures of prokaryotes using only genomic \emph{k}-mers
distribution},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3106--3108},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac289},
doi = {10.1093/BIOINFORMATICS/BTAC289},
timestamp = {Tue, 28 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangLLCYSTGM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangLM22,
author = {Xiaoyan Wang and
Hongduo Liu and
Shuangge Ma},
title = {GEInfo: an {R} package for gene-environment interaction analysis incorporating
prior information},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3139--3140},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac301},
doi = {10.1093/BIOINFORMATICS/BTAC301},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangLM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangLPWZ22,
author = {Tianying Wang and
Wodan Ling and
Anna M. Plantinga and
Michael C. Wu and
Xiang Zhan},
title = {Testing microbiome association using integrated quantile regression
models},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {419--425},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab668},
doi = {10.1093/BIOINFORMATICS/BTAB668},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangLPWZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangLRPCRDGB22,
author = {Bo Wang and
Andy Law and
Tim Regan and
Nicholas Parkinson and
Joby Cole and
Clark D. Russell and
David H. Dockrell and
Michael U. Gutmann and
J. Kenneth Baillie},
title = {Systematic comparison of ranking aggregation methods for gene lists
in experimental results},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4927--4933},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac621},
doi = {10.1093/BIOINFORMATICS/BTAC621},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangLRPCRDGB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangLZ22,
author = {Yansu Wang and
Ximei Luo and
Quan Zou},
title = {Effector-GAN: prediction of fungal effector proteins based on pretrained
deep representation learning methods and generative adversarial networks},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3541--3548},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac374},
doi = {10.1093/BIOINFORMATICS/BTAC374},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangLZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangLZ22a,
author = {Yuge Wang and
Tianyu Liu and
Hongyu Zhao},
title = {ResPAN: a powerful batch correction model for scRNA-seq data through
residual adversarial networks},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {3942--3949},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac427},
doi = {10.1093/BIOINFORMATICS/BTAC427},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangLZ22a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangSHHZ22,
author = {Meiling Wang and
Wei Shao and
Xiaoke Hao and
Shuo Huang and
Daoqiang Zhang},
title = {Identify connectome between genotypes and brain network phenotypes
via deep self-reconstruction sparse canonical correlation analysis},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2323--2332},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac074},
doi = {10.1093/BIOINFORMATICS/BTAC074},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangSHHZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangTTWGA22,
author = {Jie Wang and
Nazia Tabassum and
Tanjin Taher Toma and
Yibo Wang and
Andreas Gahlmann and
Scott T. Acton},
title = {3D {GAN} image synthesis and dataset quality assessment for bacterial
biofilm},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4598--4604},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac529},
doi = {10.1093/BIOINFORMATICS/BTAC529},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangTTWGA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangW22,
author = {Xiaqiong Wang and
Yalu Wen},
title = {A penalized linear mixed model with generalized method of moments
estimators for complex phenotype prediction},
journal = {Bioinform.},
volume = {38},
number = {23},
pages = {5222--5228},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac659},
doi = {10.1093/BIOINFORMATICS/BTAC659},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangWZHY22,
author = {Xiao Wang and
Jia Wang and
Han Zhang and
Shenwei Huang and
Yanbin Yin},
title = {{HDMC:} a novel deep learning-based framework for removing batch effects
in single-cell RNA-seq data},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1295--1303},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab821},
doi = {10.1093/BIOINFORMATICS/BTAB821},
timestamp = {Thu, 22 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangWZHY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangWZLRWCL22,
author = {Qin Wang and
Jun Wei and
Yuzhe Zhou and
Mingzhi Lin and
Ruobing Ren and
Sheng Wang and
Shuguang Cui and
Zhen Li},
title = {Prior knowledge facilitates low homologous protein secondary structure
prediction with {DSM} distillation},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3574--3581},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac351},
doi = {10.1093/BIOINFORMATICS/BTAC351},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangWZLRWCL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangXZGLZLWWTWZ22,
author = {Shixiang Wang and
Yi Xiong and
Longfei Zhao and
Kai Gu and
Yin Li and
Fei Zhao and
Jianfeng Li and
Mingjie Wang and
Haitao Wang and
Ziyu Tao and
Tao Wu and
Yichao Zheng and
Xuejun Li and
Xue{-}Song Liu},
title = {UCSCXenaShiny: an {R/CRAN} package for interactive analysis of {UCSC}
Xena data},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {527--529},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab561},
doi = {10.1093/BIOINFORMATICS/BTAB561},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangXZGLZLWWTWZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangYMWL22,
author = {Yawei Wang and
Yuning Yang and
Zhiqiang Ma and
Ka{-}Chun Wong and
Xiangtao Li},
title = {{EDCNN:} identification of genome-wide RNA-binding proteins using
evolutionary deep convolutional neural network},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {678--686},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab739},
doi = {10.1093/BIOINFORMATICS/BTAB739},
timestamp = {Mon, 09 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangYMWL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangYWZG22,
author = {Xingze Wang and
Guoxian Yu and
Jun Wang and
Azlan Mohd Zain and
Wei Guo},
title = {Lung cancer subtype diagnosis using weakly-paired multi-omics data},
journal = {Bioinform.},
volume = {38},
number = {22},
pages = {5092--5099},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac643},
doi = {10.1093/BIOINFORMATICS/BTAC643},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangYWZG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangZD22,
author = {Weiwen Wang and
Xiwen Zhang and
Dao{-}Qing Dai},
title = {springD2A: capturing uncertainty in disease-drug association prediction
with model integration},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1353--1360},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab820},
doi = {10.1093/BIOINFORMATICS/BTAB820},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangZD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangZYLTXGLDYHL22,
author = {Xi Wang and
Xiang Zhou and
Qinglin Yan and
Shaofeng Liao and
Wenqin Tang and
Peiyu Xu and
Yangzhenyu Gao and
Qian Li and
Zhihui Dou and
Weishan Yang and
Beifang Huang and
Jinhong Li and
Zhuqing Zhang},
title = {{LLPSDB} v2.0: an updated database of proteins undergoing liquid-liquid
phase separation \emph{in vitro}},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {2010--2014},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac026},
doi = {10.1093/BIOINFORMATICS/BTAC026},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangZYLTXGLDYHL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangZZS22,
author = {Hai{-}Yun Wang and
Jian{-}Ping Zhao and
Chun{-}Hou Zheng and
Yan{-}Sen Su},
title = {scCNC: a method based on capsule network for clustering scRNA-seq
data},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3703--3709},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac393},
doi = {10.1093/BIOINFORMATICS/BTAC393},
timestamp = {Wed, 04 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangZZS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WarmerdamLDF22,
author = {Robert Warmerdam and
Pauline Lanting and
Patrick Deelen and
Lude Franke},
title = {Id{\'{e}}fix: identifying accidental sample mix-ups in biobanks
using polygenic scores},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1059--1066},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab783},
doi = {10.1093/BIOINFORMATICS/BTAB783},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WarmerdamLDF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WegnerJLKZSJLKSHK22,
author = {Philipp Wegner and
Geena Mariya Jose and
Vanessa Lage{-}Rupprecht and
Sepehr Golriz Khatami and
Bide Zhang and
Stephan Springstubbe and
Marc Jacobs and
Thomas Linden and
Cindy Ku and
Bruce Schultz and
Martin Hofmann{-}Apitius and
Alpha Tom Kodamullil},
title = {Common data model for {COVID-19} datasets},
journal = {Bioinform.},
volume = {38},
number = {24},
pages = {5466--5468},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac651},
doi = {10.1093/BIOINFORMATICS/BTAC651},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WegnerJLKZSJLKSHK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WegnerSUDSGSBSK22,
author = {Philipp Wegner and
Sebastian Schaaf and
Mischa Uebachs and
Daniel Domingo{-}Fern{\'{a}}ndez and
Yasamin Salimi and
Stephan Gebel and
Astghik Sargsyan and
Colin Birkenbihl and
Stephan Springstubbe and
Thomas Klockgether and
Juliane Fluck and
Martin Hofmann{-}Apitius and
Alpha Tom Kodamullil},
title = {Integrative data semantics through a model-enabled data stewardship},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3850--3852},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac375},
doi = {10.1093/BIOINFORMATICS/BTAC375},
timestamp = {Mon, 24 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WegnerSUDSGSBSK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WeiARML22,
author = {Chih{-}Hsuan Wei and
Alexis Allot and
Kevin Riehle and
Aleksandar Milosavljevic and
Zhiyong Lu},
title = {tmVar 3.0: an improved variant concept recognition and normalization
tool},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4449--4451},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac537},
doi = {10.1093/BIOINFORMATICS/BTAC537},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WeiARML22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WeiDW22,
author = {Xiajie Wei and
Jiayi Dong and
Fei Wang},
title = {scPreGAN, a deep generative model for predicting the response of single-cell
expression to perturbation},
journal = {Bioinform.},
volume = {38},
number = {13},
pages = {3377--3384},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac357},
doi = {10.1093/BIOINFORMATICS/BTAC357},
timestamp = {Mon, 25 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WeiDW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WeiLJW22,
author = {Xin Wei and
Ziyi Li and
Hongkai Ji and
Hao Wu},
title = {EDClust: an {EM-MM} hybrid method for cell clustering in multiple-subject
single-cell {RNA} sequencing},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2692--2699},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac168},
doi = {10.1093/BIOINFORMATICS/BTAC168},
timestamp = {Mon, 13 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WeiLJW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WeiLLWL22,
author = {Yu Wei and
Shanshan Li and
Zhonglin Li and
Ziwei Wan and
Jianping Lin},
title = {Interpretable-ADMET: a web service for {ADMET} prediction and optimization
based on deep neural representation},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2863--2871},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac192},
doi = {10.1093/BIOINFORMATICS/BTAC192},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WeiLLWL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WeiYSMW22,
author = {Lesong Wei and
Xiucai Ye and
Tetsuya Sakurai and
Zengchao Mu and
Leyi Wei},
title = {ToxIBTL: prediction of peptide toxicity based on information bottleneck
and transfer learning},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1514--1524},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac006},
doi = {10.1093/BIOINFORMATICS/BTAC006},
timestamp = {Fri, 22 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WeiYSMW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WeiZTY22,
author = {Yanming Wei and
Quan Zou and
Furong Tang and
Liang Yu},
title = {{WMSA:} a novel method for multiple sequence alignment of {DNA} sequences},
journal = {Bioinform.},
volume = {38},
number = {22},
pages = {5019--5025},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac658},
doi = {10.1093/BIOINFORMATICS/BTAC658},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WeiZTY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WeidnerSWILK22,
author = {Felix M. Weidner and
Julian D. Schwab and
Silke D. Werle and
Nensi Ikonomi and
Ludwig Lausser and
Hans A. Kestler},
title = {Response to the letter to the editor: On the feasibility of dynamical
analysis of network models of biochemical regulation},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3676},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac318},
doi = {10.1093/BIOINFORMATICS/BTAC318},
timestamp = {Mon, 08 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WeidnerSWILK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WeitzWKELGER22,
author = {Philippe Weitz and
Yinxi Wang and
Kimmo Kartasalo and
Lars Egevad and
Johan Lindberg and
Henrik Gr{\"{o}}nberg and
Martin Eklund and
Mattias Rantalainen},
title = {Transcriptome-wide prediction of prostate cancer gene expression from
histopathology images using co-expression-based convolutional neural
networks},
journal = {Bioinform.},
volume = {38},
number = {13},
pages = {3462--3469},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac343},
doi = {10.1093/BIOINFORMATICS/BTAC343},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WeitzWKELGER22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WenJZ22,
author = {Bo Wen and
Eric J. Jaehnig and
Bing Zhang},
title = {OmicsEV: a tool for comprehensive quality evaluation of omics data
tables},
journal = {Bioinform.},
volume = {38},
number = {24},
pages = {5463--5465},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac698},
doi = {10.1093/BIOINFORMATICS/BTAC698},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WenJZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WertenbroekRXTD22,
author = {Rick Wertenbroek and
Simone Rubinacci and
Ioannis Xenarios and
Yann Thoma and
Olivier Delaneau},
title = {{XSI} - a genotype compression tool for compressive genomics in large
biobanks},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3778--3784},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac413},
doi = {10.1093/BIOINFORMATICS/BTAC413},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WertenbroekRXTD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WiedemannKMZBSA22,
author = {Jakub Wiedemann and
Jacek Kaczor and
Maciej Milostan and
Tomasz Zok and
Jacek Blazewicz and
Marta Szachniuk and
Maciej Antczak},
title = {RNAloops: a database of {RNA} multiloops},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4200--4205},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac484},
doi = {10.1093/BIOINFORMATICS/BTAC484},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WiedemannKMZBSA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WienbrandtE22,
author = {Lars Wienbrandt and
David Ellinghaus},
title = {\emph{EagleImp}: fast and accurate genome-wide phasing and imputation
in a single tool},
journal = {Bioinform.},
volume = {38},
number = {22},
pages = {4999--5006},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac637},
doi = {10.1093/BIOINFORMATICS/BTAC637},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WienbrandtE22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WiltonS22,
author = {Richard Wilton and
Alexander S. Szalay},
title = {Performance optimization in {DNA} short-read alignment},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2081--2087},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac066},
doi = {10.1093/BIOINFORMATICS/BTAC066},
timestamp = {Wed, 18 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WiltonS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WindelsMP22,
author = {Sam F. L. Windels and
No{\"{e}}l Malod{-}Dognin and
Natasa Przulj},
title = {Identifying cellular cancer mechanisms through pathway-driven data
integration},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4344--4351},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac493},
doi = {10.1093/BIOINFORMATICS/BTAC493},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WindelsMP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WirthMTD22,
author = {Wytamma Wirth and
Simon Mutch and
Robert Turnbull and
Sebasti{\'{a}}n Duch{\^{e}}ne},
title = {Phytest: quality control for phylogenetic analyses},
journal = {Bioinform.},
volume = {38},
number = {22},
pages = {5124--5125},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac664},
doi = {10.1093/BIOINFORMATICS/BTAC664},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WirthMTD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WittigMHABBDGGN22,
author = {Alice Wittig and
F{\'{a}}bio Miranda and
Martin H{\"{o}}lzer and
Tom Altenburg and
Jakub M. Bartoszewicz and
Sebastian Beyvers and
Marius A. Dieckmann and
Ulrich Genske and
Sven H. Giese and
Melania Nowicka and
Hugues Richard and
Henning Schiebenhoefer and
Anna{-}Juliane Schmachtenberg and
Paul Sieben and
Ming Tang and
Julius Tembrockhaus and
Bernhard Y. Renard and
Stephan Fuchs},
title = {CovRadar: continuously tracking and filtering SARS-CoV-2 mutations
for genomic surveillance},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4223--4225},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac411},
doi = {10.1093/BIOINFORMATICS/BTAC411},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WittigMHABBDGGN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WongL22,
author = {Christina Wong and
Bo Li},
title = {AutoCAT: automated cancer-associated TCRs discovery from TCR-seq data},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {589--591},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab661},
doi = {10.1093/BIOINFORMATICS/BTAB661},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WongL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Wright22,
author = {Erik Scott Wright},
title = {FindNonCoding: rapid and simple detection of non-coding RNAs in genomes},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {841--843},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab708},
doi = {10.1093/BIOINFORMATICS/BTAB708},
timestamp = {Wed, 20 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Wright22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WuLWH22,
author = {Jiashuo Wu and
Xiangmei Li and
Qian Wang and
Junwei Han},
title = {DRviaSPCN: a software package for drug repurposing in cancer via a
subpathway crosstalk network},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4975--4977},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac611},
doi = {10.1093/BIOINFORMATICS/BTAC611},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WuLWH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WuRFLAH22,
author = {Gang Wu and
Marc D. Ruben and
Lauren J. Francey and
Yin Yeng Lee and
Ron C. Anafi and
John B. Hogenesch},
title = {An \emph{in silico} genome-wide screen for circadian clock strength
in human samples},
journal = {Bioinform.},
volume = {38},
number = {24},
pages = {5375--5382},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac686},
doi = {10.1093/BIOINFORMATICS/BTAC686},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WuRFLAH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WuZLWTC22,
author = {Qiong Wu and
Xubin Zheng and
Kwong{-}Sak Leung and
Man Hon Wong and
Stephen Kwok{-}Wing Tsui and
Lixin Cheng},
title = {meGPS: a multi-omics signature for hepatocellular carcinoma detection
integrating methylome and transcriptome data},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3513--3522},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac379},
doi = {10.1093/BIOINFORMATICS/BTAC379},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WuZLWTC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X22,
title = {Correction to: MetaSquare: an integrated metadatabase of 16S rRNA
gene amplicon for microbiome taxonomic classification},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3154},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac285},
doi = {10.1093/BIOINFORMATICS/BTAC285},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/X22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X22a,
title = {Correction to: Topological analysis as a tool for detection of abnormalities
in protein-protein interaction data},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4997},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac607},
doi = {10.1093/BIOINFORMATICS/BTAC607},
timestamp = {Fri, 17 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X22a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X22b,
title = {Correction to: Integrative data semantics through a model-enabled
data stewardship},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4998},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac635},
doi = {10.1093/BIOINFORMATICS/BTAC635},
timestamp = {Fri, 17 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X22b.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X22c,
title = {Correction to: Efficient permutation-based genome-wide association
studies for normal and skewed phenotypic distributions},
journal = {Bioinform.},
volume = {38},
number = {22},
pages = {5149},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac690},
doi = {10.1093/BIOINFORMATICS/BTAC690},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/X22c.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/X22d,
title = {Correction to: plotsr: visualizing structural similarities and rearrangements
between multiple genomes},
journal = {Bioinform.},
volume = {38},
number = {23},
pages = {5328},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac661},
doi = {10.1093/BIOINFORMATICS/BTAC661},
timestamp = {Fri, 17 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/X22d.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XiaoCHWCY22,
author = {Jiashun Xiao and
Mingxuan Cai and
Xianghong Hu and
Xiang Wan and
Gang Chen and
Can Yang},
title = {{XPXP:} improving polygenic prediction by cross-population and cross-phenotype
analysis},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {1947--1955},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac029},
doi = {10.1093/BIOINFORMATICS/BTAC029},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/XiaoCHWCY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XiaoKPY22,
author = {Di Xiao and
Hani Jieun Kim and
Ignatius Pang and
Pengyi Yang},
title = {Functional analysis of the stable phosphoproteome reveals cancer vulnerabilities},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {1956--1963},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac015},
doi = {10.1093/BIOINFORMATICS/BTAC015},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/XiaoKPY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XiaoL22,
author = {Zhixia Xiao and
Hon{-}Ming Lam},
title = {ShinySyn: a Shiny/R application for the interactive visualization
and integration of macro- and micro-synteny data},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4406--4408},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac503},
doi = {10.1093/BIOINFORMATICS/BTAC503},
timestamp = {Tue, 06 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/XiaoL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XieHHZ22,
author = {Shaohui Xie and
Xiaotian He and
Shan He and
Zexuan Zhu},
title = {{CURC:} a CUDA-based reference-free read compressor},
journal = {Bioinform.},
volume = {38},
number = {12},
pages = {3294--3296},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac333},
doi = {10.1093/BIOINFORMATICS/BTAC333},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/XieHHZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XieX22,
author = {Ziwei Xie and
Jinbo Xu},
title = {Deep graph learning of inter-protein contacts},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {947--953},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab761},
doi = {10.1093/BIOINFORMATICS/BTAB761},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/XieX22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XinLJZWBQ22,
author = {Ying Xin and
Pin Lyu and
Junyao Jiang and
Fengquan Zhou and
Jie Wang and
Seth Blackshaw and
Jiang Qian},
title = {LRLoop: a method to predict feedback loops in cell-cell communication},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4117--4126},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac447},
doi = {10.1093/BIOINFORMATICS/BTAC447},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/XinLJZWBQ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XingYLZZGHY22,
author = {Xiaohan Xing and
Fan Yang and
Hang Li and
Jun Zhang and
Yu Zhao and
Mingxuan Gao and
Junzhou Huang and
Jianhua Yao},
title = {Multi-level attention graph neural network based on co-expression
gene modules for disease diagnosis and prognosis},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2178--2186},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac088},
doi = {10.1093/BIOINFORMATICS/BTAC088},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/XingYLZZGHY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XiongLWFZXLHLCJ22,
author = {Jiacheng Xiong and
Zhaojun Li and
Guangchao Wang and
Zunyun Fu and
Feisheng Zhong and
Tingyang Xu and
Xiaomeng Liu and
Ziming Huang and
Xiaohong Liu and
Kaixian Chen and
Hualiang Jiang and
Mingyue Zheng},
title = {Multi-instance learning of graph neural networks for aqueous pKa prediction},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {792--798},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab714},
doi = {10.1093/BIOINFORMATICS/BTAB714},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/XiongLWFZXLHLCJ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XuBSH22,
author = {Yang Xu and
Simon J. Baumgart and
Christian M. Stegmann and
Sikander Hayat},
title = {{MACA:} marker-based automatic cell-type annotation for single-cell
expression data},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1756--1760},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab840},
doi = {10.1093/BIOINFORMATICS/BTAB840},
timestamp = {Wed, 31 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/XuBSH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XuDM22,
author = {Yang Xu and
Priyojit Das and
Rachel Patton McCord},
title = {{SMILE:} mutual information learning for integration of single-cell
omics data},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {476--486},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab706},
doi = {10.1093/BIOINFORMATICS/BTAB706},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/XuDM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XuLX22,
author = {Zhongyuan Xu and
Jiawei Luo and
Zehao Xiong},
title = {scSemiGAN: a single-cell semi-supervised annotation and dimensionality
reduction framework based on generative adversarial network},
journal = {Bioinform.},
volume = {38},
number = {22},
pages = {5042--5048},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac652},
doi = {10.1093/BIOINFORMATICS/BTAC652},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/XuLX22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XuNAG22,
author = {Yuanwei Xu and
Katrina Nash and
Animesh Acharjee and
Georgios V. Gkoutos},
title = {{CACONET:} a novel classification framework for microbial correlation
networks},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1639--1647},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab879},
doi = {10.1093/BIOINFORMATICS/BTAB879},
timestamp = {Fri, 13 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/XuNAG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XueZWX22,
author = {Min{-}Qi Xue and
Xi{-}Liang Zhu and
Ge Wang and
Ying{-}Ying Xu},
title = {DULoc: quantitatively unmixing protein subcellular location patterns
in immunofluorescence images based on deep learning features},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {827--833},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab730},
doi = {10.1093/BIOINFORMATICS/BTAB730},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/XueZWX22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YaacoubGGSC22,
author = {Jean Charle Yaacoub and
James Gleave and
Francesco Gentile and
Abraham C. Stern and
Artem Cherkasov},
title = {{DD-GUI:} a graphical user interface for deep learning-accelerated
virtual screening of large chemical libraries (Deep Docking)},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1146--1148},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab771},
doi = {10.1093/BIOINFORMATICS/BTAB771},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YaacoubGGSC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YaishO22,
author = {Ofir Yaish and
Yaron Orenstein},
title = {Computational modeling of mRNA degradation dynamics using deep neural
networks},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {1087--1101},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab800},
doi = {10.1093/BIOINFORMATICS/BTAB800},
timestamp = {Wed, 23 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YaishO22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YanDLZWW22,
author = {Cheng Yan and
Guihua Duan and
Na Li and
Lishen Zhang and
Fang{-}Xiang Wu and
Jianxin Wang},
title = {{PDMDA:} predicting deep-level miRNA-disease associations with graph
neural networks and sequence features},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2226--2234},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac077},
doi = {10.1093/BIOINFORMATICS/BTAC077},
timestamp = {Wed, 18 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YanDLZWW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YanLGCWL22,
author = {Ke Yan and
Hongwu Lv and
Yichen Guo and
Yongyong Chen and
Hao Wu and
Bin Liu},
title = {TPpred-ATMV: therapeutic peptide prediction by adaptive multi-view
tensor learning model},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2712--2718},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac200},
doi = {10.1093/BIOINFORMATICS/BTAC200},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YanLGCWL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YangCK22,
author = {Dongchan Yang and
Taesu Chung and
Dongsup Kim},
title = {DeepLUCIA: predicting tissue-specific chromatin loops using Deep Learning-based
Universal Chromatin Interaction Annotator},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3501--3512},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac373},
doi = {10.1093/BIOINFORMATICS/BTAC373},
timestamp = {Mon, 08 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YangCK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YangCWWJZL22,
author = {Hai Yang and
Rui Chen and
Quan Wang and
Qiang Wei and
Ying Ji and
Xue Zhong and
Bingshan Li},
title = {{TVAR:} assessing tissue-specific functional effects of non-coding
variants with deep learning},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4697--4704},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac608},
doi = {10.1093/BIOINFORMATICS/BTAC608},
timestamp = {Mon, 15 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YangCWWJZL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YangMZZWZ22,
author = {Runmin Yang and
Jingjing Ma and
Shu Zhang and
Yu Zheng and
Lusheng Wang and
Daming Zhu},
title = {mzMD: visualization-oriented {MS} data storage and retrieval},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2333--2340},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac098},
doi = {10.1093/BIOINFORMATICS/BTAC098},
timestamp = {Thu, 10 Nov 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YangMZZWZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YangSVHLC22,
author = {Ran Yang and
Alexandra M. Stendahl and
Katinka A Vigh{-}Conrad and
Madison Held and
Ana C. Lima and
Donald F. Conrad},
title = {{SATINN:} an automated neural network-based classification of testicular
sections allows for high-throughput histopathology of mouse mutants},
journal = {Bioinform.},
volume = {38},
number = {23},
pages = {5288--5298},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac673},
doi = {10.1093/BIOINFORMATICS/BTAC673},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YangSVHLC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YangYS22,
author = {Bo Yang and
Yan Yang and
Xueping Su},
title = {Deep structure integrative representation of multi-omics data for
cancer subtyping},
journal = {Bioinform.},
volume = {38},
number = {13},
pages = {3337--3342},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac345},
doi = {10.1093/BIOINFORMATICS/BTAC345},
timestamp = {Mon, 25 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YangYS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YaoSJWW22,
author = {Junfeng Yao and
Wen Sun and
ZhongQuan Jian and
Qingqiang Wu and
Xiaoli Wang},
title = {Effective knowledge graph embeddings based on multidirectional semantics
relations for polypharmacy side effects prediction},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2315--2322},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac094},
doi = {10.1093/BIOINFORMATICS/BTAC094},
timestamp = {Wed, 28 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YaoSJWW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YeLQZGWXJZP22,
author = {Sifan Ye and
Congyu Lu and
Ye Qiu and
Heping Zheng and
Xingyi Ge and
Aiping Wu and
Zanxian Xia and
Taijiao Jiang and
Haizhen Zhu and
Yousong Peng},
title = {An atlas of human viruses provides new insights into diversity and
tissue tropism of human viruses},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3087--3093},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac275},
doi = {10.1093/BIOINFORMATICS/BTAC275},
timestamp = {Tue, 28 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YeLQZGWXJZP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YeTHKMTLCT22,
author = {Cheng Ye and
Bryan Thornlow and
Angie S. Hinrichs and
Alexander Kramer and
Cade Mirchandani and
Devika Torvi and
Robert Lanfear and
Russell Corbett{-}Detig and
Yatish Turakhia},
title = {matOptimize: a parallel tree optimization method enables online phylogenetics
for SARS-CoV-2},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3734--3740},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac401},
doi = {10.1093/BIOINFORMATICS/BTAC401},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YeTHKMTLCT22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YehASD22,
author = {Chiann{-}Ling C. Yeh and
Clara J. Amorosi and
Soyeon Showman and
Maitreya J. Dunham},
title = {PacRAT: a program to improve barcode-variant mapping from PacBio long
reads using multiple sequence alignment},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2927--2929},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac165},
doi = {10.1093/BIOINFORMATICS/BTAC165},
timestamp = {Mon, 13 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YehASD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YehL22,
author = {Yang{-}Ming Yeh and
Yi{-}Chang Lu},
title = {MSRCall: a multi-scale deep neural network to basecall Oxford Nanopore
sequences},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {3877--3884},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac435},
doi = {10.1093/BIOINFORMATICS/BTAC435},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YehL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YeungR22,
author = {Jason Yeung and
Andrew L. Routh},
title = {\emph{ViReMaShiny}: an interactive application for analysis of viral
recombination data},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4420--4422},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac522},
doi = {10.1093/BIOINFORMATICS/BTAC522},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YeungR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YiCB22,
author = {Ren Yi and
Kyunghyun Cho and
Richard Bonneau},
title = {NetTIME: a multitask and base-pair resolution framework for improved
transcription factor binding site prediction},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4762--4770},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac569},
doi = {10.1093/BIOINFORMATICS/BTAC569},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YiCB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YiWZXQZHC22,
author = {Jia{-}Cai Yi and
Chengkun Wu and
Xiao{-}Chen Zhang and
Xinyi Xiao and
Yanlong Qiu and
Wentao Zhao and
Tingjun Hou and
Dong{-}Sheng Cao},
title = {{MICER:} a pre-trained encoder-decoder architecture for molecular
image captioning},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4562--4572},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac545},
doi = {10.1093/BIOINFORMATICS/BTAC545},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YiWZXQZHC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YilmazFKCT22,
author = {Serhan Yilmaz and
Mohamad Fakhouri and
Mehmet Koyut{\"{u}}rk and
A. Erc{\"{u}}ment {\c{C}}i{\c{c}}ek and
{\"{O}}znur Tastan},
title = {Uncovering complementary sets of variants for predicting quantitative
phenotypes},
journal = {Bioinform.},
volume = {38},
number = {4},
pages = {908--917},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab803},
doi = {10.1093/BIOINFORMATICS/BTAB803},
timestamp = {Sat, 20 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YilmazFKCT22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YinLFZZZJL22,
author = {Qijin Yin and
Qiao Liu and
Zhuoran Fu and
Wanwen Zeng and
Boheng Zhang and
Xuegong Zhang and
Rui Jiang and
Hairong Lv},
title = {scGraph: a graph neural network-based approach to automatically identify
cell types},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {2996--3003},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac199},
doi = {10.1093/BIOINFORMATICS/BTAC199},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YinLFZZZJL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YoonJLK22,
author = {Wonjin Yoon and
Richard Jackson and
Aron Lagerberg and
Jaewoo Kang},
title = {Sequence tagging for biomedical extractive question answering},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3794--3801},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac397},
doi = {10.1093/BIOINFORMATICS/BTAC397},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YoonJLK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YouCS22,
author = {Yupei You and
Michael B. Clark and
Heejung Shim},
title = {NanoSplicer: accurate identification of splice junctions using Oxford
Nanopore sequencing},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3741--3748},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac359},
doi = {10.1093/BIOINFORMATICS/BTAC359},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YouCS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YuD22,
author = {Zhenhua Yu and
Fang Du},
title = {{AMC:} accurate mutation clustering from single-cell {DNA} sequencing
data},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1732--1734},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab857},
doi = {10.1093/BIOINFORMATICS/BTAB857},
timestamp = {Thu, 21 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YuD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YuH22,
author = {Huaxu Yu and
Tao Huan},
title = {{MAFFIN:} metabolomics sample normalization using maximal density
fold change with high-quality metabolic features and corrected signal
intensities},
journal = {Bioinform.},
volume = {38},
number = {13},
pages = {3429--3437},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac355},
doi = {10.1093/BIOINFORMATICS/BTAC355},
timestamp = {Mon, 25 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YuH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YuL22,
author = {Jinge Yu and
Xiangyu Luo},
title = {Identification of cell-type-specific spatially variable genes accounting
for excess zeros},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4135--4144},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac457},
doi = {10.1093/BIOINFORMATICS/BTAC457},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YuL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YuY22,
author = {Hongyang Yu and
Hongjiang C. Yu},
title = {Powerful molecule generation with simple ConvNet},
journal = {Bioinform.},
volume = {38},
number = {13},
pages = {3438--3443},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac332},
doi = {10.1093/BIOINFORMATICS/BTAC332},
timestamp = {Fri, 08 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YuY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YuanCD22,
author = {Musu Yuan and
Liang Chen and
Minghua Deng},
title = {scMRA: a robust deep learning method to annotate scRNA-seq data with
multiple reference datasets},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {738--745},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab700},
doi = {10.1093/BIOINFORMATICS/BTAB700},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YuanCD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YueH22,
author = {Ye Yue and
Yi{-}Juan Hu},
title = {A new approach to testing mediation of the microbiome at both the
community and individual taxon levels},
journal = {Bioinform.},
volume = {38},
number = {12},
pages = {3173--3180},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac310},
doi = {10.1093/BIOINFORMATICS/BTAC310},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YueH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZabelkinYBA22,
author = {Alexey Zabelkin and
Yulia Yakovleva and
Olga Bochkareva and
Nikita Alexeev},
title = {PaReBrick: PArallel REarrangements and BReaks identification toolkit},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {357--363},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab691},
doi = {10.1093/BIOINFORMATICS/BTAB691},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZabelkinYBA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZadeUSSA22,
author = {Ramin Shirali Hossein Zade and
Aysun Urhan and
Alvaro Assis de Souza and
Akash Singh and
Thomas Abeel},
title = {{HAT:} haplotype assembly tool using short and error-prone long reads},
journal = {Bioinform.},
volume = {38},
number = {24},
pages = {5352--5359},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac702},
doi = {10.1093/BIOINFORMATICS/BTAC702},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZadeUSSA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZengGH22,
author = {Wenhuan Zeng and
Anupam Gautam and
Daniel H. Huson},
title = {DeepToA: an ensemble deep-learning approach to predicting the theater
of activity of a microbiome},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4670--4676},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac584},
doi = {10.1093/BIOINFORMATICS/BTAC584},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZengGH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangCSDXCZ22,
author = {Zilong Zhang and
Feifei Cui and
Wei Su and
Lijun Dou and
Anqi Xu and
Chen Cao and
Quan Zou},
title = {webSCST: an interactive web application for single-cell RNA-sequencing
data and spatial transcriptomic data integration},
journal = {Bioinform.},
volume = {38},
number = {13},
pages = {3488--3489},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac350},
doi = {10.1093/BIOINFORMATICS/BTAC350},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangCSDXCZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangCYXWSL22,
author = {Hao Zhang and
Qixin Chang and
Zekun Yin and
Xiaoming Xu and
Yanjie Wei and
Bertil Schmidt and
Weiguo Liu},
title = {RabbitV: fast detection of viruses and microorganisms in sequencing
data on multi-core architectures},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2932--2933},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac187},
doi = {10.1093/BIOINFORMATICS/BTAC187},
timestamp = {Mon, 13 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangCYXWSL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangG22,
author = {Mengqi Zhang and
F. Richard Guo},
title = {{BSDE:} barycenter single-cell differential expression for case-control
studies},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2765--2772},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac171},
doi = {10.1093/BIOINFORMATICS/BTAC171},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangLCCS22,
author = {Shuyi Zhang and
Jacob R. Leistico and
Raymond J. Cho and
Jeffrey B. Cheng and
Jun S. Song},
title = {Spectral clustering of single-cell multi-omics data on multilayer
graphs},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3600--3608},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac378},
doi = {10.1093/BIOINFORMATICS/BTAC378},
timestamp = {Mon, 08 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangLCCS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangLCWYHD22,
author = {Lulu Zhang and
Xiao Liu and
Xiaoxiang Chen and
Antony R. Warden and
Youyi Yu and
Baozhen Huang and
Xianting Ding},
title = {SCANCell reveals diverse inter-cluster interaction patterns in systemic
lupus erythematosus across the disease spectrum},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1361--1368},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab713},
doi = {10.1093/BIOINFORMATICS/BTAB713},
timestamp = {Tue, 15 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangLCWYHD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangLMZW22,
author = {Ruiyi Zhang and
Yunan Luo and
Jianzhu Ma and
Ming Zhang and
Sheng Wang},
title = {scPretrain: multi-task self-supervised learning for cell-type classification},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1607--1614},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac007},
doi = {10.1093/BIOINFORMATICS/BTAC007},
timestamp = {Tue, 26 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangLMZW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangLZCL22,
author = {Wei Zhang and
Aiyi Liu and
Zhiwei Zhang and
Guanjie Chen and
Qizhai Li},
title = {An adaptive direction-assisted test for microbiome compositional data},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3493--3500},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac361},
doi = {10.1093/BIOINFORMATICS/BTAC361},
timestamp = {Sun, 24 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangLZCL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangM22,
author = {Chao Zhang and
Siavash Mirarab},
title = {ASTRAL-Pro 2: ultrafast species tree reconstruction from multi-copy
gene family trees},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4949--4950},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac620},
doi = {10.1093/BIOINFORMATICS/BTAC620},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangNHNLW22,
author = {Jun Zhang and
Fan Nie and
Neng Huang and
Peng Ni and
Feng Luo and
Jianxin Wang},
title = {Fec: a fast error correction method based on two-rounds overlapping
and caching},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4629--4632},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac565},
doi = {10.1093/BIOINFORMATICS/BTAC565},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangNHNLW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangPKLDZ22,
author = {Peter Zhang and
Alida Palmisano and
Ravindra Kumar and
Ming{-}Chung Li and
James H. Doroshow and
Yingdong Zhao},
title = {TPWshiny: an interactive R/Shiny app to explore cell line transcriptional
responses to anti-cancer drugs},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {570--572},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab619},
doi = {10.1093/BIOINFORMATICS/BTAB619},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangPKLDZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangSMAKSQQ22,
author = {Yun Zhang and
Hao Sun and
Aishwarya Mandava and
Brian D. Aevermann and
Tobias R. Kollmann and
Richard H. Scheuermann and
Xing Qiu and
Yu Qian},
title = {FastMix: a versatile data integration pipeline for cell type-specific
biomarker inference},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4735--4744},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac585},
doi = {10.1093/BIOINFORMATICS/BTAC585},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangSMAKSQQ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangWSZ22,
author = {Ke Zhang and
Chenxi Wang and
Liping Sun and
Jie Zheng},
title = {Prediction of gene co-expression from chromatin contacts with graph
attention network},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4457--4465},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac535},
doi = {10.1093/BIOINFORMATICS/BTAC535},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangWSZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangWZZZW22,
author = {Pengyu Zhang and
Yingfu Wu and
Haoru Zhou and
Bing Zhou and
Hongming Zhang and
Hao Wu},
title = {CLNN-loop: a deep learning model to predict CTCF-mediated chromatin
loops in the different cell lines and CTCF-binding sites {(CBS)} pair
types},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4497--4504},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac575},
doi = {10.1093/BIOINFORMATICS/BTAC575},
timestamp = {Fri, 08 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangWZZZW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangXH22,
author = {Jasper Zhongyuan Zhang and
Wei Xu and
Pingzhao Hu},
title = {Tightly integrated multiomics-based deep tensor survival model for
time-to-event prediction},
journal = {Bioinform.},
volume = {38},
number = {12},
pages = {3259--3266},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac286},
doi = {10.1093/BIOINFORMATICS/BTAC286},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangXH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangYCL22,
author = {Jun Zhang and
Ke Yan and
Qingcai Chen and
Bin Liu},
title = {PreRBP-TL: prediction of species-specific RNA-binding proteins based
on transfer learning},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2135--2143},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac106},
doi = {10.1093/BIOINFORMATICS/BTAC106},
timestamp = {Fri, 29 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangYCL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangYHLHWFZWWW22,
author = {Shanzhuo Zhang and
Zhiyuan Yan and
Yueyang Huang and
Lihang Liu and
Donglong He and
Wei Wang and
Xiaomin Fang and
Xiaonan Zhang and
Fan Wang and
Hua Wu and
Haifeng Wang},
title = {HelixADMET: a robust and endpoint extensible {ADMET} system incorporating
self-supervised knowledge transfer},
journal = {Bioinform.},
volume = {38},
number = {13},
pages = {3444--3453},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac342},
doi = {10.1093/BIOINFORMATICS/BTAC342},
timestamp = {Thu, 08 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangYHLHWFZWWW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangYWSFMW22,
author = {Shuangquan Zhang and
Lili Yang and
Xiaotian Wu and
Nan Sheng and
Yuan Fu and
Anjun Ma and
Yan Wang},
title = {MMGraph: a multiple motif predictor based on graph neural network
and coexisting probability for ATAC-seq data},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4636--4638},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac572},
doi = {10.1093/BIOINFORMATICS/BTAC572},
timestamp = {Mon, 23 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangYWSFMW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhaoBWWLF22,
author = {Yiqing Zhao and
Matthew Brush and
Chen Wang and
Alex H. Wagner and
Hongfang Liu and
Robert R. Freimuth},
title = {Leveraging a pharmacogenomics knowledgebase to formulate a drug response
phenotype terminology for genomic medicine},
journal = {Bioinform.},
volume = {38},
number = {23},
pages = {5279--5287},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac646},
doi = {10.1093/BIOINFORMATICS/BTAC646},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhaoBWWLF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhaoGCWZ22,
author = {Wenyi Zhao and
Xun Gu and
Shuqing Chen and
Jian Wu and
Zhan Zhou},
title = {{MODIG:} integrating multi-omics and multi-dimensional gene network
for cancer driver gene identification based on graph attention network
model},
journal = {Bioinform.},
volume = {38},
number = {21},
pages = {4901--4907},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac622},
doi = {10.1093/BIOINFORMATICS/BTAC622},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhaoGCWZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhaoHGMTLJ22,
author = {Hongyu Zhao and
Kun Han and
Chao Gao and
Vithal Madhira and
Umit Topaloglu and
Yong Lu and
Guangxu Jin},
title = {VOC-alarm: mutation-based prediction of SARS-CoV-2 variants of concern},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3549--3556},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac370},
doi = {10.1093/BIOINFORMATICS/BTAC370},
timestamp = {Mon, 08 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhaoHGMTLJ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhaoWQW22,
author = {Sendong Zhao and
Aobo Wang and
Bing Qin and
Fei Wang},
title = {Biomedical evidence engineering for data-driven discovery},
journal = {Bioinform.},
volume = {38},
number = {23},
pages = {5270--5278},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac675},
doi = {10.1093/BIOINFORMATICS/BTAC675},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhaoWQW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhaoYWLCACL22,
author = {Yue Zhao and
Lianbo Yu and
Xue Wu and
Haoran Li and
Kevin R. Coombes and
Kin Fai Au and
Lijun Cheng and
Lang Li},
title = {{CEDA:} integrating gene expression data with CRISPR-pooled screen
data identifies essential genes with higher expression},
journal = {Bioinform.},
volume = {38},
number = {23},
pages = {5245--5252},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac668},
doi = {10.1093/BIOINFORMATICS/BTAC668},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhaoYWLCACL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhaoZZW22,
author = {Qichang Zhao and
Haochen Zhao and
Kai Zheng and
Jianxin Wang},
title = {HyperAttentionDTI: improving drug-protein interaction prediction by
sequence-based deep learning with attention mechanism},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {655--662},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab715},
doi = {10.1093/BIOINFORMATICS/BTAB715},
timestamp = {Tue, 13 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhaoZZW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhelezovD22,
author = {Gleb Zhelezov and
James H. Degnan},
title = {Trying out a million genes to find the perfect pair with \emph{RTIST}},
journal = {Bioinform.},
volume = {38},
number = {14},
pages = {3565--3573},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac349},
doi = {10.1093/BIOINFORMATICS/BTAC349},
timestamp = {Mon, 08 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhelezovD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhengLYS22,
author = {Lujing Zheng and
Zhenhuan Liu and
Yang Yang and
Hong{-}Bin Shen},
title = {Accurate inference of gene regulatory interactions from spatial gene
expression with deep contrastive learning},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {746--753},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab718},
doi = {10.1093/BIOINFORMATICS/BTAB718},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhengLYS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhengNWKS22,
author = {Lily Zheng and
Noushin Niknafs and
Laura D. Wood and
Rachel Karchin and
Robert B. Scharpf},
title = {Estimation of cancer cell fractions and clone trees from multi-region
sequencing of tumors},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3677--3683},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac367},
doi = {10.1093/BIOINFORMATICS/BTAC367},
timestamp = {Thu, 25 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhengNWKS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhengWHYCSC22,
author = {Jun{-}Jie Zheng and
Po{-}Wen Wang and
Tzu{-}Wen Huang and
Yao{-}Jong Yang and
Hua{-}Sheng Chiu and
Pavel Sumazin and
Ting{-}Wen Chen},
title = {{MOCHI:} a comprehensive cross-platform tool for amplicon-based microbiota
analysis},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4286--4292},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac494},
doi = {10.1093/BIOINFORMATICS/BTAC494},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhengWHYCSC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhongHWCL22,
author = {Jiayuan Zhong and
Chongyin Han and
Yangkai Wang and
Pei Chen and
Rui Liu},
title = {Identifying the critical state of complex biological systems by the
directed-network rank score method},
journal = {Bioinform.},
volume = {38},
number = {24},
pages = {5398--5405},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac707},
doi = {10.1093/BIOINFORMATICS/BTAC707},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhongHWCL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhongLCLPHPW22,
author = {Cheng Zhong and
Kangenbei Liao and
Wei Chen and
Qianlong Liu and
Baolin Peng and
Xuanjing Huang and
Jiajie Peng and
Zhongyu Wei},
title = {Hierarchical reinforcement learning for automatic disease diagnosis},
journal = {Bioinform.},
volume = {38},
number = {16},
pages = {3995--4001},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac408},
doi = {10.1093/BIOINFORMATICS/BTAC408},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhongLCLPHPW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhouBA22,
author = {Feng Zhou and
Adam S. Butterworth and
Jennifer L. Asimit},
title = {\emph{Flashfm-ivis}: interactive visualization for fine-mapping of
multiple quantitative traits},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4238--4242},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac453},
doi = {10.1093/BIOINFORMATICS/BTAC453},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhouBA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhouJYD22,
author = {Huiwei Zhou and
Haibin Jiang and
Weihong Yao and
Xun Du},
title = {Learning temporal difference embeddings for biomedical hypothesis
generation},
journal = {Bioinform.},
volume = {38},
number = {23},
pages = {5253--5261},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac660},
doi = {10.1093/BIOINFORMATICS/BTAC660},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhouJYD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhouRLGL22,
author = {Tong Zhou and
Jie Rong and
Yang Liu and
Weikang Gong and
Chunhua Li},
title = {An ensemble approach to predict binding hotspots in protein-RNA interactions
based on {SMOTE} data balancing and Random Grouping feature selection
strategies},
journal = {Bioinform.},
volume = {38},
number = {9},
pages = {2452--2458},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac138},
doi = {10.1093/BIOINFORMATICS/BTAC138},
timestamp = {Wed, 18 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhouRLGL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhouWZW22,
author = {Chao Zhou and
Huimin Wang and
Hongyu Zhao and
Tao Wang},
title = {fastANCOM: a fast method for analysis of compositions of microbiomes},
journal = {Bioinform.},
volume = {38},
number = {7},
pages = {2039--2041},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac060},
doi = {10.1093/BIOINFORMATICS/BTAC060},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhouWZW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhuLHZ22,
author = {Rui Zhu and
Xiongfei Li and
Sa Huang and
Xiaoli Zhang},
title = {Multimodal medical image fusion using adaptive co-occurrence filter-based
decomposition optimization model},
journal = {Bioinform.},
volume = {38},
number = {3},
pages = {818--826},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab721},
doi = {10.1093/BIOINFORMATICS/BTAB721},
timestamp = {Wed, 28 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhuLHZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhuOCFCCW22,
author = {Yiheng Zhu and
Zhenqiu Ouyang and
Wenbo Chen and
Ruiwei Feng and
Danny Z. Chen and
Ji Cao and
Jian Wu},
title = {{TGSA:} protein-protein association-based twin graph neural networks
for drug response prediction with similarity augmentation},
journal = {Bioinform.},
volume = {38},
number = {2},
pages = {461--468},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab650},
doi = {10.1093/BIOINFORMATICS/BTAB650},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhuOCFCCW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhuSH22,
author = {Zhengyi Zhu and
Glen A. Satten and
Yi{-}Juan Hu},
title = {Integrative analysis of relative abundance data and presence-absence
data of the microbiome using the {LDM}},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2915--2917},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac181},
doi = {10.1093/BIOINFORMATICS/BTAC181},
timestamp = {Mon, 13 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhuSH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhuYXLZL22,
author = {Chaoyu Zhu and
Zhihao Yang and
Xiaoqiong Xia and
Nan Li and
Fan Zhong and
Lei Liu},
title = {Multimodal reasoning based on knowledge graph embedding for specific
diseases},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2235--2245},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac085},
doi = {10.1093/BIOINFORMATICS/BTAC085},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhuYXLZL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhuangWJ22,
author = {Haotian Zhuang and
Huimin Wang and
Zhicheng Ji},
title = {findPC: An {R} package to automatically select the number of principal
components in single-cell analysis},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2949--2951},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac235},
doi = {10.1093/BIOINFORMATICS/BTAC235},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhuangWJ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhuangWNBZWML22,
author = {Yongwen Zhuang and
Brooke N. Wolford and
Kisung Nam and
Wenjian Bi and
Wei Zhou and
Cristen J. Willer and
Bhramar Mukherjee and
Seunggeun Lee},
title = {Incorporating family disease history and controlling case-control
imbalance for population-based genetic association studies},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4337--4343},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac459},
doi = {10.1093/BIOINFORMATICS/BTAC459},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhuangWNBZWML22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZielezinskiDG22,
author = {Andrzej Zielezinski and
Sebastian Deorowicz and
Adam Gudys},
title = {{PHIST:} fast and accurate prediction of prokaryotic hosts from metagenomic
viral sequences},
journal = {Bioinform.},
volume = {38},
number = {5},
pages = {1447--1449},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab837},
doi = {10.1093/BIOINFORMATICS/BTAB837},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZielezinskiDG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZiemskiAKFB22,
author = {Michal Ziemski and
Anja Adamov and
Lina Kim and
Lena Fl{\"{o}}rl and
Nicholas A. Bokulich},
title = {Reproducible acquisition, management and meta-analysis of nucleotide
sequence (meta)data using q2-fondue},
journal = {Bioinform.},
volume = {38},
number = {22},
pages = {5081--5091},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac639},
doi = {10.1093/BIOINFORMATICS/BTAC639},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZiemskiAKFB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZouYXLLLWLWW22,
author = {Danyi Zou and
Ye Yuan and
Luming Xu and
Shijun Lei and
Xingbo Li and
Xiaohuan Lu and
Xingyue Wang and
Xiaoqiong Li and
Lin Wang and
Zheng Wang},
title = {PltDB: a blood platelets-based gene expression database for disease
investigation},
journal = {Bioinform.},
volume = {38},
number = {11},
pages = {3143--3145},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac278},
doi = {10.1093/BIOINFORMATICS/BTAC278},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZouYXLLLWLWW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZurkowskiZS22,
author = {Michal Zurkowski and
Tomasz Zok and
Marta Szachniuk},
title = {DrawTetrado to create layer diagrams of {G4} structures},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3835--3836},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac394},
doi = {10.1093/BIOINFORMATICS/BTAC394},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZurkowskiZS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HeGYAS22,
title = {Overcoming the inadaptability of sparse group lasso for data with
various group structures by stacking},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1542--1549},
year = {2022},
note = {Withdrawn.},
url = {https://doi.org/10.1093/bioinformatics/btab848},
doi = {10.1093/BIOINFORMATICS/BTAB848},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HeGYAS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AhmedSCYZ21,
author = {Khandakar Tanvir Ahmed and
Jiao Sun and
Sze Cheng and
Jeongsik Yong and
Wei Zhang},
title = {Multi-omics data integration by generative adversarial network},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {179--186},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab608},
doi = {10.1093/BIOINFORMATICS/BTAB608},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/AhmedSCYZ21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AncienPVR21,
author = {Fran{\c{c}}ois Ancien and
Fabrizio Pucci and
Wim F. Vranken and
Marianne Rooman},
title = {MutaFrame - an interpretative visualization framework for deleteriousness
prediction of missense variants in the human exome},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {265--266},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab453},
doi = {10.1093/BIOINFORMATICS/BTAB453},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AncienPVR21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Arenas21,
author = {Miguel Arenas},
title = {ProteinEvolverABC: coestimation of recombination and substitution
rates in protein sequences by approximate Bayesian computation},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {58--64},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab617},
doi = {10.1093/BIOINFORMATICS/BTAB617},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Arenas21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BorellaMRR21,
author = {Matteo Borella and
Graziano Martello and
Davide Risso and
Chiara Romualdi},
title = {PsiNorm: a scalable normalization for single-cell RNA-seq data},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {164--172},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab641},
doi = {10.1093/BIOINFORMATICS/BTAB641},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BorellaMRR21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CaoHW21,
author = {Kai Cao and
Yiguang Hong and
Lin Wan},
title = {Manifold alignment for heterogeneous single-cell multi-omics data
integration using Pamona},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {211--219},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab594},
doi = {10.1093/BIOINFORMATICS/BTAB594},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CaoHW21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenZ21,
author = {Jun Chen and
Xianyang Zhang},
title = {{D-MANOVA:} fast distance-based multivariate analysis of variance
for large-scale microbiome association studies},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {286--288},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab498},
doi = {10.1093/BIOINFORMATICS/BTAB498},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenZ21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CortezHCKJ21,
author = {Mark Jayson Cortez and
Hyukpyo Hong and
Boseung Choi and
Jae Kyoung Kim and
Kresimir Josic},
title = {Hierarchical Bayesian models of transcriptional and translational
regulation processes with delays},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {187--195},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab618},
doi = {10.1093/BIOINFORMATICS/BTAB618},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CortezHCKJ21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DanilukOL21,
author = {Pawel Daniluk and
Tymoteusz Oleniecki and
Bogdan Lesyng},
title = {{DAMA:} a method for computing multiple alignments of protein structures
using local structure descriptors},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {80--85},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab571},
doi = {10.1093/BIOINFORMATICS/BTAB571},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DanilukOL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FangH21,
author = {Xiunan Fang and
Joshua W. K. Ho},
title = {FlowGrid enables fast clustering of very large single-cell RNA-seq
data},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {282--283},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab521},
doi = {10.1093/BIOINFORMATICS/BTAB521},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/FangH21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FarrSF21,
author = {Elias B. Farr and
Julia M. Sattler and
Friedrich Frischknecht},
title = {{SPOT:} a web-tool enabling swift profiling of transcriptomes},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {284--285},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab541},
doi = {10.1093/BIOINFORMATICS/BTAB541},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/FarrSF21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GaoZYW21,
author = {Jianzhao Gao and
Shuangjia Zheng and
Mengting Yao and
Peikun Wu},
title = {Precise estimation of residue relative solvent accessible area from
C{\(\alpha\)} atom distance matrix using a deep learning method},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {94--98},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab616},
doi = {10.1093/BIOINFORMATICS/BTAB616},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GaoZYW21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Gonzalez-Aleman21,
author = {Roy Gonz{\'{a}}lez{-}Alem{\'{a}}n and
Daniel Platero{-}Rochart and
David Hern{\'{a}}ndez{-}Castillo and
Erix Wiliam Hern{\'{a}}ndez{-}Rodr{\'{\i}}guez and
Julio Caballero and
Fabrice Leclerc and
Luis Alberto Montero{-}Cabrera},
title = {BitQT: a graph-based approach to the quality threshold clustering
of molecular dynamics},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {73--79},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab595},
doi = {10.1093/BIOINFORMATICS/BTAB595},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Gonzalez-Aleman21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Gordon-Rodriguez21,
author = {Elliott Gordon{-}Rodr{\'{\i}}guez and
Thomas P. Quinn and
John P. Cunningham},
title = {Learning sparse log-ratios for high-throughput sequencing data},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {157--163},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab645},
doi = {10.1093/BIOINFORMATICS/BTAB645},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Gordon-Rodriguez21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HeX21,
author = {Di He and
Lei Xie},
title = {A cross-level information transmission network for hierarchical omics
data integration and phenotype prediction from a new genotype},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {204--210},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab580},
doi = {10.1093/BIOINFORMATICS/BTAB580},
timestamp = {Mon, 13 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HeX21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KatuwawalaZK21,
author = {Akila Katuwawala and
Bi Zhao and
Lukasz A. Kurgan},
title = {DisoLipPred: accurate prediction of disordered lipid-binding residues
in protein sequences with deep recurrent networks and transfer learning},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {115--124},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab640},
doi = {10.1093/BIOINFORMATICS/BTAB640},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KatuwawalaZK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KimHYYL21,
author = {Mirae Kim and
Soonwoo Hong and
Thomas E. Yankeelov and
Hsin{-}Chih Yeh and
Yen{-}Liang Liu},
title = {Deep learning-based classification of breast cancer cells using transmembrane
receptor dynamics},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {243--249},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab581},
doi = {10.1093/BIOINFORMATICS/BTAB581},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KimHYYL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiangLZZ21,
author = {Shide Liang and
Zhixiu Li and
Jian Zhan and
Yaoqi Zhou},
title = {De novo protein design by an energy function based on series expansion
in distance and orientation dependence},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {86--93},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab598},
doi = {10.1093/BIOINFORMATICS/BTAB598},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiangLZZ21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LinHTCHYLC21,
author = {Jun{-}Liang Lin and
Tsung{-}Ting Hsieh and
Yi{-}An Tung and
Xuan{-}Jun Chen and
Yu{-}Chun Hsiao and
Chia{-}Lin Yang and
Tyng{-}Luh Liu and
Chien{-}Yu Chen},
title = {ezGeno: an automatic model selection package for genomic data analysis},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {30--37},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab588},
doi = {10.1093/BIOINFORMATICS/BTAB588},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LinHTCHYLC21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuZBYYPS21,
author = {Hualin Liu and
Jinshui Zheng and
Dexin Bo and
Yun Yu and
Weixing Ye and
Donghai Peng and
Ming Sun},
title = {BtToxin{\_}Digger: a comprehensive and high-throughput pipeline for
mining toxin protein genes from Bacillus thuringiensis},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {250--251},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab506},
doi = {10.1093/BIOINFORMATICS/BTAB506},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuZBYYPS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuZHWZZ21,
author = {Jun Liu and
Kai{-}Long Zhao and
Guang{-}Xing He and
Liu{-}Jing Wang and
Xiao{-}Gen Zhou and
Gui{-}Jun Zhang},
title = {A de novo protein structure prediction by iterative partition sampling,
topology adjustment and residue-level distance deviation optimization},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {99--107},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab620},
doi = {10.1093/BIOINFORMATICS/BTAB620},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuZHWZZ21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MagnoDM21,
author = {Ramiro Magno and
Isabel Duarte and
Ana{-}Teresa Maia},
title = {quincunx: an {R} package to query, download and wrangle {PGS} Catalog
data},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {294--296},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab522},
doi = {10.1093/BIOINFORMATICS/BTAB522},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MagnoDM21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MaheCSQVDR21,
author = {Fr{\'{e}}d{\'{e}}ric Mah{\'{e}} and
Lucas Czech and
Alexandros Stamatakis and
Christopher Quince and
Colomban de Vargas and
Micah Dunthorn and
Torbj{\o}rn Rognes},
title = {Swarm v3: towards tera-scale amplicon clustering},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {267--269},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab493},
doi = {10.1093/BIOINFORMATICS/BTAB493},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MaheCSQVDR21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Mary-HuardDMR21,
author = {Tristan Mary{-}Huard and
Sarmistha Das and
Indranil Mukhopadhyay and
St{\'{e}}phane Robin},
title = {Querying multiple sets of P-values through composed hypothesis testing},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {141--148},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab592},
doi = {10.1093/BIOINFORMATICS/BTAB592},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Mary-HuardDMR21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MeleshkoHK21,
author = {Dmitry Meleshko and
Iman Hajirasouliha and
Anton I. Korobeynikov},
title = {coronaSPAdes: from biosynthetic gene clusters to {RNA} viral assemblies},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {1--8},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab597},
doi = {10.1093/BIOINFORMATICS/BTAB597},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MeleshkoHK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MotonoYSH21,
author = {Chie Motono and
Shunsuke Yanagida and
Miwa Sato and
Takatsugu Hirokawa},
title = {MDContactCom: a tool to identify differences of protein molecular
dynamics from two {MD} simulation trajectories in terms of interresidue
contacts},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {273--274},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab538},
doi = {10.1093/BIOINFORMATICS/BTAB538},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MotonoYSH21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MurgasMSMASR21,
author = {Kevin A. Murgas and
Yanlin Ma and
Lidea K. Shahidi and
Sayan Mukherjee and
Andrew S. Allen and
Darryl Shibata and
Marc D. Ryser},
title = {A Bayesian hierarchical model to estimate {DNA} methylation conservation
in colorectal tumors},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {22--29},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab637},
doi = {10.1093/BIOINFORMATICS/BTAB637},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MurgasMSMASR21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NikolaienkoLK21,
author = {Oleksii Nikolaienko and
Per Eystein L{\o}nning and
Stian Knappskog},
title = {ramr: an R/Bioconductor package for detection of rare aberrantly methylated
regions},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {133--140},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab586},
doi = {10.1093/BIOINFORMATICS/BTAB586},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/NikolaienkoLK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/OlsonW21,
author = {Andrew Olson and
Doreen Ware},
title = {Ranked choice voting for representative transcripts with TRaCE},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {261--264},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab542},
doi = {10.1093/BIOINFORMATICS/BTAB542},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/OlsonW21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ParkLKLCK21,
author = {Sungjoon Park and
Dohoon Lee and
Youngkuk Kim and
Sangsoo Lim and
Heejoon Chae and
Sun Kim},
title = {BioVLAB-Cancer-Pharmacogenomics: tumor heterogeneity and pharmacogenomics
analysis of multi-omics data from tumor on the cloud},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {275--277},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab478},
doi = {10.1093/BIOINFORMATICS/BTAB478},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ParkLKLCK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Prive21,
author = {Florian Priv{\'{e}}},
title = {Optimal linkage disequilibrium splitting},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {255--256},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab519},
doi = {10.1093/BIOINFORMATICS/BTAB519},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Prive21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PryszczN21,
author = {Leszek P. Pryszcz and
Eva Maria Novoa},
title = {ModPhred: an integrative toolkit for the analysis and storage of nanopore
sequencing {DNA} and {RNA} modification data},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {257--260},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab539},
doi = {10.1093/BIOINFORMATICS/BTAB539},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PryszczN21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ReisCM21,
author = {Pedro B. P. S. Reis and
Djork{-}Arn{\'{e}} Clevert and
Miguel Machuqueiro},
title = {pKPDB: a protein data bank extension database of pKa and pI theoretical
values},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {297--298},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab518},
doi = {10.1093/BIOINFORMATICS/BTAB518},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ReisCM21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SalazarRHAS21,
author = {Guillem Salazar and
Hans{-}Joachim Ruscheweyh and
Falk Hildebrand and
Silvia G. Acinas and
Shinichi Sunagawa},
title = {mTAGs: taxonomic profiling using degenerate consensus reference sequences
of ribosomal {RNA} genes},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {270--272},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab465},
doi = {10.1093/BIOINFORMATICS/BTAB465},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SalazarRHAS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SchwarzGKSVD21,
author = {Dominik Schwarz and
Guy Georges and
Sebastian Kelm and
Jiye Shi and
Anna Vangone and
Charlotte M. Deane},
title = {Co-evolutionary distance predictions contain flexibility information},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {65--72},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab562},
doi = {10.1093/BIOINFORMATICS/BTAB562},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SchwarzGKSVD21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShaoHWHCWMC21,
author = {Dan Shao and
Lan Huang and
Yan Wang and
Kai He and
Xueteng Cui and
Yao Wang and
Qin Ma and
Juan Cui},
title = {DeepSec: a deep learning framework for secreted protein discovery
in human body fluids},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {228--235},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab545},
doi = {10.1093/BIOINFORMATICS/BTAB545},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShaoHWHCWMC21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SinghA21,
author = {Dilawar Singh and
Steven S. Andrews},
title = {Python interfaces for the Smoldyn simulator},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {291--293},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab530},
doi = {10.1093/BIOINFORMATICS/BTAB530},
timestamp = {Sun, 22 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SinghA21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SohnLL21,
author = {Michael B. Sohn and
Jiarui Lu and
Hongzhe Li},
title = {A compositional mediation model for a binary outcome: Application
to microbiome studies},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {16--21},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab605},
doi = {10.1093/BIOINFORMATICS/BTAB605},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SohnLL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SongY21,
author = {Jian Song and
Changbin Yu},
title = {Alpha-XIC: a deep neural network for scoring the coelution of peak
groups improves peptide identification by data-independent acquisition
mass spectrometry},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {38--43},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab544},
doi = {10.1093/BIOINFORMATICS/BTAB544},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SongY21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SukysG21,
author = {Augustinas Sukys and
Ramon Grima},
title = {MomentClosure.jl: automated moment closure approximations in Julia},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {289--290},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab469},
doi = {10.1093/BIOINFORMATICS/BTAB469},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SukysG21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TylerFK21,
author = {Jonathan Tyler and
Daniel B. Forger and
Jae Kyoung Kim},
title = {Inferring causality in biological oscillators},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {196--203},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab623},
doi = {10.1093/BIOINFORMATICS/BTAB623},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/TylerFK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangJZL21,
author = {Chao Wang and
Ying Ju and
Quan Zou and
Chen Lin},
title = {DeepAc4C: a convolutional neural network model with hybrid features
composed of physicochemical patterns and distributed representation
information for identification of N4-acetylcytidine in mRNA},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {52--57},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab611},
doi = {10.1093/BIOINFORMATICS/BTAB611},
timestamp = {Tue, 06 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangJZL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WoodhouseSSPFWA21,
author = {Margaret Woodhouse and
Shatabdi Sen and
David A. Schott and
John L. Portwood II and
Michael Freeling and
Justin W. Walley and
Carson M. Andorf and
James C. Schnable},
title = {qTeller: a tool for comparative multi-genomic gene expression analysis},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {236--242},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab604},
doi = {10.1093/BIOINFORMATICS/BTAB604},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WoodhouseSSPFWA21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XinWBLCWWSDZ21,
author = {Junyi Xin and
Yanling Wu and
Shuai Ben and
Shuwei Li and
Haiyan Chu and
Meilin Wang and
Molin Wang and
Mingyang Song and
Mulong Du and
Zhengdong Zhang},
title = {CoSMeD: a user-friendly web server to estimate 5-year survival probability
of left-sided and right-sided colorectal cancer patients using molecular
data},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {278--281},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab523},
doi = {10.1093/BIOINFORMATICS/BTAB523},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/XinWBLCWWSDZ21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XuVZZ21,
author = {Anthony Xu and
Aravind Venkateswaran and
Lianguizi Zhou and
Andreas Zankl},
title = {Ontoclick: a web browser extension to facilitate biomedical knowledge
curation},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {301--302},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab520},
doi = {10.1093/BIOINFORMATICS/BTAB520},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/XuVZZ21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XuWM21,
author = {Gang Xu and
Qinghua Wang and
Jianpeng Ma},
title = {{OPUS-X:} an open-source toolkit for protein torsion angles, secondary
structure, solvent accessibility, contact map predictions and 3D folding},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {108--114},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab633},
doi = {10.1093/BIOINFORMATICS/BTAB633},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/XuWM21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YanMGCLD21,
author = {Jun Yan and
Zhongsong Man and
Lu Gao and
Lei Cai and
Qian Lu and
Jiahong Dong},
title = {The role of CpG island methylator phenotype in the clinical course
of hepatocellular carcinoma},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {9--15},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab600},
doi = {10.1093/BIOINFORMATICS/BTAB600},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YanMGCLD21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YatesACDLLNSHK21,
author = {Andrew D. Yates and
Jeremy Adams and
Somesh Chaturvedi and
Robert Davies and
Matthew R. Laird and
Rasko Leinonen and
Rishi Nag and
Nathan C. Sheffield and
Oliver Hofmann and
Thomas M. Keane},
title = {Refget: standardized access to reference sequences},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {299--300},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab524},
doi = {10.1093/BIOINFORMATICS/BTAB524},
timestamp = {Thu, 25 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YatesACDLLNSHK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YuSY21,
author = {Fulong Yu and
Vijay G. Sankaran and
Guo{-}Cheng Yuan},
title = {CUT{\&}RUNTools 2.0: a pipeline for single-cell and bulk-level
CUT{\&}RUN and CUT{\&}Tag data analysis},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {252--254},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab507},
doi = {10.1093/BIOINFORMATICS/BTAB507},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YuSY21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YuanCZZY21,
author = {Qianmu Yuan and
Jianwen Chen and
Huiying Zhao and
Yaoqi Zhou and
Yuedong Yang},
title = {Structure-aware protein-protein interaction site prediction using
deep graph convolutional network},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {125--132},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab643},
doi = {10.1093/BIOINFORMATICS/BTAB643},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YuanCZZY21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZaitzeffLMHS21,
author = {Alexander Zaitzeff and
Nick Leiby and
Francis C. Motta and
Steven B. Haase and
Jed Singer},
title = {Improved datasets and evaluation methods for the automatic prediction
of DNA-binding proteins},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {44--51},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab603},
doi = {10.1093/BIOINFORMATICS/BTAB603},
timestamp = {Wed, 08 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZaitzeffLMHS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZenereRGA21,
author = {Alberto Zenere and
Olof Rundquist and
Mika Gustafsson and
Claudio Altafini},
title = {Using high-throughput multi-omics data to investigate structural balance
in elementary gene regulatory network motifs},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {173--178},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab577},
doi = {10.1093/BIOINFORMATICS/BTAB577},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZenereRGA21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhouC21,
author = {Xin Zhou and
Xiaodong Cai},
title = {Joint eQTL mapping and inference of gene regulatory network improves
power of detecting both cis- and trans-eQTLs},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {149--156},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab609},
doi = {10.1093/BIOINFORMATICS/BTAB609},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhouC21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZuoZ21,
author = {Mei Zuo and
Yang Zhang},
title = {A span-based joint model for extracting entities and relations of
bacteria biotopes},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {220--227},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab593},
doi = {10.1093/BIOINFORMATICS/BTAB593},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZuoZ21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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