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Gene ontologies  
PLOS Computational Biology  
GeneCOCOA: Detecting context-specific functions of individual genes using co-expression data

Simonida Zehr, Sebastian Wolf, Thomas Oellerich, Matthias S. Leisegang, Ralf P. Brandes, Marcel H. Schulz, Timothy Warwick

Software | published 31 Mar 2025 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012278

Views: 98Citations: 0Saves: 0 • Shares: 0

Prediction of virus-host associations using protein language models and multiple instance learning

Dan Liu, Francesca Young, Kieran D. Lamb, David L. Robertson, Ke Yuan

Research Article | published 19 Nov 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012597

Views: 1968Citations: 2Saves: 0 • Shares: 6

A deep learning model for prediction of autism status using whole-exome sequencing data

Qing Wu, Eric M. Morrow, Ece D. Gamsiz Uzun

Research Article | published 08 Nov 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012468

Views: 1863Citations: 1Saves: 12 • Shares: 1

BootCellNet, a resampling-based procedure, promotes unsupervised identification of cell populations via robust inference of gene regulatory networks

Yutaro Kumagai

Research Article | published 30 Sep 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012480

Views: 1104Citations: 0Saves: 0 • Shares: 0

Construct prognostic models of multiple myeloma with pathway information incorporated

Shuo Wang, ShanJin Wang, Wei Pan, YuYang Yi, Junyan Lu

Research Article | published 10 Sep 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012444

Views: 897Citations: 0Saves: 5 • Shares: 4

MAGICAL: A multi-class classifier to predict synthetic lethal and viable interactions using protein-protein interaction network

Anubha Dey, Suresh Mudunuri, Manjari Kiran

Research Article | published 26 Aug 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012336

Views: 1566Citations: 1Saves: 7 • Shares: 5

scaDA: A novel statistical method for differential analysis of single-cell chromatin accessibility sequencing data

Fengdi Zhao, Xin Ma, Bing Yao, Qing Lu, Li Chen

Methods | published 02 Aug 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011854

Views: 1039Citations: 3Saves: 9 • Shares: 0

Reassessing the modularity of gene co-expression networks using the Stochastic Block Model

Diogo Melo, Luisa F. Pallares, Julien F. Ayroles

Research Article | published 29 Jul 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012300

Views: 1781Citations: 3Saves: 10 • Shares: 10

Interpretable online network dictionary learning for inferring long-range chromatin interactions

Vishal Rana, Jianhao Peng, Chao Pan, Hanbaek Lyu, Albert Cheng, Minji Kim, Olgica Milenkovic

Research Article | published 16 May 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012095

Views: 1045Citations: 0Saves: 0 • Shares: 0

Identification of Low-Complexity Domains by Compositional Signatures Reveals Class-Specific Frequencies and Functions Across the Domains of Life

Sean M. Cascarina, Eric D. Ross

Research Article | published 15 May 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011372

Views: 858Citations: 0Saves: 0 • Shares: 0

Joint representation of molecular networks from multiple species improves gene classification

Christopher A. Mancuso, Kayla A. Johnson, Renming Liu, Arjun Krishnan

Research Article | published 10 Jan 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011773

Views: 1422Citations: 3Saves: 0 • Shares: 0

Ten simple rules for writing a PLOS Computational Biology quick tips article

Patricia M. Palagi, Russell Schwartz, Scott Markel, B. F. Francis Ouellette

Education | published 21 Dec 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011689

Views: 1723Citations: 0Saves: 4 • Shares: 10

Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation

Sarvesh Nikumbh, Boris Lenhard

Methods | published 20 Nov 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011491

Views: 1204Citations: 2Saves: 12 • Shares: 16

DeepGenePrior: A deep learning model for prioritizing genes affected by copy number variants

Zahra Rahaie, Hamid R. Rabiee, Hamid Alinejad-Rokny

Research Article | published 24 Jul 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011249

Views: 1957Citations: 6Saves: 21 • Shares: 4

Detection of genes with differential expression dispersion unravels the role of autophagy in cancer progression

Christophe Le Priol, Chloé-Agathe Azencott, Xavier Gidrol

Research Article | published 09 Mar 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010342

Views: 2081Citations: 1Saves: 9 • Shares: 2

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