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PLOS Computational Biology  
Large scale paired antibody language models

Henry Kenlay, Frédéric A. Dreyer, Aleksandr Kovaltsuk, Dom Miketa, Douglas Pires, Charlotte M. Deane

Research Article | published 06 Dec 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012646

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Rapid prediction of key residues for foldability by machine learning model enables the design of highly functional libraries with hyperstable constrained peptide scaffolds

Fei Cai, Yuehua Wei, Daniel Kirchhofer, Andrew Chang, Yingnan Zhang

Research Article | published 18 Nov 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012609

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Ten simple rules for the sharing of bacterial genotype—Phenotype data on antimicrobial resistance

Leonid Chindelevitch, Maarten van Dongen, Heather Graz, Antonio Pedrotta, Anita Suresh, Swapna Uplekar, Elita Jauneikaite, Nicole Wheeler

Education | published 22 Jun 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011129

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HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph

Joshua Daniel Rubin, Nicola Alexandra Vogel, Shyam Gopalakrishnan, Peter Wad Sackett, Gabriel Renaud

Research Article | published 07 Jun 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011148

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AC-PCoA: Adjustment for confounding factors using principal coordinate analysis

Yu Wang, Fengzhu Sun, Wei Lin, Shuqin Zhang

Research Article | published 13 Jul 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010184

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The accuracy of absolute differential abundance analysis from relative count data

Kimberly E. Roche, Sayan Mukherjee

Research Article | published 11 Jul 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010284

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SavvyCNV: Genome-wide CNV calling from off-target reads

Thomas W. Laver, Elisa De Franco, Matthew B. Johnson, Kashyap A. Patel, Sian Ellard, Michael N. Weedon, Sarah E. Flanagan, Matthew N. Wakeling

Research Article | published 16 Mar 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1009940

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Tool evaluation for the detection of variably sized indels from next generation whole genome and targeted sequencing data

Ning Wang, Vladislav Lysenkov, Katri Orte, Veli Kairisto, Juhani Aakko, Sofia Khan, Laura L. Elo

Research Article | published 17 Feb 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1009269

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MitoScape: A big-data, machine-learning platform for obtaining mitochondrial DNA from next-generation sequencing data

Larry N. Singh, Brian Ennis, Bryn Loneragan, Noah L. Tsao, M. Isabel G. Lopez Sanchez, Jianping Li, Patrick Acheampong, Oanh Tran, Ian A. Trounce, Yuankun Zhu, Prasanth Potluri, Regeneron Genetics Center , Beverly S. Emanuel, Daniel J. Rader, Zoltan Arany, Scott M. Damrauer, Adam C. Resnick, Stewart A. Anderson, Douglas C. Wallace

Research Article | published 11 Nov 2021 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1009594

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Bioinformatics in Sudan: Status and challenges case study: The National University-Sudan

Sofia B. Mohamed, Sumaya Kambal, Sabah A. E. Ibrahim, Esra Abdalwhab, Abdalla Munir, Arwa Ibrahim, Qurashi Mohamed Ali

Education | published 21 Oct 2021 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1009462

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VCF2CAPS–A high-throughput CAPS marker design from VCF files and its test-use on a genotyping-by-sequencing (GBS) dataset

Wojciech Wesołowski, Beata Domnicz, Joanna Augustynowicz, Marek Szklarczyk

Research Article | published 20 May 2021 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1008980

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Sequence deeper without sequencing more: Bayesian resolution of ambiguously mapped reads

Rohan N. Shah, Alexander J. Ruthenburg

Research Article | published 19 Apr 2021 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1008926

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PASA: Proteomic analysis of serum antibodies web server

Oren Avram, Aya Kigel, Anna Vaisman-Mentesh, Sharon Kligsberg, Shai Rosenstein, Yael Dror, Tal Pupko, Yariv Wine

Research Article | published 25 Jan 2021 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1008607

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NGS-PrimerPlex: High-throughput primer design for multiplex polymerase chain reactions

Andrey Kechin, Viktoria Borobova, Ulyana Boyarskikh, Evgeniy Khrapov, Sergey Subbotin, Maxim Filipenko

Research Article | published 30 Dec 2020 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1008468

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Using B cell receptor lineage structures to predict affinity

Duncan K. Ralph, Frederick A. Matsen IV

Research Article | published 11 Nov 2020 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1008391

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