Covasim: An agent-based model of COVID-19 dynamics and interventions
Kerr, Cliff C, Stuart, Robyn M, Mistry, Dina, Abeysuriya, Romesh G, Rosenfeld, Katherine, Hart, Gregory R, Núñez, Rafael C, Cohen, Jamie A, Selvaraj, Prashanth, Hagedorn, Brittany, George, Lauren, Jastrzebski, Michal, Izzo, Amanda S, Fowler, Greer, Palmer, Anna, Delport, Dominic, Scott, Nick, Kelly, Sherrie L, Bennette, Caroline S, Wagner, Bradley G, Chang, Stewart T, Oron, Assaf P, Wenger, Edward A, Panovska-Griffiths, Jasmina, Famulare, Michael, Klein, Daniel J
Published in PLoS computational biology (26.07.2021)
Published in PLoS computational biology (26.07.2021)
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Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads
Wick, Ryan R, Judd, Louise M, Gorrie, Claire L, Holt, Kathryn E
Published in PLoS computational biology (01.06.2017)
Published in PLoS computational biology (01.06.2017)
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MUMmer4: A fast and versatile genome alignment system
Marçais, Guillaume, Delcher, Arthur L, Phillippy, Adam M, Coston, Rachel, Salzberg, Steven L, Zimin, Aleksey
Published in PLoS computational biology (01.01.2018)
Published in PLoS computational biology (01.01.2018)
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Integrating Hi-C links with assembly graphs for chromosome-scale assembly
Ghurye, Jay, Rhie, Arang, Walenz, Brian P, Schmitt, Anthony, Selvaraj, Siddarth, Pop, Mihai, Phillippy, Adam M, Koren, Sergey
Published in PLoS computational biology (01.08.2019)
Published in PLoS computational biology (01.08.2019)
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MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data
Huson, Daniel H, Beier, Sina, Flade, Isabell, Górska, Anna, El-Hadidi, Mohamed, Mitra, Suparna, Ruscheweyh, Hans-Joachim, Tappu, Rewati
Published in PLoS computational biology (01.06.2016)
Published in PLoS computational biology (01.06.2016)
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Transcriptomics technologies
Lowe, Rohan, Shirley, Neil, Bleackley, Mark, Dolan, Stephen, Shafee, Thomas
Published in PLoS computational biology (01.05.2017)
Published in PLoS computational biology (01.05.2017)
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Deep convolutional networks do not classify based on global object shape
Baker, Nicholas, Lu, Hongjing, Erlikhman, Gennady, Kellman, Philip J
Published in PLoS computational biology (01.12.2018)
Published in PLoS computational biology (01.12.2018)
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New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx
Mounir, Mohamed, Lucchetta, Marta, Silva, Tiago C, Olsen, Catharina, Bontempi, Gianluca, Chen, Xi, Noushmehr, Houtan, Colaprico, Antonio, Papaleo, Elena
Published in PLoS computational biology (01.03.2019)
Published in PLoS computational biology (01.03.2019)
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Sequence determinants of protein phase behavior from a coarse-grained model
Dignon, Gregory L, Zheng, Wenwei, Kim, Young C, Best, Robert B, Mittal, Jeetain
Published in PLoS computational biology (01.01.2018)
Published in PLoS computational biology (01.01.2018)
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Systems biology informed deep learning for inferring parameters and hidden dynamics
Yazdani, Alireza, Lu, Lu, Raissi, Maziar, Karniadakis, George Em
Published in PLoS computational biology (18.11.2020)
Published in PLoS computational biology (18.11.2020)
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Metacoder: An R package for visualization and manipulation of community taxonomic diversity data
Foster, Zachary S L, Sharpton, Thomas J, Grünwald, Niklaus J
Published in PLoS computational biology (01.02.2017)
Published in PLoS computational biology (01.02.2017)
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ProMod3-A versatile homology modelling toolbox
Studer, Gabriel, Tauriello, Gerardo, Bienert, Stefan, Biasini, Marco, Johner, Niklaus, Schwede, Torsten
Published in PLoS computational biology (28.01.2021)
Published in PLoS computational biology (28.01.2021)
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Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments
Van Valen, David A, Kudo, Takamasa, Lane, Keara M, Macklin, Derek N, Quach, Nicolas T, DeFelice, Mialy M, Maayan, Inbal, Tanouchi, Yu, Ashley, Euan A, Covert, Markus W
Published in PLoS computational biology (01.11.2016)
Published in PLoS computational biology (01.11.2016)
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OpenABM-Covid19-An agent-based model for non-pharmaceutical interventions against COVID-19 including contact tracing
Hinch, Robert, Probert, William J M, Nurtay, Anel, Kendall, Michelle, Wymant, Chris, Hall, Matthew, Lythgoe, Katrina, Bulas Cruz, Ana, Zhao, Lele, Stewart, Andrea, Ferretti, Luca, Montero, Daniel, Warren, James, Mather, Nicole, Abueg, Matthew, Wu, Neo, Legat, Olivier, Bentley, Katie, Mead, Thomas, Van-Vuuren, Kelvin, Feldner-Busztin, Dylan, Ristori, Tommaso, Finkelstein, Anthony, Bonsall, David G, Abeler-Dörner, Lucie, Fraser, Christophe
Published in PLoS computational biology (01.07.2021)
Published in PLoS computational biology (01.07.2021)
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