Sergei L. Kosakovsky Pond

Publication Activity (10 Years)

Years Active: 2005-2024
Publications (10 Years): 6

Top Topics

Learning Platform

Protein Function

Single Nucleotide Polymorphisms

Data Visualization

Top Venues

PLoS Comput. Biol.

Publications

Alexander G. Lucaci, William E. Brew, Jason Lamanna, Avery Selberg, Vincenzo Carnevale, Anna R. Moore, Sergei L. Kosakovsky Pond
The evolution of mammalian Rem2: unraveling the impact of purifying selection and coevolution on protein function, and implications for human disorders. Frontiers Bioinform. 4 (2024)
Marcos A. Caraballo-Ortiz, Sayaka Miura, Maxwell D. Sanderford, Tenzin Dolker, Qiqing Tao, Steven Weaver, Sergei L. Kosakovsky Pond, Sudhir Kumar
TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity. Bioinform. 38 (10) (2022)
Sayaka Miura, Koichiro Tamura, Qiqing Tao, Louise A. Huuki, Sergei L. Kosakovsky Pond, Jessica Priest, Jiamin Deng, Sudhir Kumar
A new method for inferring timetrees from temporally sampled molecular sequences. PLoS Comput. Biol. 16 (1) (2020)
Kemal Eren, Steven Weaver, Robert Ketteringham, Morné Valentyn, Melissa Laird Smith, Venkatesh Kumar, Sanjay Mohan, Sergei L. Kosakovsky Pond, Ben Murrell
Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons. PLoS Comput. Biol. 14 (12) (2018)
Stephen D. Shank, Steven Weaver, Sergei L. Kosakovsky Pond
phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics. BMC Bioinform. 19 (1) (2018)
Ramon Lorenzo-Redondo, Helen R. Fryer, Trevor Bedford, Eun-Young Kim, John A. C. Archer, Sergei L. Kosakovsky Pond, Yoon-Seok Chung, Sudhir Penugonda, Jeffrey G. Chipman, Courtney V. Fletcher, Timothy W. Schacker, Michael H. Malim, Andrew Rambaut, Ashley T. Haase, Angela R. McLean, Steven M. Wolinsky
. reply. Nat. 551 (7681) (2017)
Paul Thatcher Edlefsen, Morgane Rolland, Tomer Hertz, Sodsai Tovanabutra, Andrew J. Gartland, Allan C. deCamp, Craig A. Magaret, Hasan Ahmed, Raphael Gottardo, Michal Juraska, Connor McCoy, Brendan B. Larsen, Eric Sanders-Buell, Chris Carrico, Sergey Menis, Meera Bose, Miguel A. Arroyo, Robert J. O'Connell, Sorachai Nitayaphan, Punnee Pitisuttithum, Jaranit Kaewkungwal, Supachai Rerks-Ngarm, Merlin L. Robb, Tatsiana Kirys, Ivelin Georgiev, Peter D. Kwong, Konrad Scheffler, Sergei L. Kosakovsky Pond, Jonathan M. Carlson, Nelson Michael, William R. Schief, James I. Mullins, Jerome H. Kim, Peter B. Gilbert
: Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial. PLoS Comput. Biol. 11 (2) (2015)
N. Lance Hepler, Konrad Scheffler, Steven Weaver, Ben Murrell, Douglas D. Richman, Dennis R. Burton, Pascal Poignard, Davey M. Smith, Sergei L. Kosakovsky Pond
IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform. PLoS Comput. Biol. 10 (9) (2014)
Konrad Scheffler, N. Lance Hepler, Martin D. Smith, Wayne Delport, Art F. Y. Poon, Douglas D. Richman, Sergei L. Kosakovsky Pond
Workshop: Error correction, noise filtering, and phylogenetic analysis of HIV sequences using the 454 platform. ICCABS (2012)
Ben Murrell, Tulio de Oliveira, Chris Seebregts, Sergei L. Kosakovsky Pond, Konrad Scheffler
Modeling HIV-1 Drug Resistance as Episodic Directional Selection. PLoS Comput. Biol. 8 (5) (2012)
Philippe Lemey, Vladimir N. Minin, Filip Bielejec, Sergei L. Kosakovsky Pond, Marc A. Suchard
A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection. Bioinform. 28 (24) (2012)
Sergei L. Kosakovsky Pond
Computational analysis of HIV-1 evolution and epidemiology. BIBM Workshops (2011)
Wayne Delport, Konrad Scheffler, Gordon Botha, Mike B. Gravenor, Spencer V. Muse, Sergei L. Kosakovsky Pond
CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences. PLoS Comput. Biol. 6 (8) (2010)
Wayne Delport, Art F. Y. Poon, Simon D. W. Frost, Sergei L. Kosakovsky Pond
Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinform. 26 (19) (2010)
Sergei L. Kosakovsky Pond, David Posada, Eric Stawiski, Colombe Chappey, Art F. Y. Poon, Gareth Hughes, Esther Fearnhill, Mike B. Gravenor, Andrew J. Leigh Brown, Simon D. W. Frost
An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1. PLoS Comput. Biol. 5 (11) (2009)
David C. Nickle, Nebojsa Jojic, David Heckerman, Vladimir Jojic, Darko Kirovski, Morgane Rolland, Sergei L. Kosakovsky Pond, James I. Mullins
Comparison of Immunogen Designs That Optimize Peptide Coverage: Reply to Fischer et al. PLoS Comput. Biol. 4 (1) (2008)
Art F. Y. Poon, Fraser I. Lewis, Simon D. W. Frost, Sergei L. Kosakovsky Pond
Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models. Bioinform. 24 (17) (2008)
Art F. Y. Poon, Fraser I. Lewis, Sergei L. Kosakovsky Pond, Simon D. W. Frost
An Evolutionary-Network Model Reveals Stratified Interactions in the V3 Loop of the HIV-1 Envelope. PLoS Comput. Biol. 3 (11) (2007)
David C. Nickle, Morgane Rolland, Mark A. Jensen, Sergei L. Kosakovsky Pond, Wenjie Deng, Mark Seligman, David Heckerman, James I. Mullins, Nebojsa Jojic
Coping with Viral Diversity in HIV Vaccine Design. PLoS Comput. Biol. 3 (4) (2007)
Wen-Yu Chung, Samir Wadhawan, Radek Szklarczyk, Sergei L. Kosakovsky Pond, Anton Nekrutenko
A First Look at ARFome: Dual-Coding Genes in Mammalian Genomes. PLoS Comput. Biol. 3 (5) (2007)
Art F. Y. Poon, Fraser I. Lewis, Sergei L. Kosakovsky Pond, Simon D. W. Frost
Evolutionary Interactions between N-Linked Glycosylation Sites in the HIV-1 Envelope. PLoS Comput. Biol. 3 (1) (2007)
Philippe Lemey, Sergei L. Kosakovsky Pond, Alexei J. Drummond, Oliver G. Pybus, Beth Shapiro, Helena Barroso, Nuno Taveira, Andrew Rambaut
Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics. PLoS Comput. Biol. 3 (2) (2007)
Sergei L. Kosakovsky Pond, Simon D. W. Frost, Zehava Grossman, Michael B. Gravenor, Douglas D. Richman, Andrew J. Leigh Brown
Adaptation to Different Human Populations by HIV-1 Revealed by Codon-Based Analyses. PLoS Comput. Biol. 2 (6) (2006)
Sergei L. Kosakovsky Pond, David Posada, Michael B. Gravenor, Christopher H. Woelk, Simon D. W. Frost
GARD: a genetic algorithm for recombination detection. Bioinform. 22 (24) (2006)
Sergei L. Kosakovsky Pond, Simon D. W. Frost
Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinform. 21 (10) (2005)
Sergei L. Kosakovsky Pond, Simon D. W. Frost, Spencer V. Muse
HyPhy: hypothesis testing using phylogenies. Bioinform. 21 (5) (2005)