Sergei L. Kosakovsky Pond

According to our database, Sergei L. Kosakovsky Pond authored at least 25 papers between 2005 and 2022.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2022

TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity.

Marcos A. Caraballo-Ortiz, Sayaka Miura, Maxwell D. Sanderford, Tenzin Dolker, Qiqing Tao, Steven Weaver, Sergei L. Kosakovsky Pond, Sudhir Kumar

Bioinform., 2022

2020

A new method for inferring timetrees from temporally sampled molecular sequences.

Sayaka Miura, Koichiro Tamura, Qiqing Tao, Louise A. Huuki, Sergei L. Kosakovsky Pond, Jessica Priest, Jiamin Deng, Sudhir Kumar

PLoS Comput. Biol., 2020

2018

Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons.

Kemal Eren, Steven Weaver, Robert Ketteringham, Morné Valentyn, Melissa Laird Smith, Venkatesh Kumar, Sanjay Mohan, Sergei L. Kosakovsky Pond, Ben Murrell

PLoS Comput. Biol., 2018

phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics.

Stephen D. Shank, Steven Weaver, Sergei L. Kosakovsky Pond

BMC Bioinform., 2018

2017

Lorenzo-Redondo <i>et al</i>. reply.

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

Nat., 2017

2015

: Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial.

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

PLoS Comput. Biol., 2015

2014

IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform.

N. Lance Hepler, Konrad Scheffler, Steven Weaver, Ben Murrell, Douglas D. Richman, Dennis R. Burton, Pascal Poignard, Davey M. Smith, Sergei L. Kosakovsky Pond

PLoS Comput. Biol., 2014

2012

Modeling HIV-1 Drug Resistance as Episodic Directional Selection.

Ben Murrell, Tulio de Oliveira, Chris Seebregts, Sergei L. Kosakovsky Pond, Konrad Scheffler

PLoS Comput. Biol., 2012

A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection.

Philippe Lemey, Vladimir N. Minin, Filip Bielejec, Sergei L. Kosakovsky Pond, Marc A. Suchard

Bioinform., 2012

Workshop: Error correction, noise filtering, and phylogenetic analysis of HIV sequences using the 454 platform.

Konrad Scheffler, N. Lance Hepler, Martin D. Smith, Wayne Delport, Art F. Y. Poon, Douglas D. Richman, Sergei L. Kosakovsky Pond

Proceedings of the IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, 2012

2011

Computational analysis of HIV-1 evolution and epidemiology.

Sergei L. Kosakovsky Pond

Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2011

2010

CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences.

Wayne Delport, Konrad Scheffler, Gordon Botha, Mike B. Gravenor, Spencer V. Muse, Sergei L. Kosakovsky Pond

PLoS Comput. Biol., 2010

Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology.

Wayne Delport, Art F. Y. Poon, Simon D. W. Frost, Sergei L. Kosakovsky Pond

Bioinform., 2010

2009

An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1.

Sergei L. Kosakovsky Pond, David Posada, Eric W. Stawiski, Colombe Chappey, Art F. Y. Poon, Gareth Hughes, Esther Fearnhill, Mike B. Gravenor, Andrew J. Leigh Brown, Simon D. W. Frost

PLoS Comput. Biol., 2009

2008

Comparison of Immunogen Designs That Optimize Peptide Coverage: Reply to Fischer et al.

David C. Nickle, Nebojsa Jojic, David Heckerman, Vladimir Jojic, Darko Kirovski, Morgane Rolland, Sergei L. Kosakovsky Pond, James I. Mullins

PLoS Comput. Biol., 2008

Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models.

Art F. Y. Poon, Fraser I. Lewis, Simon D. W. Frost, Sergei L. Kosakovsky Pond

Bioinform., 2008

2007

An Evolutionary-Network Model Reveals Stratified Interactions in the V3 Loop of the HIV-1 Envelope.

Art F. Y. Poon, Fraser I. Lewis, Sergei L. Kosakovsky Pond, Simon D. W. Frost

PLoS Comput. Biol., 2007

Evolutionary Interactions between N-Linked Glycosylation Sites in the HIV-1 Envelope.

Art F. Y. Poon, Fraser I. Lewis, Sergei L. Kosakovsky Pond, Simon D. W. Frost

PLoS Comput. Biol., 2007

Coping with Viral Diversity in HIV Vaccine Design.

David C. Nickle, Morgane Rolland, Mark A. Jensen, Sergei L. Kosakovsky Pond, Wenjie Deng, Mark Seligman, David Heckerman, James I. Mullins, Nebojsa Jojic

PLoS Comput. Biol., 2007

Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics.

Philippe Lemey, Sergei L. Kosakovsky Pond, Alexei J. Drummond, Oliver G. Pybus, Beth Shapiro, Helena Barroso, Nuno Taveira, Andrew Rambaut

PLoS Comput. Biol., 2007

A First Look at ARFome: Dual-Coding Genes in Mammalian Genomes.

Wen-Yu Chung, Samir Wadhawan, Radek Szklarczyk, Sergei L. Kosakovsky Pond, Anton Nekrutenko

PLoS Comput. Biol., 2007

2006

Adaptation to Different Human Populations by HIV-1 Revealed by Codon-Based Analyses.

Sergei L. Kosakovsky Pond, Simon D. W. Frost, Zehava Grossman, Michael B. Gravenor, Douglas D. Richman, Andrew J. Leigh Brown

PLoS Comput. Biol., 2006

GARD: a genetic algorithm for recombination detection.

Sergei L. Kosakovsky Pond, David Posada, Michael B. Gravenor, Christopher H. Woelk, Simon D. W. Frost

Bioinform., 2006

2005

HyPhy: hypothesis testing using phylogenies.

Sergei L. Kosakovsky Pond, Simon D. W. Frost, Spencer V. Muse

Bioinform., 2005

Datamonkey: rapid detection of selective pressure on individual sites of codon alignments.

Sergei L. Kosakovsky Pond, Simon D. W. Frost

Bioinform., 2005