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Sergei L. Kosakovsky Pond
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2020 – today
- 2024
- [j24]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) - 2022
- [j23]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): 2719-2726 (2022) - 2020
- [j22]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)
2010 – 2019
- 2018
- [j21]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): 276:1-276:5 (2018) - [j20]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) - 2017
- [j19]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:
Lorenzo-Redondo et al. reply. Nat. 551(7681): E10-E10 (2017) - 2015
- [j18]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) - 2014
- [j17]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) - 2012
- [j16]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): 3248-3256 (2012) - [j15]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) - [c2]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: 1 - 2011
- [c1]Sergei L. Kosakovsky Pond:
Computational analysis of HIV-1 evolution and epidemiology. BIBM Workshops 2011: 60-63 - 2010
- [j14]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): 2455-2457 (2010) - [j13]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)
2000 – 2009
- 2009
- [j12]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:
An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1. PLoS Comput. Biol. 5(11) (2009) - 2008
- [j11]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): 1949-1950 (2008) - [j10]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) - 2007
- [j9]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) - [j8]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) - [j7]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) - [j6]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) - [j5]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) - 2006
- [j4]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): 3096-3098 (2006) - [j3]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) - 2005
- [j2]Sergei L. Kosakovsky Pond, Simon D. W. Frost, Spencer V. Muse:
HyPhy: hypothesis testing using phylogenies. Bioinform. 21(5): 676-679 (2005) - [j1]Sergei L. Kosakovsky Pond, Simon D. W. Frost:
Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinform. 21(10): 2531-2533 (2005)
Coauthor Index
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last updated on 2024-07-09 22:01 CEST by the dblp team
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