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ORCIDSergei L. Kosakovsky Pond
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Journal Articles
- 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) - 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) - 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) - 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)
Conference and Workshop Papers
- 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
Informal and Other Publications
- 2024
- [i1]Hannah Kim, Sergei L. Kosakovsky Pond, Stephen MacNeil:
WIP: Identifying Tutorial Affordances for Interdisciplinary Learning Environments. CoRR abs/2408.14576 (2024)
Coauthor Index
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last updated on 2024-10-08 21:27 CEST by the dblp team
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