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22 results for Pond,+Sergei+LKosakovsky

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ArticlesPeer ReviewedFull Text
Detecting Individual Sites Subject to Episodic Diversifying Selection
Author / Creator:Murrell, Ben ; Wertheim, Joel O. ; Moola, Sasha ; Weighill, Thomas ; Scheffler, Konrad ; Kosakovsky Pond, Sergei L.
Publisher:United States: Public Library of Science
Journal title:PLoS genetics, 2012-07, Vol.8 (7), p.e1002764-e1002764
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Social and Genetic Networks of HIV-1 Transmission in New York City
Author / Creator:Wertheim, Joel O. ; Kosakovsky Pond, Sergei L. ; Forgione, Lisa A. ; Mehta, Sanjay R. ; Murrell, Ben ; Shah, Sharmila ; Smith, Davey M. ; Scheffler, Konrad ; Torian, Lucia V.
Publisher:United States: Public Library of Science
Journal title:PLoS pathogens, 2017-01, Vol.13 (1), p.e1006000-e1006000
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Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage
Author / Creator:Farrer, Rhys A ; Weinert, Lucy A ; Bielby, Jon ; Garner, Trenton W. J ; Balloux, Francois ; Clare, Frances ; Bosch, Jaime ; Cunningham, Andrew A ; Weldon, Che ; du Preez, Louis H ; Anderson, Lucy ; Pond, Sergei L. Kosakovsky ; Shahar-Golan, Revital ; Henk, Daniel A ; Fisher, Matthew C
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2011-11, Vol.108 (46), p.18732-18736
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Neutralizing Antibody Responses Drive the Evolution of Human Immunodeficiency Virus Type 1 Envelope during Recent HIV Infection
Author / Creator:Simon D. W. Frost ; Wrin, Terri ; Davey M. Smith ; Sergei L. Kosakovsky Pond ; Liu, Yang ; Paxinos, Ellen ; Chappey, Colombe ; Justin Galovich ; Jeff Beauchaine ; Petropoulos, Christos J. ; Little, Susan J. ; Richman, Douglas D. ; Martin, Malcolm A.
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2005-12, Vol.102 (51), p.18514-18519
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A Genetic Algorithm Approach to Detecting Lineage-Specific Variation in Selection Pressure
Author / Creator:Kosakovsky Pond, Sergei L ; Frost, Simon D W
Publisher:Oxford: Oxford University Press
Journal title:Molecular biology and evolution, 2005-03, Vol.22 (3), p.478-485
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Assigning and visualizing germline genes in antibody repertoires
Author / Creator:Frost, Simon D. W. ; Murrell, Ben ; Hossain, A. S. Md. Mukarram ; Silverman, Gregg J. ; Pond, Sergei L. Kosakovsky
Publisher:England: The Royal Society
Journal title:Philosophical transactions of the Royal Society of London. Series B. Biological sciences, 2015-09, Vol.370 (1676), p.20140240-20140240
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Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics
Author / Creator:Lemey, Philippe ; Kosakovsky Pond, Sergei L ; Drummond, Alexei J ; Pybus, Oliver G ; Shapiro, Beth ; Barroso, Helena ; Taveira, Nuno ; Rambaut, Andrew
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2007-02, Vol.3 (2), p.e29
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Adaptation to Different Human Populations by HIV-1 Revealed by Codon-Based Analyses
Author / Creator:Kosakovsky Pond, Sergei L ; Frost, Simon D. W ; Grossman, Zehava ; Gravenor, Michael B ; Richman, Douglas D ; Brown, Andrew J. Leigh
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2006-06, Vol.2 (6), p.e62-e62
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Modeling HIV-1 Drug Resistance as Episodic Directional Selection
Author / Creator:Murrell, Ben ; de Oliveira, Tulio ; Seebregts, Chris ; Kosakovsky Pond, Sergei L. ; Scheffler, Konrad
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2012-05, Vol.8 (5), p.e1002507
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IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform: e1003842
Author / Creator:Hepler, N Lance ; Scheffler, Konrad ; Weaver, Steven ; Murrell, Ben ; Richman, Douglas D ; Burton, Dennis R ; Poignard, Pascal ; Smith, Davey M ; Pond, Sergei LKosakovsky
Publisher:San Francisco: Public Library of Science
Journal title:PLoS computational biology, 2014-09, Vol.10 (9)
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An Evolutionary-Network Model Reveals Stratified Interactions in the V3 Loop of the HIV-1 Envelope
Author / Creator:Poon, Art F. Y ; Lewis, Fraser I ; Pond, Sergei L. Kosakovsky ; Frost, Simon D. W
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2007-11, Vol.3 (11), p.e231-e231
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Coping with Viral Diversity in HIV Vaccine Design
Author / Creator:Nickle, David C ; Rolland, Morgane ; Jensen, Mark A ; Pond, Sergei L. Kosakovsky ; Deng, Wenjie ; Seligman, Mark ; Heckerman, David ; Mullins, James I ; Jojic, Nebojsa
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2007-04, Vol.3 (4), p.e75-e75
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A Dirichlet Process Model for Detecting Positive Selection in Protein-Coding DNA Sequences
Author / Creator:Huelsenbeck, John P. ; Jain, Sonia ; Frost, Simon W. D. ; Pond, Sergei L. Kosakovsky
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2006-04, Vol.103 (16), p.6263-6268
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Phylodynamic Reconstruction Reveals Norovirus GII.4 Epidemic Expansions and their Molecular Determinants: e1000884
Author / Creator:Siebenga, J Joukje ; Lemey, Philippe ; Pond, Sergei LKosakovsky ; Rambaut, Andrew ; Vennema, Harry ; Koopmans, Marion
Publisher:San Francisco: Public Library of Science
Journal title:PLoS pathogens, 2010-05, Vol.6 (5)
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CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences: e1000885
Author / Creator:Delport, Wayne ; Scheffler, Konrad ; Botha, Gordon ; Gravenor, Mike B ; Muse, Spencer V ; Pond, Sergei LKosakovsky
Publisher:San Francisco: Public Library of Science
Journal title:PLoS computational biology, 2010-08, Vol.6 (8)
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Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial: e1003973
Author / Creator:Edlefsen, Paul T ; Rolland, Morgane ; Hertz, Tomer ; Tovanabutra, Sodsai ; Gartland, Andrew J ; deCamp, Allan C ; Magaret, Craig A ; Ahmed, Hasan ; Gottardo, Raphael ; Juraska, Michal ; McCoy, Connor ; Larsen, Brendan B ; Sanders-Buell, Eric ; Carrico, Chris ; Menis, Sergey ; Bose, Meera ; Arroyo, Miguel A ; O'Connell, Robert J ; Nitayaphan, Sorachai ; Pitisuttithum, Punnee ; Kaewkungwal, Jaranit ; Rerks-Ngarm, Supachai ; Robb, Merlin L ; Kirys, Tatsiana ; Georgiev, Ivelin S ; Kwong, Peter D ; Scheffler, Konrad ; Pond, Sergei LKosakovsky ; Carlson, Jonathan M ; Michael, Nelson L ; Schief, William R ; Mullins, James I ; Kim, Jerome H ; Gilbert, Peter B ; Team, RV144 Sequencing
Publisher:San Francisco: Public Library of Science
Journal title:PLoS computational biology, 2015-02, Vol.11 (2)
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Evolutionary Interactions between N-Linked Glycosylation Sites in the HIV-1 Envelope
Author / Creator:Poon, Art F. Y ; Lewis, Fraser I ; Pond, Sergei L. Kosakovsky ; Frost, Simon D. W
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2007-01, Vol.3 (1), p.e11-e11
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Comparative Analysis of Cell-Associated HIV DNA Levels in Cerebrospinal Fluid and Peripheral Blood by Droplet Digital PCR: e0139510
Author / Creator:Oliveira, Michelli Fariade ; Gianella, Sara ; Letendre, Scott ; Scheffler, Konrad ; Pond, Sergei LKosakovsky ; Smith, Davey M ; Strain, Matt ; Ellis, Ronald J
Journal title:PloS one, 2015-10, Vol.10 (10)
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Adaptation to Human Populations Is Revealed by Within-Host Polymorphisms in HIV-1 and Hepatitis C Virus
Author / Creator:Poon, Art F. Y ; Kosakovsky Pond, Sergei L. ; Bennett, Phil ; Richman, Douglas D ; Leigh Brown, Andrew J. ; Frost, Simon D. W
Publisher:United States: Public Library of Science
Journal title:PLoS pathogens, 2007-03, Vol.3 (3), p.e45-e45
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An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1: e1000581
Author / Creator:Pond, Sergei LKosakovsky ; Posada, David ; Stawiski, Eric ; Chappey, Colombe ; Poon, Art FY ; Hughes, Gareth ; Fearnhill, Esther ; Gravenor, Mike B ; Brown, Andrew JLeigh ; Frost, Simon DW
Publisher:San Francisco: Public Library of Science
Journal title:PLoS computational biology, 2009-11, Vol.5 (11)
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Detecting Individual Sites Subject to Episodic Diversifying Selection

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Social and Genetic Networks of HIV-1 Transmission in New York City

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Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage

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Neutralizing Antibody Responses Drive the Evolution of Human Immunodeficiency Virus Type 1 Envelope during Recent HIV Infection

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A Genetic Algorithm Approach to Detecting Lineage-Specific Variation in Selection Pressure

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Assigning and visualizing germline genes in antibody repertoires

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

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

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Modeling HIV-1 Drug Resistance as Episodic Directional Selection

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IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform: e1003842

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

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Coping with Viral Diversity in HIV Vaccine Design

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A Dirichlet Process Model for Detecting Positive Selection in Protein-Coding DNA Sequences

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Phylodynamic Reconstruction Reveals Norovirus GII.4 Epidemic Expansions and their Molecular Determinants: e1000884

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CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences: e1000885

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Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial: e1003973

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

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Comparative Analysis of Cell-Associated HIV DNA Levels in Cerebrospinal Fluid and Peripheral Blood by Droplet Digital PCR: e0139510

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Adaptation to Human Populations Is Revealed by Within-Host Polymorphisms in HIV-1 and Hepatitis C Virus

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An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1: e1000581

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