On the Validity of Evolutionary Models with Site-Specific Parameters

by Scheffler, Konrad, Murrell, Ben, Kosakovsky Pond, Sergei L.
Published 2014

Using HIV Transmission Networks to Investigate Community Effects in HIV Prevention Trials

by Wertheim, Joel O., Kosakovsky Pond, Sergei L., Little, Susan J., De Gruttola, Victor
Published 2011

Modeling HIV-1 Drug Resistance as Episodic Directional Selection

by Murrell, Ben, de Oliveira, Tulio, Seebregts, Chris, Kosakovsky Pond, Sergei L., Scheffler, Konrad
Published 2012

Detecting Individual Sites Subject to Episodic Diversifying Selection

by Murrell, Ben, Wertheim, Joel O., Moola, Sasha, Weighill, Thomas, Scheffler, Konrad, Kosakovsky Pond, Sergei L.
Published 2012

Suppressors of RNAi from plant viruses are subject to episodic positive selection

by Murray, Gemma G. R., Kosakovsky Pond, Sergei L., Obbard, Darren J.
Published 2013

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

by Kosakovsky Pond, Sergei L, Frost, Simon D. W, Grossman, Zehava, Gravenor, Michael B, Richman, Douglas D, Brown, Andrew J. Leigh
Published 2006

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

by Lemey, Philippe, Kosakovsky Pond, Sergei L, Drummond, Alexei J, Pybus, Oliver G, Shapiro, Beth, Barroso, Helena, Taveira, Nuno, Rambaut, Andrew
Published 2007

HIV-Specific Probabilistic Models of Protein Evolution

by Nickle, David C., Heath, Laura, Jensen, Mark A., Gilbert, Peter B., Mullins, James I., Kosakovsky Pond, Sergei L.
Published 2007

A Massively Parallel Sequencing Approach Uncovers Ancient Origins and High Genetic Variability of Endangered Przewalski's Horses

by Goto, Hiroki, Ryder, Oliver A., Fisher, Allison R., Schultz, Bryant, Kosakovsky Pond, Sergei L., Nekrutenko, Anton, Makova, Kateryna D.
Published 2011

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

by Poon, Art F. Y, Kosakovsky Pond, Sergei L., Bennett, Phil, Richman, Douglas D, Leigh Brown, Andrew J., Frost, Simon D. W
Published 2007

Using HIV Networks to Inform Real Time Prevention Interventions

by Little, Susan J., Kosakovsky Pond, Sergei L., Anderson, Christy M., Young, Jason A., Wertheim, Joel O., Mehta, Sanjay R., May, Susanne, Smith, Davey M.
Published 2014

Compartmentalized HIV rebound in the central nervous system after interruption of antiretroviral therapy

by Gianella, Sara, Kosakovsky Pond, Sergei L., Oliveira, Michelli F., Scheffler, Konrad, Strain, Matt C., De la Torre, Antonio, Letendre, Scott, Smith, Davey M., Ellis, Ronald J.
Published 2016

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

by de Oliveira, Michelli Faria, Gianella, Sara, Letendre, Scott, Scheffler, Konrad, Kosakovsky Pond, Sergei L., Smith, Davey M., Strain, Matt, Ellis, Ronald J.
Published 2015

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

by Hepler, N. Lance, Scheffler, Konrad, Weaver, Steven, Murrell, Ben, Richman, Douglas D., Burton, Dennis R., Poignard, Pascal, Smith, Davey M., Kosakovsky Pond, Sergei L.
Published 2014

Broadly Neutralizing Antibody Responses in a Large Longitudinal Sub-Saharan HIV Primary Infection Cohort

by Landais, Elise, Huang, Xiayu, Havenar-Daughton, Colin, Murrell, Ben, Price, Matt A., Wickramasinghe, Lalinda, Ramos, Alejandra, Bian, Charoan B., Simek, Melissa, Allen, Susan, Karita, Etienne, Kilembe, William, Lakhi, Shabir, Inambao, Mubiana, Kamali, Anatoli, Sanders, Eduard J., Anzala, Omu, Edward, Vinodh, Bekker, Linda-Gail, Tang, Jianming, Gilmour, Jill, Kosakovsky-Pond, Sergei L., Phung, Pham, Wrin, Terri, Crotty, Shane, Godzik, Adam, Poignard, Pascal
Published 2016

Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus

by Tully, Damien C., Ogilvie, Colin B., Batorsky, Rebecca E., Bean, David J., Power, Karen A., Ghebremichael, Musie, Bedard, Hunter E., Gladden, Adrianne D., Seese, Aaron M., Amero, Molly A., Lane, Kimberly, McGrath, Graham, Bazner, Suzane B., Tinsley, Jake, Lennon, Niall J., Henn, Matthew R., Brumme, Zabrina L., Norris, Philip J., Rosenberg, Eric S., Mayer, Kenneth H., Jessen, Heiko, Kosakovsky Pond, Sergei L., Walker, Bruce D., Altfeld, Marcus, Carlson, Jonathan M., Allen, Todd M.
Published 2016