Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection
Smith, Martin D, Wertheim, Joel O, Weaver, Steven, Murrell, Ben, Scheffler, Konrad, Kosakovsky Pond, Sergei L
Published in Molecular biology and evolution (01.05.2015)
Published in Molecular biology and evolution (01.05.2015)
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Journal Article
Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes
Weaver, Steven, Shank, Stephen D, Spielman, Stephanie J, Li, Michael, Muse, Spencer V, Kosakovsky Pond, Sergei L
Published in Molecular biology and evolution (01.03.2018)
Published in Molecular biology and evolution (01.03.2018)
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Journal Article
Detecting individual sites subject to episodic diversifying selection
Murrell, Ben, Wertheim, Joel O, Moola, Sasha, Weighill, Thomas, Scheffler, Konrad, Kosakovsky Pond, Sergei L
Published in PLoS genetics (01.07.2012)
Published in PLoS genetics (01.07.2012)
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Journal Article
RELAX: detecting relaxed selection in a phylogenetic framework
Wertheim, Joel O, Murrell, Ben, Smith, Martin D, Kosakovsky Pond, Sergei L, Scheffler, Konrad
Published in Molecular biology and evolution (01.03.2015)
Published in Molecular biology and evolution (01.03.2015)
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Journal Article
Gene-wide identification of episodic selection
Murrell, Ben, Weaver, Steven, Smith, Martin D, Wertheim, Joel O, Murrell, Sasha, Aylward, Anthony, Eren, Kemal, Pollner, Tristan, Martin, Darren P, Smith, Davey M, Scheffler, Konrad, Kosakovsky Pond, Sergei L
Published in Molecular biology and evolution (01.05.2015)
Published in Molecular biology and evolution (01.05.2015)
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Journal Article
Persistent HIV-1 replication maintains the tissue reservoir during therapy
Lorenzo-Redondo, Ramon, Fryer, Helen R, Bedford, Trevor, Kim, Eun-Young, Archer, John, Pond, Sergei L Kosakovsky, Chung, Yoon-Seok, Penugonda, Sudhir, Chipman, Jeffrey, Fletcher, Courtney V, Schacker, Timothy W, Malim, Michael H, Rambaut, Andrew, Haase, Ashley T, McLean, Angela R, Wolinsky, Steven M
Published in Nature (London) (04.02.2016)
Published in Nature (London) (04.02.2016)
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Journal Article
Purifying Selection Can Obscure the Ancient Age of Viral Lineages
Wertheim, Joel O., Kosakovsky Pond, Sergei L.
Published in Molecular Biology and Evolution (01.12.2011)
Published in Molecular Biology and Evolution (01.12.2011)
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Web Resource
The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages
Martin, Darren P., Weaver, Steven, Tegally, Houriiyah, San, James Emmanuel, Shank, Stephen D., Wilkinson, Eduan, Lucaci, Alexander G., Giandhari, Jennifer, Naidoo, Sureshnee, Pillay, Yeshnee, Singh, Lavanya, Lessells, Richard J., Gupta, Ravindra K., Wertheim, Joel O., Nekturenko, Anton, Murrell, Ben, Harkins, Gordon W., Lemey, Philippe, MacLean, Oscar A., Robertson, David L., de Oliveira, Tulio, Kosakovsky Pond, Sergei L.
Published in Cell (30.09.2021)
Published in Cell (30.09.2021)
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Journal Article
Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology
Delport, Wayne, Poon, Art F. Y., Frost, Simon D. W., Kosakovsky Pond, Sergei L.
Published in Bioinformatics (01.10.2010)
Published in Bioinformatics (01.10.2010)
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Journal Article
Evolutionary origins of human herpes simplex viruses 1 and 2
Wertheim, Joel O, Smith, Martin D, Smith, Davey M, Scheffler, Konrad, Kosakovsky Pond, Sergei L
Published in Molecular biology and evolution (01.09.2014)
Published in Molecular biology and evolution (01.09.2014)
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Journal Article
Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage
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
Published in Proceedings of the National Academy of Sciences - PNAS (15.11.2011)
Published in Proceedings of the National Academy of Sciences - PNAS (15.11.2011)
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Journal Article
The Global Transmission Network of HIV-1
Wertheim, Joel O., Brown, Andrew J. Leigh, Hepler, N. Lance, Mehta, Sanjay R., Richman, Douglas D., Smith, Davey M., Pond, Sergei L. Kosakovsky
Published in The Journal of infectious diseases (15.01.2014)
Published in The Journal of infectious diseases (15.01.2014)
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Journal Article
HyPhy: hypothesis testing using phylogenies
Pond, Sergei L. Kosakovsky, Frost, Simon D. W., Muse, Spencer V.
Published in Bioinformatics (01.03.2005)
Published in Bioinformatics (01.03.2005)
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Journal Article
Social and Genetic Networks of HIV-1 Transmission in New York City
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
Published in PLoS pathogens (01.01.2017)
Published in PLoS pathogens (01.01.2017)
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Journal Article
Neutral Theory and Rapidly Evolving Viral Pathogens
Frost, Simon D W, Magalis, Brittany Rife, Kosakovsky Pond, Sergei L
Published in Molecular Biology and Evolution (01.06.2018)
Published in Molecular Biology and Evolution (01.06.2018)
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Web Resource
Broadly Neutralizing Antibody Responses in a Large Longitudinal Sub-Saharan HIV Primary Infection Cohort
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 in PLoS pathogens (01.01.2016)
Published in PLoS pathogens (01.01.2016)
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