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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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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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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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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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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The biological and clinical significance of emerging SARS-CoV-2 variants
Tao, Kaiming, Tzou, Philip L., Nouhin, Janin, Gupta, Ravindra K., de Oliveira, Tulio, Kosakovsky Pond, Sergei L., Fera, Daniela, Shafer, Robert W.
Published in Nature reviews. Genetics (01.12.2021)
Published in Nature reviews. Genetics (01.12.2021)
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Predicting the mutational drivers of future SARS-CoV-2 variants of concern
Maher, M Cyrus, Bartha, Istvan, Weaver, Steven, di Iulio, Julia, Ferri, Elena, Soriaga, Leah, Lempp, Florian A, Hie, Brian L, Bryson, Bryan, Berger, Bonnie, Robertson, David L, Snell, Gyorgy, Corti, Davide, Virgin, Herbert W, Kosakovsky Pond, Sergei L, Telenti, Amalio
Published in Science translational medicine (23.02.2022)
Published in Science translational medicine (23.02.2022)
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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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Using HIV networks to inform real time prevention interventions
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 in PloS one (05.06.2014)
Published in PloS one (05.06.2014)
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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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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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HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies
Kosakovsky Pond, Sergei L, Poon, Art F Y, Velazquez, Ryan, Weaver, Steven, Hepler, N Lance, Murrell, Ben, Shank, Stephen D, Magalis, Brittany Rife, Bouvier, Dave, Nekrutenko, Anton, Wisotsky, Sadie, Spielman, Stephanie J, Frost, Simon D W, Muse, Spencer V
Published in Molecular biology and evolution (01.01.2020)
Published in Molecular biology and evolution (01.01.2020)
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Claudin-Low Breast Cancer; Clinical & Pathological Characteristics
Dias, Kay, Dvorkin-Gheva, Anna, Hallett, Robin M, Wu, Ying, Hassell, John, Pond, Gregory R, Levine, Mark, Whelan, Tim, Bane, Anita L
Published in PloS one (03.01.2017)
Published in PloS one (03.01.2017)
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Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen
MacLean, Oscar A, Lytras, Spyros, Weaver, Steven, Singer, Joshua B, Boni, Maciej F, Lemey, Philippe, Kosakovsky Pond, Sergei L, Robertson, David L
Published in PLoS biology (12.03.2021)
Published in PLoS biology (12.03.2021)
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