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
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
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
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
HIV-TRACE (TRAnsmission Cluster Engine): a Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens
Kosakovsky Pond, Sergei L, Weaver, Steven, Leigh Brown, Andrew J, Wertheim, Joel O
Published in Molecular biology and evolution (01.07.2018)
Published in Molecular biology and evolution (01.07.2018)
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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
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
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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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
Statistics and Truth in Phylogenomics
Kumar, Sudhir, Filipski, Alan J., Battistuzzi, Fabia U., Kosakovsky Pond, Sergei L., Tamura, Koichiro
Published in Molecular biology and evolution (01.02.2012)
Published in Molecular biology and evolution (01.02.2012)
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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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