Sergei L Kosakovsky Pond

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Simon DW FrostMicrosoft PremonitionVerified email at microsoft.com
Davey SmithProfessor of Medicine, University of California, San DiegoVerified email at ucsd.edu
Joel WertheimUniversity of California San DiegoVerified email at ucsd.edu
Konrad SchefflerIlluminaVerified email at illumina.com
Ben MurrellDepartment of Microbiology, Tumor and Cell Biology, Karolinska InstitutetVerified email at ki.se
Susan LittleUniversity of California San DiegoVerified email at health.ucsd.edu
Art FY PoonWestern UniversityVerified email at uwo.ca
Steven WeaverInstitute for Genomics and Evolutionary Medicine, Temple UniversityVerified email at temple.edu
Spencer MuseProfessor of Statistics, North Carolina State UniversityVerified email at ncsu.edu
Wayne DelportSimplify Genomics, IncVerified email at simplifygenomics.com
Darren MartinUniversity of Cape TownVerified email at uct.ac.za
Mike GravenorProfessor of Biostatistics and Epidemiology, Swansea UniversityVerified email at swan.ac.uk
Anton NekrutenkoPenn State UniversityVerified email at nekrut.org
Stephen D. ShankTemple UniversityVerified email at temple.edu
CHRISTOPHER WOELKMERCK EXPLORATORY SCIENCE CENTERVerified email at merck.com
Philippe LemeyFull Professor, KU LeuvenVerified email at kuleuven.be
Robert ShaferProfessor of Medicine, Stanford UniversityVerified email at stanford.edu
Martin D SmithSoftware Developer, Pacific Biosciences of CaliforniaVerified email at pacificbiosciences.com
David L RobertsonProfessor, CVR Bioinformatics, MRC-University of Glasgow Centre for Virus ResearchVerified email at glasgow.ac.uk
David PosadaProfessor of Genetics, CINBIO, University of Vigo, SpainVerified email at uvigo.es

Sergei L Kosakovsky Pond

Professor of Biology, Institute for Genomics and Evolutionary Medicine, Temple University

Verified email at temple.edu - Homepage

Viral evolution phylogenetics evolutionary modeling algorithms


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HyPhy: hypothesis testing using phylogenies SLK Pond, SDW Frost, SV Muse Bioinformatics 21 (5), 676-679, 2005	3028	2005
Not so different after all: a comparison of methods for detecting amino acid sites under selection SL Kosakovsky Pond, SDW Frost Molecular biology and evolution 22 (5), 1208-1222, 2005	2050	2005
Datamonkey: rapid detection of selective pressure on individual sites of codon alignments SLK Pond, SDW Frost Bioinformatics 21 (10), 2531-2533, 2005	1426	2005
Detecting individual sites subject to episodic diversifying selection B Murrell, JO Wertheim, S Moola, T Weighill, K Scheffler, ... PLoS genetics 8 (7), e1002764, 2012	1351	2012
Genomics and epidemiology of the P. 1 SARS-CoV-2 lineage in Manaus, Brazil NR Faria, TA Mellan, C Whittaker, IM Claro, DS Candido, S Mishra, ... Science 372 (6544), 815-821, 2021	1286	2021
Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology W Delport, AFY Poon, SDW Frost, SL Kosakovsky Pond Bioinformatics 26 (19), 2455-2457, 2010	1237	2010
Detection of a SARS-CoV-2 variant of concern in South Africa H Tegally, E Wilkinson, M Giovanetti, A Iranzadeh, V Fonseca, ... Nature 592 (7854), 438-443, 2021	1219	2021
Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa H Tegally, E Wilkinson, M Giovanetti, A Iranzadeh, V Fonseca, ... medrxiv, 2020.12. 21.20248640, 2020	1113	2020
Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa R Viana, S Moyo, DG Amoako, H Tegally, C Scheepers, CL Althaus, ... Nature 603 (7902), 679-686, 2022	1007	2022
FUBAR: a fast, unconstrained bayesian approximation for inferring selection B Murrell, S Moola, A Mabona, T Weighill, D Sheward, ... Molecular biology and evolution 30 (5), 1196-1205, 2013	972	2013
Automated phylogenetic detection of recombination using a genetic algorithm SL Kosakovsky Pond, D Posada, MB Gravenor, CH Woelk, SDW Frost Molecular biology and evolution 23 (10), 1891-1901, 2006	926	2006
GARD: a genetic algorithm for recombination detection SL Kosakovsky Pond, D Posada, MB Gravenor, CH Woelk, SDW Frost Bioinformatics 22 (24), 3096-3098, 2006	782	2006
The biological and clinical significance of emerging SARS-CoV-2 variants K Tao, PL Tzou, J Nouhin, RK Gupta, T de Oliveira, SL Kosakovsky Pond, ... Nature Reviews Genetics 22 (12), 757-773, 2021	672	2021
Persistent HIV-1 replication maintains the tissue reservoir during therapy R Lorenzo-Redondo, HR Fryer, T Bedford, EY Kim, J Archer, ... Nature 530 (7588), 51-56, 2016	633	2016
Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes S Weaver, SD Shank, SJ Spielman, M Li, SV Muse, SL Kosakovsky Pond Molecular biology and evolution 35 (3), 773-777, 2018	557	2018
Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection MD Smith, JO Wertheim, S Weaver, B Murrell, K Scheffler, ... Molecular biology and evolution 32 (5), 1342-1353, 2015	525	2015
Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage RA Farrer, LA Weinert, J Bielby, TWJ Garner, F Balloux, F Clare, J Bosch, ... Proceedings of the National Academy of Sciences 108 (46), 18732-18736, 2011	473	2011
A random effects branch-site model for detecting episodic diversifying selection SL Kosakovsky Pond, B Murrell, M Fourment, SDW Frost, W Delport, ... Molecular biology and evolution 28 (11), 3033-3043, 2011	446	2011
RELAX: detecting relaxed selection in a phylogenetic framework JO Wertheim, B Murrell, MD Smith, SL Kosakovsky Pond, K Scheffler Molecular biology and evolution 32 (3), 820-832, 2015	444	2015
Gene-wide identification of episodic selection B Murrell, S Weaver, MD Smith, JO Wertheim, S Murrell, A Aylward, ... Molecular biology and evolution 32 (5), 1365-1371, 2015	393	2015

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