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 WertheimProfessor, University 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
Steven WeaverInstitute for Genomics and Evolutionary Medicine, Temple UniversityVerified email at temple.edu
Susan LittleUniversity of California San DiegoVerified email at health.ucsd.edu
Art FY PoonWestern UniversityVerified email at uwo.ca
Spencer MuseProfessor of Statistics, North Carolina State UniversityVerified email at ncsu.edu
Wayne DelportSimplify Genomics, IncVerified email at simplifygenomics.com
Stephen D. ShankTemple UniversityVerified email at temple.edu
Anton NekrutenkoPenn State UniversityVerified email at nekrut.org
Darren MartinUniversity of Cape TownVerified email at uct.ac.za
Mike GravenorProfessor of Biostatistics and Epidemiology, Swansea UniversityVerified email at swan.ac.uk
Robert ShaferProfessor of Medicine, Stanford UniversityVerified email at stanford.edu
Philippe LemeyFull Professor, KU LeuvenVerified email at kuleuven.be
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
Stephanie J SpielmanChildhood Cancer Data Lab, Alex's Lemonade Stand FoundationVerified email at ccdatalab.org
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	3329	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	1943	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	1716	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	1708	2021
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	1644	2022
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	1623	2021
Datamonkey: rapid detection of selective pressure on individual sites of codon alignments SLK Pond, SDW Frost Bioinformatics 21 (10), 2531-2533, 2005	1519	2005
Not so different after all: a comparison of methods for detecting amino acid sites under selection SLK Pond, SD Frost Mol Biol Evol 22 (5), 1208-1222, 2005	1406	2005
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	1340	2010
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	1264	2013
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	1228	2020
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	1108	2021
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	1024	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	868	2006
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	839	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	725	2015
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	710	2016
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	646	2015
Emergence of SARS-CoV-2 omicron lineages BA. 4 and BA. 5 in South Africa H Tegally, M Moir, J Everatt, M Giovanetti, C Scheepers, E Wilkinson, ... Nature medicine 28 (9), 1785-1790, 2022	625	2022
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	565	2015

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