Sergei L Kosakovsky Pond
Sergei L Kosakovsky Pond
Professor of Biology, Institute for Genomics and Evolutionary Medicine, Temple University
Verified email at temple.edu - Homepage
Title
Cited by
Cited by
Year
HyPhy: hypothesis testing using phylogenies
SLK Pond, SV Muse
Statistical methods in molecular evolution, 125-181, 2005
28532005
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
16822005
Datamonkey: rapid detection of selective pressure on individual sites of codon alignments
SLK Pond, SDW Frost
Bioinformatics 21 (10), 2531-2533, 2005
13012005
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
11252010
Detecting individual sites subject to episodic diversifying selection
B Murrell, JO Wertheim, S Moola, T Weighill, K Scheffler, SLK Pond
PLoS genet 8 (7), e1002764, 2012
9632012
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
8192006
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
6812013
GARD: a genetic algorithm for recombination detection
SL Kosakovsky Pond, D Posada, MB Gravenor, CH Woelk, SDW Frost
Bioinformatics 22 (24), 3096-3098, 2006
6612006
Persistent HIV-1 replication maintains the tissue reservoir during therapy
R Lorenzo-Redondo, HR Fryer, T Bedford, EY Kim, J Archer, SLK Pond, ...
Nature 530 (7588), 51-56, 2016
4962016
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
4142011
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
4022011
Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection
SDW Frost, T Wrin, DM Smith, SLK Pond, Y Liu, E Paxinos, C Chappey, ...
Proceedings of the National Academy of Sciences 102 (51), 18514-18519, 2005
3712005
28-way vertebrate alignment and conservation track in the UCSC Genome Browser
W Miller, K Rosenbloom, RC Hardison, M Hou, J Taylor, B Raney, ...
Genome research 17 (12), 1797-1808, 2007
2892007
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
2702015
Site-to-site variation of synonymous substitution rates
SK Pond, SV Muse
Molecular biology and evolution 22 (12), 2375-2385, 2005
2622005
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
2502018
Adaptation to different human populations by HIV-1 revealed by codon-based analyses
SLK Pond, SDW Frost, Z Grossman, MB Gravenor, DD Richman, ...
PLoS Comput Biol 2 (6), e62, 2006
2452006
Persistence of transmitted drug resistance among subjects with primary human immunodeficiency virus infection
SJ Little, SDW Frost, JK Wong, DM Smith, SLK Pond, CC Ignacio, ...
Journal of virology 82 (11), 5510-5518, 2008
2422008
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
2402015
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
2392020
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