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
28932005
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
17192005
Datamonkey: rapid detection of selective pressure on individual sites of codon alignments
SLK Pond, SDW Frost
Bioinformatics 21 (10), 2531-2533, 2005
13182005
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
11422010
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
9992012
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
8232006
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
7042013
GARD: a genetic algorithm for recombination detection
SL Kosakovsky Pond, D Posada, MB Gravenor, CH Woelk, SDW Frost
Bioinformatics 22 (24), 3096-3098, 2006
6752006
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
5112016
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
4332020
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
4192011
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
4062011
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
3722005
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
2932015
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
2922007
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
2692018
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
2622015
Site-to-site variation of synonymous substitution rates
SK Pond, SV Muse
Molecular biology and evolution 22 (12), 2375-2385, 2005
2622005
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
2482015
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
2482006
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