| HyPhy: hypothesis testing using phylogenies SLK Pond, SV Muse Statistical methods in molecular evolution, 125-181, 2005 | 2484 | 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 | 1443 | 2005 |
| Datamonkey: rapid detection of selective pressure on individual sites of codon alignments SLK Pond, SDW Frost Bioinformatics 21 (10), 2531-2533, 2005 | 1177 | 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 | 1019* | 2010 |
| 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 | 730 | 2006 |
| Detecting individual sites subject to episodic diversifying selection B Murrell, JO Wertheim, S Moola, T Weighill, K Scheffler, SLK Pond PLoS genetics 8 (7), e1002764, 2012 | 727 | 2012 |
| GARD: a genetic algorithm for recombination detection SL Kosakovsky Pond, D Posada, MB Gravenor, CH Woelk, SDW Frost Bioinformatics 22 (24), 3096-3098, 2006 | 562 | 2006 |
| 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 | 481 | 2013 |
| 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 | 364 | 2011 |
| 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, 2016 | 360 | 2016 |
| 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 | 353 | 2005 |
| 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 | 347 | 2011 |
| 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 | 267 | 2007 |
| Site-to-site variation of synonymous substitution rates SK Pond, SV Muse Molecular biology and evolution 22 (12), 2375-2385, 2005 | 248 | 2005 |
| 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 | 231 | 2008 |
| Adaptation to different human populations by HIV-1 revealed by codon-based analyses SLK Pond, SDW Frost, Z Grossman, MB Gravenor, DD Richman, ... PLoS computational biology 2 (6), e62, 2006 | 223 | 2006 |
| A genetic algorithm approach to detecting lineage-specific variation in selection pressure SLK Pond, SDW Frost Molecular biology and evolution 22 (3), 478-485, 2004 | 205 | 2004 |
| Characterization of human immunodeficiency virus type 1 (HIV-1) envelope variation and neutralizing antibody responses during transmission of HIV-1 subtype B SDW Frost, Y Liu, SLK Pond, C Chappey, T Wrin, CJ Petropoulos, ... Journal of virology 79 (10), 6523-6527, 2005 | 172 | 2005 |
| Statistics and truth in phylogenomics S Kumar, AJ Filipski, FU Battistuzzi, SL Kosakovsky Pond, K Tamura Molecular biology and evolution 29 (2), 457-472, 2011 | 166 | 2011 |
| Broadly neutralizing antibody responses in a large longitudinal sub-Saharan HIV primary infection cohort E Landais, X Huang, C Havenar-Daughton, B Murrell, MA Price, ... PLoS pathogens 12 (1), e1005369, 2016 | 165 | 2016 |
Simon DW FrostMicrosoft ResearchVerified email at microsoft.com
