| 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 | 1356* | 2010 |
| HyPhy 2.5—a customizable platform for evolutionary hypothesis testing using phylogenies SL Kosakovsky Pond, AFY Poon, R Velazquez, S Weaver, NL Hepler, ... Molecular biology and evolution 37 (1), 295-299, 2020 | 470 | 2020 |
| Compensating for our load of mutations: freezing the meltdown of small populations A Poon, SP Otto Evolution 54 (5), 1467-1479, 2000 | 215 | 2000 |
| Ancestral reconstruction JB Joy, RH Liang, RM McCloskey, T Nguyen, AFY Poon PLoS computational biology 12 (7), e1004763, 2016 | 214 | 2016 |
| Near real-time monitoring of HIV transmission hotspots from routine HIV genotyping: an implementation case study AFY Poon, R Gustafson, P Daly, L Zerr, SE Demlow, J Wong, CK Woods, ... The lancet HIV 3 (5), e231-e238, 2016 | 210 | 2016 |
| An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1 SL Kosakovsky Pond, D Posada, E Stawiski, C Chappey, AFY Poon, ... PLoS computational biology 5 (11), e1000581, 2009 | 198 | 2009 |
| The rate of compensatory mutation in the DNA bacteriophage φX174 A Poon, L Chao Genetics 170 (3), 989-999, 2005 | 193 | 2005 |
| Characterizing HIV transmission networks across the United States JL Aldous, SK Pond, A Poon, S Jain, H Qin, JS Kahn, M Kitahata, ... Clinical Infectious Diseases 55 (8), 1135-1143, 2012 | 154 | 2012 |
| Immune-driven recombination and loss of control after HIV superinfection H Streeck, B Li, AFY Poon, A Schneidewind, AD Gladden, KA Power, ... The Journal of experimental medicine 205 (8), 1789-1796, 2008 | 147 | 2008 |
| An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope AFY Poon, FI Lewis, SLK Pond, SDW Frost PLoS computational biology 3 (11), e231, 2007 | 127 | 2007 |
| The coupon collector and the suppressor mutation: estimating the number of compensatory mutations by maximum likelihood A Poon, BH Davis, L Chao Genetics 170 (3), 1323-1332, 2005 | 119 | 2005 |
| The impact of clinical, demographic and risk factors on rates of HIV transmission: a population-based phylogenetic analysis in British Columbia, Canada AFY Poon, JB Joy, CK Woods, S Shurgold, G Colley, CJ Brumme, ... The Journal of infectious diseases 211 (6), 926-935, 2015 | 117 | 2015 |
| A maximum likelihood method for detecting directional evolution in protein sequences and its application to influenza A virus SL Kosakovsky Pond, AFY Poon, AJ Leigh Brown, SDW Frost Molecular biology and evolution 25 (9), 1809-1824, 2008 | 113 | 2008 |
| Detecting signatures of selection from DNA sequences using Datamonkey AFY Poon, SDW Frost, SLK Pond Bioinformatics for DNA Sequence Analysis, 163-183, 2009 | 111 | 2009 |
| An open-source k-mer based machine learning tool for fast and accurate subtyping of HIV-1 genomes S Solis-Reyes, M Avino, A Poon, L Kari PloS one 13 (11), e0206409, 2018 | 104 | 2018 |
| Impacts and shortcomings of genetic clustering methods for infectious disease outbreaks AFY Poon Virus evolution 2 (2), vew031, 2016 | 101 | 2016 |
| Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models AFY Poon, FI Lewis, SDW Frost, SL Kosakovsky Pond Bioinformatics 24 (17), 1949-1950, 2008 | 99 | 2008 |
| Compensatory mutations are repeatable and clustered within proteins BH Davis, AFY Poon, MC Whitlock Proceedings of the Royal Society B: Biological Sciences 276 (1663), 1823-1827, 2009 | 94 | 2009 |
| Evolutionary interactions between N-linked glycosylation sites in the HIV-1 envelope AFY Poon, FI Lewis, SLK Pond, SDW Frost PLoS Computational Biology 3 (1), e11, 2007 | 91 | 2007 |
| Detection of mammalian virulence determinants in highly pathogenic avian influenza H5N1 viruses: multivariate analysis of published data SJ Lycett, MJ Ward, FI Lewis, AFY Poon, SL Kosakovsky Pond, ... Journal of virology 83 (19), 9901-9910, 2009 | 90 | 2009 |
Sergei L Kosakovsky PondProfessor of Biology, Institute for Genomics and Evolutionary Medicine, Temple UniversityVerified email at temple.edu