| 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 | 1134* | 2010 |
| Compensating for our load of mutations: freezing the meltdown of small populations A Poon, SP Otto Evolution 54 (5), 1467-1479, 2000 | 172 | 2000 |
| An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1 SLK Pond, D Posada, E Stawiski, C Chappey, AFY Poon, G Hughes, ... PLoS Comput Biol 5 (11), e1000581, 2009 | 164 | 2009 |
| The rate of compensatory mutation in the DNA bacteriophage φX174 A Poon, L Chao Genetics 170 (3), 989-999, 2005 | 164 | 2005 |
| 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 | 127 | 2016 |
| 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 | 124 | 2008 |
| 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 | 120 | 2012 |
| 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 Comput Biol 3 (11), e231, 2007 | 100 | 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 | 94 | 2005 |
| 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 | 93 | 2008 |
| 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 | 89 | 2015 |
| Detecting signatures of selection from DNA sequences using Datamonkey AFY Poon, SDW Frost, SLK Pond Bioinformatics for DNA Sequence Analysis, 163-183, 2009 | 86 | 2009 |
| Ancestral reconstruction JB Joy, RH Liang, RM McCloskey, T Nguyen, AFY Poon PLoS computational biology 12 (7), e1004763, 2016 | 83 | 2016 |
| Phylogenetic Analysis of Population-Based and Deep Sequencing Data to Identify Coevolving Sites in the nef Gene of HIV-1 AFY Poon, LC Swenson, WWY Dong, W Deng, SL Kosakovsky Pond, ... Molecular biology and evolution 27 (4), 819-832, 2010 | 80* | 2010 |
| 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 | 77 | 2007 |
| 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 | 73 | 2008 |
| Phylogenetic Analysis of Population-Based and Deep Sequencing Data to Identify Coevolving Sites in the nef Gene of HIV-1 AFY Poon, LC Swenson, WWY Dong, W Deng, SL Kosakovsky Pond, ... Molecular biology and evolution 27 (4), 819-832, 2010 | 71 | 2010 |
| Evolutionary fingerprinting of genes SL Kosakovsky Pond, K Scheffler, MB Gravenor, AFY Poon, SDW Frost Molecular biology and evolution 27 (3), 520-536, 2010 | 69 | 2010 |
| Phylogenetic clustering of hepatitis C virus among people who inject drugs in Vancouver, Canada B Jacka, T Applegate, M Krajden, A Olmstead, PR Harrigan, BDL Marshall, ... Hepatology 60 (5), 1571-1580, 2014 | 65 | 2014 |
| 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 | 65 | 2009 |
Sergei L Kosakovsky PondProfessor of Biology, Institute for Genomics and Evolutionary Medicine, Temple UniversityVerified email at temple.edu
