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Art FY Poon
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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
1341*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
4062020
Compensating for our load of mutations: freezing the meltdown of small populations
A Poon, SP Otto
Evolution 54 (5), 1467-1479, 2000
2152000
Ancestral reconstruction
JB Joy, RH Liang, RM McCloskey, T Nguyen, AFY Poon
PLoS computational biology 12 (7), e1004763, 2016
2032016
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
2022016
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
1922009
The rate of compensatory mutation in the DNA bacteriophage φX174
A Poon, L Chao
Genetics 170 (3), 989-999, 2005
1882005
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
1502012
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
1432008
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
1252007
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
1172015
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
1162005
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
1132008
Detecting signatures of selection from DNA sequences using Datamonkey
AFY Poon, SDW Frost, SLK Pond
Bioinformatics for DNA Sequence Analysis, 163-183, 2009
1102009
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
1012018
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
982008
Impacts and shortcomings of genetic clustering methods for infectious disease outbreaks
AFY Poon
Virus evolution 2 (2), vew031, 2016
962016
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
912009
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
912007
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
86*2010
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