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A. Poon · SciRah

Researcher profile · Semantic Scholar

A. Poon

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A. Poon — researcher profile on SciRah

h-index: 36
Works: 120
Citations: 5,792

Most-cited papers

HyPhy 2.5 - a customizable platform for evolutionary hypothesis testing using phylogenies.
Sergei L. Kosakovsky Pond, A. Poon, Ryan Velazquez, S. Weaver +10 more
2019Molecular biology and evolution678 citations Open access
Semantic Scholar
An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1
Sergei L. Kosakovsky Pond, D. Posada, Eric W. Stawiski, C. Chappey +6 more
2009PLoS Comput. Biol.257 citations Open access
Semantic Scholar
Near real-time monitoring of HIV transmission hotspots from routine HIV genotyping: an implementation case study
A. Poon, R. Gustafson, P. Daly, Laura Zerr +9 more
2016The Lancet HIV177 citations Open access
Semantic Scholar
Ancestral Reconstruction
J. Joy, R. Liang, Rosemary M. McCloskey, T. Nguyen +1 more
2016PLoS Comput. Biol.170 citations Open access
Semantic Scholar
Characterizing HIV transmission networks across the United States.
Jeannette L. Aldous, Sergei L. Kosakovsky Pond, A. Poon, Sonia Jain +8 more
2012Clinical Infectious Diseases125 citations Open access
Semantic Scholar
Impacts and shortcomings of genetic clustering methods for infectious disease outbreaks
A. Poon
2016Virus Evolution94 citations Open access
Semantic Scholar
An open-source k-mer based machine learning tool for fast and accurate subtyping of HIV-1 genomes
Stephen Solis-Reyes, Mariano Avino, A. Poon, L. Kari
2018bioRxiv91 citations Open access
Semantic Scholar
Detecting signatures of selection from DNA sequences using Datamonkey.
A. Poon, S. Frost, Sergei L Kosakovsky Pond
2009Methods in molecular biology89 citations
Semantic Scholar
Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1.
A. Poon, L. Swenson, W. Dong, W. Deng +6 more
2010Molecular biology and evolution73 citations Open access
Semantic Scholar
Evolutionary fingerprinting of genes.
Sergei L Kosakovsky Pond, K. Scheffler, M. Gravenor, A. Poon +1 more
2010Molecular biology and evolution70 citations Open access
Semantic Scholar
Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison
O. Ratmann, Emma B. Hodcroft, M. Pickles, A. Cori +20 more
2016Molecular biology and evolution63 citations Open access
Semantic Scholar
Phylogenetic approach to recover integration dates of latent HIV sequences within-host
B. Jones, Natalie N. Kinloch, J. Horacsek, B. Ganase +7 more
2018Proceedings of the National Academy of Sciences of the United States of America59 citations Open access
Semantic Scholar
The Influence of Hepatitis C Virus Genetic Region on Phylogenetic Clustering Analysis
F. Lamoury, B. Jacka, Sofia R. Bartlett, Rowena A. Bull +8 more
2015PLoS ONE57 citations Open access
Semantic Scholar
HIV Drug Resistance Testing by High-Multiplex “Wide” Sequencing on the MiSeq Instrument
H. Lapointe, W. Dong, Guinevere Q. Lee, D. Bangsberg +8 more
2015Antimicrobial Agents and Chemotherapy55 citations Open access
Semantic Scholar
Reconstructing the Dynamics of HIV Evolution within Hosts from Serial Deep Sequence Data
A. Poon, L. Swenson, E. Bunnik, Diana Edo-Matas +3 more
2012PLoS Comput. Biol.48 citations Open access
Semantic Scholar
Genotypic and Functional Impact of HIV-1 Adaptation to Its Host Population during the North American Epidemic
Laura A. Cotton, Xiaomei T. Kuang, A. Le, J. Carlson +25 more
2014PLoS Genetics47 citations Open access
Semantic Scholar
Addressing ethical challenges in US-based HIV phylogenetic research.
Liza Dawson, N. Benbow, F. Fletcher, Seble G. Kassaye +14 more
2020Journal of Infectious Diseases46 citations Open access
Semantic Scholar
Evidence of Pervasive Biologically Functional Secondary Structures within the Genomes of Eukaryotic Single-Stranded DNA Viruses
Brejnev Muhire, M. Golden, B. Murrell, P. Lefeuvre +11 more
2013Journal of Virology46 citations Open access
Semantic Scholar
Phylogenetic estimation of the temporal spread of hepatitis C genotype 1a in North America: a retrospective phylogenetic study
J. Joy, Rosemary M. McCloskey, Thuy Nguyen, R. Liang +7 more
2016Lancet. Infectious Diseases (Print)45 citations Open access
Semantic Scholar
Mapping the Shapes of Phylogenetic Trees from Human and Zoonotic RNA Viruses
A. Poon, Lorne W. Walker, Heather Murray, Rosemary M. McCloskey +2 more
2013PLoS ONE41 citations Open access
Semantic Scholar
Genetic Cluster Analysis for HIV Prevention
M. K. Grabowski, J. Herbeck, A. Poon
2018Current HIV/AIDS Reports40 citations Open access
Semantic Scholar
Dates of HIV infection can be estimated for seroprevalent patients by coalescent analysis of serial next-generation sequencing data
A. Poon, Rachel A. McGovern, T. Mo, D. Knapp +4 more
2011AIDS (London)40 citations Open access
Semantic Scholar
Phylodynamic Inference with Kernel ABC and Its Application to HIV Epidemiology
A. Poon
2015Molecular biology and evolution39 citations Open access
Semantic Scholar
Ageing in Escherichia coli requires damage by an extrinsic agent.
C. Rang, An-Nie Y. Peng, A. Poon, L. Chao
2012Microbiology38 citations Open access
Semantic Scholar
HIV Diversity and Genetic Compartmentalization in Blood and Testes during Suppressive Antiretroviral Therapy
Rachel L. Miller, Rosalie Ponte, B. Jones, N. Kinloch +11 more
2019Journal of Virology37 citations Open access
Semantic Scholar
HIV-1 Nef Protein Structures Associated with Brain Infection and Dementia Pathogenesis
S. Lamers, A. Poon, M. McGrath
2011PLoS ONE35 citations Open access
Semantic Scholar
Transmitted Drug Resistance in the CFAR Network of Integrated Clinical Systems Cohort: Prevalence and Effects on Pre-Therapy CD4 and Viral Load
A. Poon, Jeannette L. Aldous, W. C. Mathews, M. Kitahata +6 more
2011PLoS ONE34 citations Open access
Semantic Scholar
A model-based clustering method to detect infectious disease transmission outbreaks from sequence variation
Rosemary M. McCloskey, A. Poon
2017bioRxiv32 citations Open access
Semantic Scholar
Promises and pitfalls of Illumina sequencing for HIV resistance genotyping.
C. Brumme, A. Poon
2017Virus Research32 citations
Semantic Scholar
Higher sequence diversity in the vaginal tract than in blood at early HIV-1 infection
K. Klein, G. Nickel, I. Nankya, Fred Kyeyune +13 more
2018PLoS Pathogens28 citations Open access
Semantic Scholar
Genetic Diversity, Compartmentalization, and Age of HIV Proviruses Persisting in CD4+ T Cell Subsets during Long-Term Combination Antiretroviral Therapy
B. Jones, Rachel L. Miller, N. Kinloch, Olivia Tsai +12 more
2019Journal of Virology27 citations Open access
Semantic Scholar
Absence of HIV-1 Drug Resistance Mutations Supports the Use of Dolutegravir in Uganda
E. Ndashimye, Mariano Avino, Fred Kyeyune, I. Nankya +7 more
2018AIDS Research and Human Retroviruses27 citations Open access
Semantic Scholar
A molecular phylogenetics-based approach for identifying recent hepatitis C virus transmission events.
A. Olmstead, J. Joy, V. Montoya, Iris Luo +10 more
2015Infection, Genetics and Evolution26 citations Open access
Semantic Scholar
Genomic epidemiology of the first two waves of SARS-CoV-2 in Canada
Angela McLaughlin, V. Montoya, Rachel L. Miller, Gideon J. Mordecai +3 more
2022eLife24 citations Open access
Semantic Scholar
Transmission of hepatitis C virus infection among younger and older people who inject drugs in Vancouver, Canada
B. Jacka, T. Applegate, A. Poon, J. Raghwani +16 more
2016Journal of Hepatology23 citations Open access
Semantic Scholar
Prolonged and Substantial Discordance in Prevalence of Raltegravir-Resistant HIV-1 in Plasma versus PBMC Samples Revealed by 454 “Deep” Sequencing
Guinevere Q. Lee, L. Swenson, A. Poon, Jeffrey N. Martin +3 more
2012PLoS ONE23 citations Open access
Semantic Scholar
Parsing Social Network Survey Data from Hidden Populations Using Stochastic Context-Free Grammars
A. Poon, K. Brouwer, S. Strathdee, Michelle Firestone-Cruz +4 more
2009PLoS ONE22 citations Open access
Semantic Scholar
Comparative analysis of HIV sequences in real time for public health
J. Wertheim, Connor Chato, A. Poon
2019Current Opinion in HIV and AIDS21 citations
Semantic Scholar
In Vitro Selection of Clinically Relevant Bevirimat Resistance Mutations Revealed by “Deep” Sequencing of Serially Passaged, Quasispecies-Containing Recombinant HIV-1
D. Knapp, P. Harrigan, A. Poon, Z. Brumme +2 more
2010Journal of Clinical Microbiology20 citations Open access
Semantic Scholar
Differential evolution of a CXCR4-using HIV-1 strain in CCR5wt/wt and CCR5∆32/∆32 hosts revealed by longitudinal deep sequencing and phylogenetic reconstruction
A. Le, Jeremy M. G. Taylor, W. Dong, Rosemary M. McCloskey +6 more
2015Scientific Reports19 citations Open access
Semantic Scholar
Accumulation of integrase strand transfer inhibitor resistance mutations confers high-level resistance to dolutegravir in non-B subtype HIV-1 strains from patients failing raltegravir in Uganda.
E. Ndashimye, Mariano Avino, Abayomi S. Olabode, A. Poon +10 more
2020Nephrology, Dialysis and Transplantation18 citations Open access
Semantic Scholar
Tree shape‐based approaches for the comparative study of cophylogeny
Mariano Avino, Garway T. Ng, Yi-Ying He, Mathias S. Renaud +2 more
2018bioRxiv18 citations Open access
Semantic Scholar
Selection in Coastal Synechococcus (Cyanobacteria) Populations Evaluated from Environmental Metagenomes
Vera Tai, A. Poon, I. Paulsen, B. Palenik
2011PLoS ONE18 citations Open access
Semantic Scholar
Network science inspires novel tree shape statistics
L. Chindelevitch, Maryam Hayati, A. Poon, C. Colijn
2019bioRxiv17 citations Open access
Semantic Scholar
node.dating: dating ancestors in phylogenetic trees in R
B. Jones, A. Poon
2017Bioinform.17 citations Open access
Semantic Scholar
Protease polymorphisms in HIV-1 subtype CRF01_AE represent selection by antiretroviral therapy and host immune pressure
W. Manosuthi, David M. Butler, Josué Pérez-Santiago, A. Poon +6 more
2010AIDS (London)17 citations Open access
Semantic Scholar
CoVizu: Rapid analysis and visualization of the global diversity of SARS-CoV-2 genomes
Roux-Cil Ferreira, Emmanuel Wong, Gopi Gugan, Kaitlyn E Wade +6 more
2021bioRxiv16 citations Open access
Semantic Scholar
Public health in genetic spaces: a statistical framework to optimize cluster-based outbreak detection
Connor Chato, M. Kalish, A. Poon
2019bioRxiv16 citations Open access
Semantic Scholar
Role of co-expressed APOBEC3F and APOBEC3G in inducing HIV-1 drug resistance
Nazanin Mohammadzadeh, Robin P. Love, Richard Gibson, E. Arts +2 more
2019Heliyon16 citations Open access
Semantic Scholar
Sensitive detection of HIV-1 resistance to Zidovudine and impact on treatment outcomes in low- to middle-income countries
Richard Gibson, G. Nickel, Michael Crawford, Fred Kyeyune +10 more
2017Infectious Diseases of Poverty16 citations Open access
Semantic Scholar

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