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Items: 1 to 50 of 81

1.

Phylogenetic measures of indel rate variation among the HIV-1 group M subtypes.

Palmer J, Poon AFY.

Virus Evol. 2019 Jul 21;5(2):vez022. doi: 10.1093/ve/vez022. eCollection 2019 Jul.

2.

Tree shape-based approaches for the comparative study of cophylogeny.

Avino M, Ng GT, He Y, Renaud MS, Jones BR, Poon AFY.

Ecol Evol. 2019 May 29;9(12):6756-6771. doi: 10.1002/ece3.5185. eCollection 2019 Jun.

3.

HIV Diversity and Genetic Compartmentalization in Blood and Testes during Suppressive Antiretroviral Therapy.

Miller RL, Ponte R, Jones BR, Kinloch NN, Omondi FH, Jenabian MA, Dupuy FP, Fromentin R, Brassard P, Mehraj V, Chomont N, Poon AFY, Joy JB, Brumme ZL, Routy JP; ORCHID Study Group.

J Virol. 2019 Aug 13;93(17). pii: e00755-19. doi: 10.1128/JVI.00755-19. Print 2019 Sep 1.

PMID:
31189714
4.

Role of co-expressed APOBEC3F and APOBEC3G in inducing HIV-1 drug resistance.

Mohammadzadeh N, Love RP, Gibson R, Arts EJ, Poon AFY, Chelico L.

Heliyon. 2019 Apr 16;5(4):e01498. doi: 10.1016/j.heliyon.2019.e01498. eCollection 2019 Apr.

5.

Comparative analysis of HIV sequences in real time for public health.

Wertheim JO, Chato C, Poon AFY.

Curr Opin HIV AIDS. 2019 May;14(3):213-220. doi: 10.1097/COH.0000000000000539.

PMID:
30882486
6.

Evidence for a recombinant origin of HIV-1 Group M from genomic variation.

Olabode AS, Avino M, Ng GT, Abu-Sardanah F, Dick DW, Poon AFY.

Virus Evol. 2019 Jan 22;5(1):vey039. doi: 10.1093/ve/vey039. eCollection 2019 Jan.

7.

First-line HIV treatment failures in non-B subtypes and recombinants: a cross-sectional analysis of multiple populations in Uganda.

Poon AFY, Ndashimye E, Avino M, Gibson R, Kityo C, Kyeyune F, Nankya I, Quiñones-Mateu ME, Arts EJ; The Ugandan Drug Resistance Study Team.

AIDS Res Ther. 2019 Jan 22;16(1):3. doi: 10.1186/s12981-019-0218-2.

8.

A systematic, deep sequencing-based methodology for identification of mixed-genotype hepatitis C virus infections.

Olmstead AD, Montoya V, Chui CK, Dong W, Joy JB, Tai V, Poon AFY, Nguyen T, Brumme CJ, Martinello M, Matthews GV, Richard Harrigan P, Dore GJ, Applegate TL, Grebely J, Howe AYM.

Infect Genet Evol. 2019 Apr;69:76-84. doi: 10.1016/j.meegid.2019.01.016. Epub 2019 Jan 14.

PMID:
30654177
9.

Detecting Amino Acid Coevolution with Bayesian Graphical Models.

Avino M, Poon AFY.

Methods Mol Biol. 2019;1851:105-122. doi: 10.1007/978-1-4939-8736-8_6.

PMID:
30298394
10.

Phylogenetic approach to recover integration dates of latent HIV sequences within-host.

Jones BR, Kinloch NN, Horacsek J, Ganase B, Harris M, Harrigan PR, Jones RB, Brockman MA, Joy JB, Poon AFY, Brumme ZL.

Proc Natl Acad Sci U S A. 2018 Sep 18;115(38):E8958-E8967. doi: 10.1073/pnas.1802028115. Epub 2018 Sep 5.

11.

HIV-1 Transmission Clustering and Phylodynamics Highlight the Important Role of Young Men Who Have Sex with Men.

Dennis AM, Volz E, Frost ASMSDW, Hossain M, Poon AFY, Rebeiro PF, Vermund SH, Sterling TR, Kalish ML.

AIDS Res Hum Retroviruses. 2018 Oct;34(10):879-888. doi: 10.1089/AID.2018.0039. Epub 2018 Aug 23.

12.

Quantitation of the latent HIV-1 reservoir from the sequence diversity in viral outgrowth assays.

Poon AFY, Prodger JL, Lynch BA, Lai J, Reynolds SJ, Kasule J, Capoferri AA, Lamers SL, Rodriguez CW, Bruno D, Porcella SF, Martens C, Quinn TC, Redd AD.

Retrovirology. 2018 Jul 5;15(1):47. doi: 10.1186/s12977-018-0426-1.

13.

Quantifying the Aftermath: Recent Outbreaks Among People Who Inject Drugs and the Utility of Phylodynamics.

Poon AFY, Dearlove BL.

J Infect Dis. 2018 May 25;217(12):1854-1857. doi: 10.1093/infdis/jiy132. No abstract available.

14.

Genetic Cluster Analysis for HIV Prevention.

Grabowski MK, Herbeck JT, Poon AFY.

Curr HIV/AIDS Rep. 2018 Apr;15(2):182-189. doi: 10.1007/s11904-018-0384-1. Review.

15.

Absence of HIV-1 Drug Resistance Mutations Supports the Use of Dolutegravir in Uganda.

Ndashimye E, Avino M, Kyeyune F, Nankya I, Gibson RM, Nabulime E, Poon AFY, Kityo C, Mugyenyi P, Quiñones-Mateu ME, Arts EJ.

AIDS Res Hum Retroviruses. 2018 May;34(5):404-414. doi: 10.1089/AID.2017.0205. Epub 2018 Feb 26.

16.

Sensitive detection of HIV-1 resistance to Zidovudine and impact on treatment outcomes in low- to middle-income countries.

Gibson RM, Nickel G, Crawford M, Kyeyune F, Venner C, Nankya I, Nabulime E, Ndashimye E, Poon AFY, Salata RA, Kityo C, Mugyenyi P, Quiñones-Mateu ME, Arts EJ.

Infect Dis Poverty. 2017 Dec 4;6(1):163. doi: 10.1186/s40249-017-0377-0.

17.

What Proportion of HIV-Infected Foreign-Born Individuals in the United States Have Been Infected After Immigrating to the United States?

Herbeck JT, Kerani RP, Poon AFY.

J Acquir Immune Defic Syndr. 2018 Apr 1;77(4):e35-e36. doi: 10.1097/QAI.0000000000001594. No abstract available.

18.

A model-based clustering method to detect infectious disease transmission outbreaks from sequence variation.

McCloskey RM, Poon AFY.

PLoS Comput Biol. 2017 Nov 13;13(11):e1005868. doi: 10.1371/journal.pcbi.1005868. eCollection 2017 Nov.

19.

Potential for immune-driven viral polymorphisms to compromise antiretroviral-based preexposure prophylaxis for prevention of HIV-1 infection.

Gatanaga H, Brumme ZL, Adland E, Reyes-Terán G, Avila-Rios S, Mejía-Villatoro CR, Hayashida T, Chikata T, Van Tran G, Van Nguyen K, Meza RI, Palou EY, Valenzuela-Ponce H, Pascale JM, Porras-Cortés G, Manzanero M, Lee GQ, Martin JN, Carrington MN, John M, Mallal S, Poon AFY, Goulder P, Takiguchi M, Oka S; International HIV Adaptation Collaborative.

AIDS. 2017 Sep 10;31(14):1935-1943. doi: 10.1097/QAD.0000000000001575.

PMID:
28650381
20.

node.dating: dating ancestors in phylogenetic trees in R.

Jones BR, Poon AFY.

Bioinformatics. 2017 Mar 15;33(6):932-934. doi: 10.1093/bioinformatics/btw744.

21.

Impacts and shortcomings of genetic clustering methods for infectious disease outbreaks.

Poon AF.

Virus Evol. 2016 Oct 20;2(2):vew031. doi: 10.1093/ve/vew031. eCollection 2016 Jul.

22.

Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.

Ratmann O, Hodcroft EB, Pickles M, Cori A, Hall M, Lycett S, Colijn C, Dearlove B, Didelot X, Frost S, Hossain AS, Joy JB, Kendall M, Kühnert D, Leventhal GE, Liang R, Plazzotta G, Poon AF, Rasmussen DA, Stadler T, Volz E, Weis C, Leigh Brown AJ, Fraser C; PANGEA-HIV Consortium.

Mol Biol Evol. 2017 Jan;34(1):185-203. doi: 10.1093/molbev/msw217. Epub 2016 Oct 7.

23.

Genotypic susceptibility score (GSS) and CD4+ T cell recovery in HIV-1 patients with suppressed viral load.

Gonzalez-Serna A, Glas AC, Brumme CJ, Poon AF, Nohpal De La Rosa A, Mudrikova T, Dias Lima V, Wensing AM, Harrigan R.

J Antimicrob Chemother. 2017 Feb;72(2):496-503. doi: 10.1093/jac/dkw455. Epub 2016 Dec 20.

PMID:
27999069
24.

Promises and pitfalls of Illumina sequencing for HIV resistance genotyping.

Brumme CJ, Poon AFY.

Virus Res. 2017 Jul 15;239:97-105. doi: 10.1016/j.virusres.2016.12.008. Epub 2016 Dec 18. Review.

PMID:
27993623
25.

Reconstructing contact network parameters from viral phylogenies.

McCloskey RM, Liang RH, Poon AF.

Virus Evol. 2016 Oct 30;2(2):vew029. eCollection 2016 Jul.

26.

Ancestral Reconstruction.

Joy JB, Liang RH, McCloskey RM, Nguyen T, Poon AF.

PLoS Comput Biol. 2016 Jul 12;12(7):e1004763. doi: 10.1371/journal.pcbi.1004763. eCollection 2016 Jul. No abstract available.

27.

Deep sequencing increases hepatitis C virus phylogenetic cluster detection compared to Sanger sequencing.

Montoya V, Olmstead A, Tang P, Cook D, Janjua N, Grebely J, Jacka B, Poon AF, Krajden M.

Infect Genet Evol. 2016 Sep;43:329-37. doi: 10.1016/j.meegid.2016.06.015. Epub 2016 Jun 6.

PMID:
27282472
28.

Near real-time monitoring of HIV transmission hotspots from routine HIV genotyping: an implementation case study.

Poon AF, Gustafson R, Daly P, Zerr L, Demlow SE, Wong J, Woods CK, Hogg RS, Krajden M, Moore D, Kendall P, Montaner JS, Harrigan PR.

Lancet HIV. 2016 May;3(5):e231-8. doi: 10.1016/S2352-3018(16)00046-1. Epub 2016 Apr 7.

29.

The spread of hepatitis C virus genotype 1a in North America: a retrospective phylogenetic study.

Joy JB, McCloskey RM, Nguyen T, Liang RH, Khudyakov Y, Olmstead A, Krajden M, Ward JW, Harrigan PR, Montaner JSG, Poon AFY.

Lancet Infect Dis. 2016 Jun;16(6):698-702. doi: 10.1016/S1473-3099(16)00124-9. Epub 2016 Mar 30.

30.

Transmission of hepatitis C virus infection among younger and older people who inject drugs in Vancouver, Canada.

Jacka B, Applegate T, Poon AF, Raghwani J, Harrigan PR, DeBeck K, Milloy MJ, Krajden M, Olmstead A, Joy JB, Marshall BD, Hayashi K, Pybus OG, Lima VD, Magiorkinis G, Montaner J, Lamoury F, Dore GJ, Wood E, Grebely J.

J Hepatol. 2016 Jun;64(6):1247-55. doi: 10.1016/j.jhep.2016.02.031. Epub 2016 Feb 26.

31.

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.

Le AQ, Taylor J, Dong W, McCloskey R, Woods C, Danroth R, Hayashi K, Milloy MJ, Poon AF, Brumme ZL.

Sci Rep. 2015 Dec 3;5:17607. doi: 10.1038/srep17607.

32.

Population-Level Immune-Mediated Adaptation in HIV-1 Polymerase during the North American Epidemic.

Kinloch NN, MacMillan DR, Le AQ, Cotton LA, Bangsberg DR, Buchbinder S, Carrington M, Fuchs J, Harrigan PR, Koblin B, Kushel M, Markowitz M, Mayer K, Milloy MJ, Schechter MT, Wagner T, Walker BD, Carlson JM, Poon AF, Brumme ZL.

J Virol. 2015 Nov 11;90(3):1244-58. doi: 10.1128/JVI.02353-15. Print 2016 Feb 1.

33.

HIV drug resistance testing by high-multiplex "wide" sequencing on the MiSeq instrument.

Lapointe HR, Dong W, Lee GQ, Bangsberg DR, Martin JN, Mocello AR, Boum Y, Karakas A, Kirkby D, Poon AF, Harrigan PR, Brumme CJ.

Antimicrob Agents Chemother. 2015 Nov;59(11):6824-33. doi: 10.1128/AAC.01490-15. Epub 2015 Aug 17.

34.

Global Database-Driven Assessment of HIV-1 Adaptation to the Immune Repertoires of Human Populations.

Karakas A, Brumme ZL, Poon AF.

J Virol. 2015 Oct;89(20):10693-5. doi: 10.1128/JVI.01355-15. Epub 2015 Aug 5.

35.

The Influence of Hepatitis C Virus Genetic Region on Phylogenetic Clustering Analysis.

Lamoury FM, Jacka B, Bartlett S, Bull RA, Wong A, Amin J, Schinkel J, Poon AF, Matthews GV, Grebely J, Dore GJ, Applegate TL.

PLoS One. 2015 Jul 20;10(7):e0131437. doi: 10.1371/journal.pone.0131437. eCollection 2015.

36.

Development and Validation of Two Screening Assays for the Hepatitis C Virus NS3 Q80K Polymorphism Associated with Reduced Response to Combination Treatment Regimens Containing Simeprevir.

Chui CK, Dong WW, Joy JB, Poon AF, Dong WY, Mo T, Woods CK, Beatty C, Hew H, Harrigan PR, Brumme CJ.

J Clin Microbiol. 2015 Sep;53(9):2942-50. doi: 10.1128/JCM.00650-15. Epub 2015 Jul 1.

37.

Phylodynamic Inference with Kernel ABC and Its Application to HIV Epidemiology.

Poon AF.

Mol Biol Evol. 2015 Sep;32(9):2483-95. doi: 10.1093/molbev/msv123. Epub 2015 May 25.

38.

A molecular phylogenetics-based approach for identifying recent hepatitis C virus transmission events.

Olmstead AD, Joy JB, Montoya V, Luo I, Poon AF, Jacka B, Lamoury F, Applegate T, Montaner J, Khudyakov Y, Grebely J, Cook D, Harrigan PR, Krajden M.

Infect Genet Evol. 2015 Jul;33:101-9. doi: 10.1016/j.meegid.2015.04.017. Epub 2015 Apr 24.

39.

Global origin and transmission of hepatitis C virus nonstructural protein 3 Q80K polymorphism.

McCloskey RM, Liang RH, Joy JB, Krajden M, Montaner JS, Harrigan PR, Poon AF.

J Infect Dis. 2015 Apr 15;211(8):1288-95. doi: 10.1093/infdis/jiu613. Epub 2014 Nov 10.

PMID:
25389307
40.

The impact of clinical, demographic and risk factors on rates of HIV transmission: a population-based phylogenetic analysis in British Columbia, Canada.

Poon AF, Joy JB, Woods CK, Shurgold S, Colley G, Brumme CJ, Hogg RS, Montaner JS, Harrigan PR.

J Infect Dis. 2015 Mar 15;211(6):926-35. doi: 10.1093/infdis/jiu560. Epub 2014 Oct 13.

41.

Phylogenetic clustering of hepatitis C virus among people who inject drugs in Vancouver, Canada.

Jacka B, Applegate T, Krajden M, Olmstead A, Harrigan PR, Marshall B, DeBeck K, Milloy MJ, Lamoury F, Pybus OG, Lima VD, Magiorkinis G, Montoya V, Montaner J, Joy J, Woods C, Dobrer S, Dore GJ, Poon AF, Grebely J.

Hepatology. 2014 Nov;60(5):1571-1580. doi: 10.1002/hep.27310. Epub 2014 Sep 29.

42.

"Deep" sequencing accuracy and reproducibility using Roche/454 technology for inferring co-receptor usage in HIV-1.

Knapp DJ, McGovern RA, Poon AF, Zhong X, Chan D, Swenson LC, Dong W, Harrigan PR.

PLoS One. 2014 Jun 24;9(6):e99508. doi: 10.1371/journal.pone.0099508. eCollection 2014.

43.

Theoretical and experimental assessment of degenerate primer tagging in ultra-deep applications of next-generation sequencing.

Liang RH, Mo T, Dong W, Lee GQ, Swenson LC, McCloskey RM, Woods CK, Brumme CJ, Ho CK, Schinkel J, Joy JB, Harrigan PR, Poon AF.

Nucleic Acids Res. 2014 Jul;42(12):e98. doi: 10.1093/nar/gku355. Epub 2014 May 7.

44.

Genotypic and functional impact of HIV-1 adaptation to its host population during the North American epidemic.

Cotton LA, Kuang XT, Le AQ, Carlson JM, Chan B, Chopera DR, Brumme CJ, Markle TJ, Martin E, Shahid A, Anmole G, Mwimanzi P, Nassab P, Penney KA, Rahman MA, Milloy MJ, Schechter MT, Markowitz M, Carrington M, Walker BD, Wagner T, Buchbinder S, Fuchs J, Koblin B, Mayer KH, Harrigan PR, Brockman MA, Poon AF, Brumme ZL.

PLoS Genet. 2014 Apr 24;10(4):e1004295. doi: 10.1371/journal.pgen.1004295. eCollection 2014 Apr.

45.

An evaluation of phylogenetic methods for reconstructing transmitted HIV variants using longitudinal clonal HIV sequence data.

McCloskey RM, Liang RH, Harrigan PR, Brumme ZL, Poon AF.

J Virol. 2014 Jun;88(11):6181-94. doi: 10.1128/JVI.00483-14. Epub 2014 Mar 19.

46.

Mapping the shapes of phylogenetic trees from human and zoonotic RNA viruses.

Poon AF, Walker LW, Murray H, McCloskey RM, Harrigan PR, Liang RH.

PLoS One. 2013 Nov 1;8(11):e78122. doi: 10.1371/journal.pone.0078122. eCollection 2013.

47.

Replication fitness of multiple nonnucleoside reverse transcriptase-resistant HIV-1 variants in the presence of etravirine measured by 454 deep sequencing.

Brumme CJ, Huber KD, Dong W, Poon AF, Harrigan PR, Sluis-Cremer N.

J Virol. 2013 Aug;87(15):8805-7. doi: 10.1128/JVI.00335-13. Epub 2013 May 29.

48.

Maraviroc treatment in non-R5-HIV-1-infected patients results in the selection of extreme CXCR4-using variants with limited effect on the total viral setpoint.

McGovern RA, Symons J, Poon AF, Harrigan PR, van Lelyveld SF, Hoepelman AI, van Ham PM, Dong W, Wensing AM, Nijhuis M.

J Antimicrob Chemother. 2013 Sep;68(9):2007-14. doi: 10.1093/jac/dkt153. Epub 2013 May 14.

PMID:
23677920
49.

Use of cellular HIV DNA to predict virologic response to maraviroc: performance of population-based and deep sequencing.

Swenson LC, Dong WW, Mo T, Demarest J, Chapman D, Ellery S, Heera J, Valdez H, Poon AF, Harrigan PR.

Clin Infect Dis. 2013 Jun;56(11):1659-66. doi: 10.1093/cid/cit105. Epub 2013 Feb 21.

PMID:
23429552
50.

Comparison of population and 454 "deep" sequence analysis for HIV type 1 tropism versus the original trofile assay in non-B subtypes.

Lee GQ, Harrigan PR, Dong W, Poon AF, Heera J, Demarest J, Rinehart A, Chapman D, Valdez H, Portsmouth S.

AIDS Res Hum Retroviruses. 2013 Jun;29(6):979-84. doi: 10.1089/AID.2012.0338. Epub 2013 Mar 6.

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