Arthur F. Poon, Ph.D. - Publications

Affiliations: 
University of California, San Diego, La Jolla, CA 

39 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2015 Karakas A, Brumme ZL, Poon AF. Global Database-Driven Assessment of HIV-1 Adaptation to the Immune Repertoires of Human Populations. Journal of Virology. 89: 10693-5. PMID 26246562 DOI: 10.1128/JVI.01355-15  1
2015 Poon AF. Phylodynamic Inference with Kernel ABC and Its Application to HIV Epidemiology. Molecular Biology and Evolution. 32: 2483-95. PMID 26006189 DOI: 10.1093/molbev/msv123  1
2015 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. A molecular phylogenetics-based approach for identifying recent hepatitis C virus transmission events. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 33: 101-9. PMID 25917496 DOI: 10.1016/j.meegid.2015.04.017  1
2015 McCloskey RM, Liang RH, Joy JB, Krajden M, Montaner JS, Harrigan PR, Poon AF. Global origin and transmission of hepatitis C virus nonstructural protein 3 Q80K polymorphism. The Journal of Infectious Diseases. 211: 1288-95. PMID 25389307 DOI: 10.1093/infdis/jiu613  1
2015 Poon AF, Joy JB, Woods CK, Shurgold S, Colley G, Brumme CJ, Hogg RS, Montaner JS, Harrigan PR. The impact of clinical, demographic and risk factors on rates of HIV transmission: a population-based phylogenetic analysis in British Columbia, Canada. The Journal of Infectious Diseases. 211: 926-35. PMID 25312037 DOI: 10.1093/infdis/jiu560  1
2015 Lamoury FMJ, Jacka B, Bartlett S, Bull RA, Wong A, Amin J, Schinkel J, Poon AF, Matthews GV, Grebely J, Dore GJ, Applegate TL. The influence of hepatitis C virus genetic region on phylogenetic clustering analysis Plos One. 10. DOI: 10.1371/journal.pone.0131437  1
2014 Knapp DJ, McGovern RA, Poon AF, Zhong X, Chan D, Swenson LC, Dong W, Harrigan PR. "Deep" sequencing accuracy and reproducibility using Roche/454 technology for inferring co-receptor usage in HIV-1. Plos One. 9: e99508. PMID 24959876 DOI: 10.1371/journal.pone.0099508  1
2014 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. Theoretical and experimental assessment of degenerate primer tagging in ultra-deep applications of next-generation sequencing. Nucleic Acids Research. 42: e98. PMID 24810852 DOI: 10.1093/nar/gku355  1
2014 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, ... ... Poon AF, et al. Genotypic and functional impact of HIV-1 adaptation to its host population during the North American epidemic. Plos Genetics. 10: e1004295. PMID 24762668 DOI: 10.1371/Journal.Pgen.1004295  1
2014 McCloskey RM, Liang RH, Harrigan PR, Brumme ZL, Poon AF. An evaluation of phylogenetic methods for reconstructing transmitted HIV variants using longitudinal clonal HIV sequence data. Journal of Virology. 88: 6181-94. PMID 24648453 DOI: 10.1128/JVI.00483-14  1
2013 Poon AF, Walker LW, Murray H, McCloskey RM, Harrigan PR, Liang RH. Mapping the shapes of phylogenetic trees from human and zoonotic RNA viruses. Plos One. 8: e78122. PMID 24223766 DOI: 10.1371/Journal.Pone.0078122  1
2013 Brumme CJ, Huber KD, Dong W, Poon AF, Harrigan PR, Sluis-Cremer N. Replication fitness of multiple nonnucleoside reverse transcriptase-resistant HIV-1 variants in the presence of etravirine measured by 454 deep sequencing. Journal of Virology. 87: 8805-7. PMID 23720723 DOI: 10.1128/Jvi.00335-13  1
2013 McGovern RA, Symons J, Poon AF, Harrigan PR, van Lelyveld SF, Hoepelman AI, van Ham PM, Dong W, Wensing AM, Nijhuis M. 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. The Journal of Antimicrobial Chemotherapy. 68: 2007-14. PMID 23677920 DOI: 10.1093/jac/dkt153  1
2013 Swenson LC, Dong WW, Mo T, Demarest J, Chapman D, Ellery S, Heera J, Valdez H, Poon AF, Harrigan PR. Use of cellular HIV DNA to predict virologic response to maraviroc: performance of population-based and deep sequencing. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. 56: 1659-66. PMID 23429552 DOI: 10.1093/cid/cit105  1
2013 Lee GQ, Harrigan PR, Dong W, Poon AF, Heera J, Demarest J, Rinehart A, Chapman D, Valdez H, Portsmouth S. Comparison of population and 454 "deep" sequence analysis for HIV type 1 tropism versus the original trofile assay in non-B subtypes. Aids Research and Human Retroviruses. 29: 979-84. PMID 23350534 DOI: 10.1089/AID.2012.0338  1
2013 Knapp DJ, McGovern RA, Dong W, Poon AF, Swenson LC, Zhong X, Woods CK, Harrigan PR. Factors influencing the sensitivity and specificity of conventional sequencing in human immunodeficiency virus type 1 tropism testing. Journal of Clinical Microbiology. 51: 444-51. PMID 23175258 DOI: 10.1128/JCM.00739-12  1
2012 Poon AF, Swenson LC, Bunnik EM, Edo-Matas D, Schuitemaker H, van 't Wout AB, Harrigan PR. Reconstructing the dynamics of HIV evolution within hosts from serial deep sequence data. Plos Computational Biology. 8: e1002753. PMID 23133358 DOI: 10.1371/journal.pcbi.1002753  1
2012 Lee GQ, Swenson LC, Poon AF, Martin JN, Hatano H, Deeks SG, Harrigan PR. Prolonged and substantial discordance in prevalence of raltegravir-resistant HIV-1 in plasma versus PBMC samples revealed by 454 "deep" sequencing. Plos One. 7: e46181. PMID 23049972 DOI: 10.1371/journal.pone.0046181  1
2012 Aldous JL, Pond SK, Poon A, Jain S, Qin H, Kahn JS, Kitahata M, Rodriguez B, Dennis AM, Boswell SL, Haubrich R, Smith DM. Characterizing HIV transmission networks across the United States. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. 55: 1135-43. PMID 22784872 DOI: 10.1093/Cid/Cis612  1
2012 Rang CU, Peng AY, Poon AF, Chao L. Ageing in Escherichia coli requires damage by an extrinsic agent. Microbiology (Reading, England). 158: 1553-9. PMID 22422756 DOI: 10.1099/Mic.0.057240-0  0.72
2012 Gonzalez-Serna A, McGovern RA, Harrigan PR, Vidal F, Poon AF, Ferrando-Martinez S, Abad MA, Genebat M, Leal M, Ruiz-Mateos E. Correlation of the virological response to short-term maraviroc monotherapy with standard and deep-sequencing-based genotypic tropism prediction methods. Antimicrobial Agents and Chemotherapy. 56: 1202-7. PMID 22143533 DOI: 10.1128/AAC.05857-11  1
2011 Tai V, Poon AF, Paulsen IT, Palenik B. Selection in coastal Synechococcus (cyanobacteria) populations evaluated from environmental metagenomes. Plos One. 6: e24249. PMID 21931665 DOI: 10.1371/Journal.Pone.0024249  1
2011 Poon AF, McGovern RA, Mo T, Knapp DJ, Brenner B, Routy JP, Wainberg MA, Harrigan PR. Dates of HIV infection can be estimated for seroprevalent patients by coalescent analysis of serial next-generation sequencing data. Aids (London, England). 25: 2019-26. PMID 21832936 DOI: 10.1097/Qad.0B013E32834B643C  1
2011 Poon AF, Aldous JL, Mathews WC, Kitahata M, Kahn JS, Saag MS, Rodríguez B, Boswell SL, Frost SD, Haubrich RH. Transmitted drug resistance in the CFAR network of integrated clinical systems cohort: prevalence and effects on pre-therapy CD4 and viral load. Plos One. 6: e21189. PMID 21701595 DOI: 10.1371/journal.pone.0021189  1
2011 Knapp DJ, Harrigan PR, Poon AF, Brumme ZL, Brockman M, Cheung PK. In vitro selection of clinically relevant bevirimat resistance mutations revealed by "deep" sequencing of serially passaged, quasispecies-containing recombinant HIV-1. Journal of Clinical Microbiology. 49: 201-8. PMID 21084518 DOI: 10.1128/Jcm.01868-10  1
2010 Manosuthi W, Butler DM, Pérez-Santiago J, Poon AF, Pillai SK, Mehta SR, Pacold ME, Richman DD, Pond SK, Smith DM. Protease polymorphisms in HIV-1 subtype CRF01_AE represent selection by antiretroviral therapy and host immune pressure. Aids (London, England). 24: 411-6. PMID 20009919 DOI: 10.1097/Qad.0B013E3283350Eef  1
2010 Poon AF, Swenson LC, Dong WW, Deng W, Kosakovsky Pond SL, Brumme ZL, Mullins JI, Richman DD, Harrigan PR, Frost SD. Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1. Molecular Biology and Evolution. 27: 819-32. PMID 19955476 DOI: 10.1093/Molbev/Msp289  1
2009 Kosakovsky Pond SL, Posada D, Stawiski E, Chappey C, Poon AF, Hughes G, Fearnhill E, Gravenor MB, Leigh Brown AJ, Frost SD. An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1. Plos Computational Biology. 5: e1000581. PMID 19956739 DOI: 10.1371/Journal.Pcbi.1000581  1
2009 Jordan PS, Poon A, Eron J, Squires K, Ignacio C, Richman DD, Smith DM. A novel codon insert in protease of clade B HIV type 1. Aids Research and Human Retroviruses. 25: 547-50. PMID 19397401 DOI: 10.1089/Aid.2008.0310  1
2009 Davis BH, Poon AF, Whitlock MC. Compensatory mutations are repeatable and clustered within proteins. Proceedings. Biological Sciences / the Royal Society. 276: 1823-7. PMID 19324785 DOI: 10.1098/Rspb.2008.1846  1
2008 Harrigan PR, Sheen CW, Gill VS, Wynhoven B, Hudson E, Lima VD, Lecocq P, Aguirre R, Poon AF, Sluis-Cremer N. Silent mutations are selected in HIV-1 reverse transcriptase and affect enzymatic efficiency. Aids (London, England). 22: 2501-8. PMID 19005273 DOI: 10.1097/Qad.0B013E328318F16C  1
2008 Streeck H, Li B, Poon AF, Schneidewind A, Gladden AD, Power KA, Daskalakis D, Bazner S, Zuniga R, Brander C, Rosenberg ES, Frost SD, Altfeld M, Allen TM. Immune-driven recombination and loss of control after HIV superinfection. The Journal of Experimental Medicine. 205: 1789-96. PMID 18625749 DOI: 10.1084/Jem.20080281  1
2008 Cachay ER, Frost SD, Poon AF, Looney D, Rostami SM, Pacold ME, Richman DD, Little SJ, Smith DM. Herpes simplex virus type 2 acquisition during recent HIV infection does not influence plasma HIV levels. Journal of Acquired Immune Deficiency Syndromes (1999). 47: 592-6. PMID 18197122 DOI: 10.1097/Qai.0B013E318163Bd87  1
2007 Poon AF, Kosakovsky Pond SL, Richman DD, Frost SD. Mapping protease inhibitor resistance to human immunodeficiency virus type 1 sequence polymorphisms within patients. Journal of Virology. 81: 13598-607. PMID 17913806 DOI: 10.1128/Jvi.01570-07  1
2006 Poon AF, Chao L. Functional origins of fitness effect-sizes of compensatory mutations in the DNA bacteriophage phiX174. Evolution; International Journal of Organic Evolution. 60: 2032-43. PMID 17133860 DOI: 10.1111/J.0014-3820.2006.Tb01841.X  1
2005 Poon A, Chao L. The rate of compensatory mutation in the DNA bacteriophage phiX174. Genetics. 170: 989-99. PMID 15911582 DOI: 10.1534/Genetics.104.039438  1
2005 Poon A, Davis BH, Chao L. The coupon collector and the suppressor mutation: estimating the number of compensatory mutations by maximum likelihood. Genetics. 170: 1323-32. PMID 15879511 DOI: 10.1534/Genetics.104.037259  1
2004 Poon A, Chao L. Drift increases the advantage of sex in RNA bacteriophage Phi6. Genetics. 166: 19-24. PMID 15020402 DOI: 10.1534/Genetics.166.1.19  1
2000 Poon A, Otto SP. Compensating for our load of mutations: freezing the meltdown of small populations. Evolution; International Journal of Organic Evolution. 54: 1467-79. PMID 11108576  1
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