User:Artpoon

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Last updated: January 15, 2010

Contents

Research Interests

Evolutionary biology, population genetics, phylogenetics, experimental evolution, HIV/AIDS, infectious diseases, mathematical biology, bioinformatics.

Education

  • Ph.D., Biology. University of California, San Diego
  • M.Sc. Zoology. University of British Columbia, Canada.
  • Hon.B.Sc., Biology. University of Toronto, Canada.

Appointments

  • Postdoctoral Employee. Division of Comparative Pathology and Medicine. Department of Pathology. University of California, San Diego.
  • Associate Research Scientist, Bioinformatics. BC Centre for Excellence in HIV/AIDS. St. Paul's Hospital, Vancouver, Canada.

Publications

  1. Manosuthi, W, DM Butler, J Prez-Santiago, AFY Poon, SK Pillai, SR Mehta, ME Pacold, DD Richman, SK Pond, DM Smith. 2009. Protease polymorphisms in HIV-1 subtype CRF01 AE represent selection by antiretroviral therapy and host immune pressure. AIDS, doi:10.1097/QAD.0b013e3283350eef.
  2. Poon, AFY, LC Swenson, WY Dong, SL Kosakovsky Pond, DD Richman, PR Harrigan, and SDW Frost. 2009. Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1. Molecular Biology and Evolution, doi:10.1093/molbev/msp289.
  3. Kosakovsky Pond, SL, D Posada, C Chappey, E Stawinski, AFY Poon, MB Gravenor, AJ Leigh Brown, and SDW Frost. 2009. An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1. PLoS Computational Biology, 5(11): e1000581.
  4. Kosakovsky Pond, SL, K Scheffler, AFY Poon, MB Gravenor, and SDW Frost. 2009. Evolutionary fingerprinting of genes. Molecular Biology and Evolution, doi:10.1093/molbev/msp260.
  5. Jordan, PS, AFY Poon, J Enron, K Squires, C Ignacio, DD Richman, and DM Smith. 2009. A novel codon insert in protease of clade B HIV type 1. AIDS Res Hum Retroviruses 25(5): 547-550.
  6. Poon, AFY, KC Brouwer, SA Strathdee, M Firestone Cruz, RM Lozada, SL Kosakovsky Pond, DD Heckathorn, and SDW Frost. 2009. Parsing social network survey data from hidden populations using stochastic context-free grammars. PLoS ONE, in press.
  7. Lycett, SJ, MJ Ward, FI Lewis, AFY Poon, SL Kosakovsky Pond, and AJ Leigh Brown. 2009. Detection of mammalian virulence determinants in highly pathogenic avian influenza H5N1 viruses: multivariate analysis of published data. J. Virol., in press.
  8. Davis, BH, AFY Poon, and MC Whitlock. 2009. Compensatory mutations are repeatable and clustered within proteins. Proc. Roy. Soc. B 276(1663): 1823-1827 .
  9. Harrigan, PR, C-W Sheen, V Gill, B Wynhoven, E Hudson, V Lima, P Lecocq, AFY Poon, and N Sluis-Cremer. 2008. Silent mutations are selected in HIV-1 reverse transcriptase and affect enzymatic efficiency. AIDS 22(18): 2501-2508.
  10. Poon, AFY, FI Lewis, SDW Frost, and SL Kosakovsky Pond. 2008. Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models. Bioinformatics 24(17): 1949-1950.
  11. Kosakovsky Pond, SL, AFY Poon, AJ Leigh Brown, and SDW Frost. 2008. A maximum likelihood method for detecting directional evolution in protein sequences and its application to Influenza A virus. Molecular Biology and Evolution 25(9): 1809-1824.
  12. Streeck, H, B Li, AFY Poon, A Schneidewind, AD Gladden, KA Power, SB Bazner, C Brander, ES Rosenberg, S Frost, M Altfeld, and TM Allen. 2008. Immune driven HIV-1 recombination and loss of control following superinfection. Journal of Experimental Medicine 206(8): 1789-1796.
  13. Kosakovsky Pond, SL, AFY Poon, CS Zarate, DM Smith, SJ Little, SK Pillai, RJ Ellis, JK Wong, AJ Leigh Brown, DD Richman, and SDW Frost. 2008. Estimating selection pressures on HIV-1 using phylogenetic likelihood models. Statistics in Medicine, 27(23): 4779-4789. doi:10.1002/sim.3192
  14. Cachay, ER, SDW Frost, AFY Poon, D Looney, SM Rostami, ME Pacold, DD Richman, SJ Little, and DM Smith. 2008. Herpes simplex virus type 2 (HSV-2) acquisition during recent HIV infection does not influence plasma HIV levels. Journal of Acquired Immune Deficiency Syndromes 47(5): 592-596.
  15. Poon, AFY, FI Lewis, SL Kosakovsky Pond, and SDW Frost. 2007. An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope. PLoS Computational Biology 3(11): e231. doi:10.1371/journal.pcbi.0030231.
  16. Poon AFY, SL Kosakovsky Pond, DD Richman, and SDW Frost. 2007. Mapping protease inhibitor resistance to HIV-1 sequence polymorphisms within patients. Journal of Virology 81(24): 13598-13607.
  17. Lapp, H, S Bala, JP Balhoff, A Bouck, N Goto, M Holder, R Holland, A Holloway, T Katayama, PO Lewis, A Mackey, BI Osborne, WH Piel, SL Kosakovsky Pond, AFY Poon, W-G Qui, JE Stajich, A Stolzfus, T Thierer, AJ Vilella, RA Vos, CM Zmasek, D Zwickl, and TJ Vision. 2007. The 2006 NESCent Phyloinformatics Hackathon: A field report. Evolutionary Bioinformatics 3: 357-366.
  18. Poon, AFY, SL Kosakovsky Pond, P Bennett, DD Richman, AJ Leigh Brown, and SDW Frost. 2007. Adaptation to human populations is revealed by within-host polymorphisms in HIV-1 and hepatitis C virus. PLoS Pathogens 3(3): e45. doi:10.1371/journal.ppat.0030045
  19. Poon, AFY, FI Lewis, SL Kosakovsky Pond, and SDW Frost. 2007. Evolutionary interactions between N-linked glycosylation sites in the HIV-1 envelope. PLoS Computational Biology 3(1): e11. doi:10.1371/journal.pcbi.0030011
  20. Poon, AFY and L Chao. 2006. Functional origins of fitness-effect sizes of compensatory mutations in the DNA bacteriophage φX174. Evolution 60(10): 2032-2043.
  21. Poon, A, BH Davis, and L Chao. 2005. The Coupon Collector and the Suppressor Mutation: estimating the number of suppressor mutations by maximum likelihood. Genetics 170(3): 1323-1332.
  22. Poon, A and L Chao. 2005. The rate of compensatory mutation in the bacteriophage φX174. Genetics 170(3): 989-999.
  23. Poon, A and L Chao. 2004. Drift increases the advantage of sex in bacteriophage φ6. Genetics 166 (1): 19-24.
  24. Poon, A and SP Otto. 2000. Compensating for our load of mutations: freezing the meltdown of small populations. Evolution 54(5): 1469-1479.

Book Chapters

  • Kosakovsky Pond, SL, AFY Poon, and SDW Frost. Estimating selection pressures on alignments of coding sequences. In The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny, 2nd ed. M Salemi and A-M Vandamme, eds. Cambridge University Press. Amazon
  • AFY Poon, SDW Frost, and Kosakovsky Pond, SL. Detecting selection in DNA sequences with Datamonkey. In Bioinformatics for DNA Sequence Analysis (Methods in Molecular Biology). Humana Press. Amazon
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