Research Topics
| Art F Y PoonSummaryAffiliation: University of California Country: USA Publications
| Collaborators
|
Detail Information
Publications
Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical modelsArt F Y Poon
Division of Comparative Pathology and Medicine, Department of Pathology, University of California, San Diego, CA 92103, USA
Bioinformatics 24:1949-50. 2008..data-monkey.org and as a stand-alone component of the phylogenetic software package HyPhy, which is freely distributed on the web (http://www.hyphy.org) as precompiled binaries and open source...- Parsing social network survey data from hidden populations using stochastic context-free grammarsArt F Y Poon
Division of Comparative Pathology and Medicine, University of California San Diego, La Jolla, California, United States of America
PLoS ONE 4:e6777. 2009..Moreover, current analytical models rely on unrealistic assumptions, e.g., that the traversal of social networks can be modeled by a Markov chain rather than a branching process... - An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelopeArt F Y Poon
Department of Pathology, University of California San Diego, La Jolla, California, United States of America
PLoS Comput Biol 3:e231. 2007..We extend our model to detect interactions between the V3 and C4 domains of the HIV-1 envelope, and account for the uncertainty in mapping substitutions to the tree with a parametric bootstrap... - Mapping protease inhibitor resistance to human immunodeficiency virus type 1 sequence polymorphisms within patientsArt F Y Poon
Department of Pathology, University of California, San Diego, La Jolla, California, USA
J Virol 81:13598-607. 2007..These positions are under strong positive selection in the PI-naive patient population, implying that other factors can produce spurious associations with resistance, e.g., mutational escape from the immune response... - Adaptation to human populations is revealed by within-host polymorphisms in HIV-1 and hepatitis C virusArt F Y Poon
Department of Pathology, University of California San Diego, La Jolla, California, United States of America
PLoS Pathog 3:e45. 2007.... - Evolutionary interactions between N-linked glycosylation sites in the HIV-1 envelopeArt F Y Poon
Department of Pathology, University of California San Diego, La Jolla, California, United States of America
PLoS Comput Biol 3:e11. 2007..This represents a potential vulnerability of rapidly evolving HIV-1 populations that may provide useful glycan-based targets for neutralizing antibodies... - Evolutionary fingerprinting of genesSergei L Kosakovsky Pond
Department of Medicine, University of California, San Diego, USA
Mol Biol Evol 27:520-36. 2010.... - A maximum likelihood method for detecting directional evolution in protein sequences and its application to influenza A virusSergei L Kosakovsky Pond
Department of Pathology, University of California, San Diego, CA, USA
Mol Biol Evol 25:1809-24. 2008..We propose a simple descriptive classification of directionally evolving sites into 5 groups based on the temporal distribution of residue frequencies and document known functional correlates, such as immune escape or host adaptation... - An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1Sergei L Kosakovsky Pond
Department of Medicine, University of California San Diego, La Jolla, California, USA
PLoS Comput Biol 5:e1000581. 2009.... - Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biologyWayne Delport
Department of Pathology, Antiviral Research Center, University of California, San Diego, CA, USA
Bioinformatics 26:2455-7. 2010..Here, we summarize the analyses options currently available on Datamonkey, and provide guidelines for their use in evolutionary biology. Availability and documentation: http://www.datamonkey.org... - Detecting signatures of selection from DNA sequences using DatamonkeyArt F Y Poon
Antiviral Research Center, Department of Pathology, University of California San Diego, La Jolla, CA, USA
Methods Mol Biol 537:163-83. 2009..org) provides a user-friendly web interface to a wide collection of state-of-the-art statistical techniques for estimating dS and dN and identifying codons and lineages under selection, even in the presence of recombinant sequences... - Functional origins of fitness effect-sizes of compensatory mutations in the DNA bacteriophage phiX174Art F Y Poon
Section of Ecology, Behavior, and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, California 92037, USA
Evolution 60:2032-43. 2006.... - Herpes simplex virus type 2 acquisition during recent HIV infection does not influence plasma HIV levelsEdward R Cachay
University of California, San Diego, La Jolla, CA 92103 8681, USA
J Acquir Immune Defic Syndr 47:592-6. 2008..5 log10 copies/mL over 11 days). The HSV-2 incidence rate was high in our cohort of recently HIV-infected individuals; however, HSV-2 acquisition did not significantly change the plasma HIV dynamics and CD4 cell levels... - Selection in coastal Synechococcus (cyanobacteria) populations evaluated from environmental metagenomesVera Tai
Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
PLoS ONE 6:e24249. 2011..By developing a means to analyze population diversity data from these environmental metagenomes, we have provided the first insight into the role of selection in the evolution of Synechococcus, a globally significant primary producer... - Immune-driven recombination and loss of control after HIV superinfectionHendrik Streeck
Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
J Exp Med 205:1789-96. 2008..These data also support a role for cellular immune pressures in driving the selection of new recombinant forms of HIV...