Research Topics
| Sergei L Kosakovsky PondSummaryAffiliation: University of California Country: USA Publications
| Collaborators
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Detail Information
Publications
Characterization of human immunodeficiency virus type 1 (HIV-1) envelope variation and neutralizing antibody responses during transmission of HIV-1 subtype BSimon D W Frost
UCSD Antiviral Research Center, 150 W Washington St, Suite 100, San Diego, CA 92103, USA
J Virol 79:6523-7. 2005..We suggest that limited genetic variation within the infecting host reduces the likelihood of selective transmission of neutralization-sensitive HIV...- 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... 
Evolution of viral genomes: interplay between selection, recombination, and other forcesSergei L Kosakovsky Pond
Department of Medicine, University of California, San Diego, CA, USA
Methods Mol Biol 856:239-72. 2012....
A simple hierarchical approach to modeling distributions of substitution ratesSergei L Kosakovsky Pond
Antiviral Research Center, University of California San Diego, San Diego, California, USA
Mol Biol Evol 22:223-34. 2005..We also demonstrate this discretization scheme in the context of codon models specifically aimed at identifying individual sites undergoing adaptive or purifying evolution...- Windshield splatter analysis with the Galaxy metagenomic pipelineSergei Kosakovsky Pond
http galaxyproject org
Genome Res 19:2144-53. 2009..To the best of our knowledge, this is also the first publication that features a live online supplement providing access to exact analyses and workflows used in the article... - Evolutionary fingerprinting of genesSergei L Kosakovsky Pond
Department of Medicine, University of California, San Diego, USA
Mol Biol Evol 27:520-36. 2010.... - GARD: a genetic algorithm for recombination detectionSergei L Kosakovsky Pond
Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
Bioinformatics 22:3096-8. 2006..The evolution of recombinant sequences can not be properly explained by a single phylogenetic tree, but several phylogenies may be used to correctly model the evolution of non-recombinant fragments... - Evolutionary model selection with a genetic algorithm: a case study using stem RNASergei L Kosakovsky Pond
Department of Pathology, University of California, San Diego, USA
Mol Biol Evol 24:159-70. 2007..In addition, the new method provides the foundation for rigorous selection and comparison of substitution models for other types of sequence data... - Automated phylogenetic detection of recombination using a genetic algorithmSergei L Kosakovsky Pond
Department of Pathology, University of California San Diego, USA
Mol Biol Evol 23:1891-901. 2006..Finally, we demonstrate that prescreening alignments with our method allows one to analyze recombinant sequences for positive selection... - 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.... - Correcting the bias of empirical frequency parameter estimators in codon modelsSergei Kosakovsky Pond
Department of Medicine, University of California San Diego, San Diego, California, United States of America
PLoS ONE 5:e11230. 2010..Our results demonstrate that there is little justification, either statistical or computational, for continued use of the -style estimators... - A random effects branch-site model for detecting episodic diversifying selectionSergei L Kosakovsky Pond
Department of Medicine, University of California San Diego, CA, USA
Mol Biol Evol 28:3033-43. 2011..Using three empirical data sets, previously analyzed for episodic selection, we discuss how modeling assumptions can influence inference in practical situations... - Datamonkey: rapid detection of selective pressure on individual sites of codon alignmentsSergei L Kosakovsky Pond
Antiviral Research Center, University of California, San Diego, CA 92103, USA
Bioinformatics 21:2531-3. 2005..AVAILABILITY: http://www.datamonkey.org. In the future, we plan to expand the collection of available analytic tools, and provide a package for installation on other systems... - A genetic algorithm approach to detecting lineage-specific variation in selection pressureSergei L Kosakovsky Pond
Antiviral Research Center, University of California San Diego, USA
Mol Biol Evol 22:478-85. 2005..We illustrate our methods on primate lysozyme sequences and compare them with previous methods applied to the same data sets... - 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... - HyPhy: hypothesis testing using phylogeniesSergei L Kosakovsky Pond
Antiviral Research Center, University of California San Diego San Diego, CA 92103, USA
Bioinformatics 21:676-9. 2005..AVAILABILITY: http://www.hyphy.org CONTACT: SUPPLEMENTARY INFORMATION: HyPhydocumentation and tutorials are available at http://www.hyphy.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... - Persistence of transmitted drug resistance among subjects with primary human immunodeficiency virus infectionSusan J Little
Department of Medicine, University of California, San Diego, San Diego, California, USA
J Virol 82:5510-8. 2008..The prolonged persistence of transmitted drug resistance strongly supports the routine use of HIV resistance genotyping for all newly diagnosed individuals... - 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... - Comparative study of methods for detecting sequence compartmentalization in human immunodeficiency virus type 1Selene Zárate
Antiviral Research Center, 150 W Washington St, Ste 100, San Diego, CA 92103, USA
J Virol 81:6643-51. 2007.... - Adaptation to different human populations by HIV-1 revealed by codon-based analysesSergei L Kosakovsky Pond
Department of Pathology, University of California San Diego, La Jolla, California, USA
PLoS Comput Biol 2:e62. 2006..Additionally, we have identified seven amino acid sites in protease and reverse transcriptase that are selected differentially in the two samples, demonstrating specific population-level adaptation of HIV to human populations... - Clinical, virologic, and immunologic correlates of HIV-1 intraclade B dual infection among men who have sex with menMary E Pacold
Department of Medicine, Stanford University, California, USA
AIDS 26:157-65. 2012..To investigate the susceptibilities to and consequences of HIV-1 dual infection... - Genetic attributes of cerebrospinal fluid-derived HIV-1 envSatish K Pillai
University of California San Diego, Department of Medicine NCIRE, La Jolla, CA 94121, USA
Brain 129:1872-83. 2006..Furthermore, neurological impairment may be influenced by mutations within the viral V3 loop sequence... - Impact of seminal cytomegalovirus replication on HIV-1 dynamics between blood and semenSara Gianella
University of California San Diego, La Jolla, California 92093 0679, USA
J Med Virol 84:1703-9. 2012..In conclusion, the effects of CMV replication on HIV-1 viral and immunologic dynamics within the male genital tract are not significant enough to perturb evolution or disrupt compartmentalization in the genital tract... - 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... - Using phylogeography to characterize the origins of the HIV-1 subtype F epidemic in RomaniaSanjay R Mehta
Department of Medicine, University of California, San Diego, CA 92103, USA
Infect Genet Evol 11:975-9. 2011..However, the geographic source and origins of this epidemic remain unclear... - A Dirichlet process model for detecting positive selection in protein-coding DNA sequencesJohn P Huelsenbeck
Section of Ecology, Behavior, and Evolution, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
Proc Natl Acad Sci U S A 103:6263-8. 2006..We implemented the model in a fully Bayesian approach, with all parameters of the model considered as random variables...