Sergei L Kosakovsky Pond

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Characterization of human immunodeficiency virus type 1 (HIV-1) envelope variation and neutralizing antibody responses during transmission of HIV-1 subtype B
    Simon D W Frost
    UCSD Antiviral Research Center, 150 W Washington St, Suite 100, San Diego, CA 92103, USA
    J Virol 79:6523-7. 2005
  2. pmc Evolutionary interactions between N-linked glycosylation sites in the HIV-1 envelope
    Art F Y Poon
    Department of Pathology, University of California San Diego, La Jolla, California, United States of America
    PLoS Comput Biol 3:e11. 2007
  3. pmc Detecting individual sites subject to episodic diversifying selection
    Ben Murrell
    Biomedical Informatics Research Division, eHealth Research and Innovation Platform, Medical Research Council, Tygerberg, South Africa
    PLoS Genet 8:e1002764. 2012
  4. pmc HIV-specific probabilistic models of protein evolution
    David C Nickle
    Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
    PLoS ONE 2:e503. 2007
  5. doi request reprint Evolution of viral genomes: interplay between selection, recombination, and other forces
    Sergei L Kosakovsky Pond
    Department of Medicine, University of California, San Diego, CA, USA
    Methods Mol Biol 856:239-72. 2012
  6. ncbi request reprint A simple hierarchical approach to modeling distributions of substitution rates
    Sergei L Kosakovsky Pond
    Antiviral Research Center, University of California San Diego, San Diego, California, USA
    Mol Biol Evol 22:223-34. 2005
  7. pmc Windshield splatter analysis with the Galaxy metagenomic pipeline
    Sergei Kosakovsky Pond
    http galaxyproject org
    Genome Res 19:2144-53. 2009
  8. pmc Evolutionary fingerprinting of genes
    Sergei L Kosakovsky Pond
    Department of Medicine, University of California, San Diego, USA
    Mol Biol Evol 27:520-36. 2010
  9. pmc An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1
    Sergei L Kosakovsky Pond
    Department of Medicine, University of California San Diego, La Jolla, California, USA
    PLoS Comput Biol 5:e1000581. 2009
  10. ncbi request reprint GARD: a genetic algorithm for recombination detection
    Sergei L Kosakovsky Pond
    Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
    Bioinformatics 22:3096-8. 2006

Detail Information

Publications32

  1. pmc Characterization of human immunodeficiency virus type 1 (HIV-1) envelope variation and neutralizing antibody responses during transmission of HIV-1 subtype B
    Simon 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...
  2. pmc Evolutionary interactions between N-linked glycosylation sites in the HIV-1 envelope
    Art 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...
  3. pmc Detecting individual sites subject to episodic diversifying selection
    Ben Murrell
    Biomedical Informatics Research Division, eHealth Research and Innovation Platform, Medical Research Council, Tygerberg, South Africa
    PLoS Genet 8:e1002764. 2012
    ..We find that episodic selection is widespread and conclude that the number of sites experiencing positive selection may have been vastly underestimated...
  4. pmc HIV-specific probabilistic models of protein evolution
    David C Nickle
    Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
    PLoS ONE 2:e503. 2007
    ..We argue that our model derivation procedure is immediately applicable to other organisms with extensive sequence data available, such as Hepatitis C and Influenza A viruses...
  5. doi request reprint Evolution of viral genomes: interplay between selection, recombination, and other forces
    Sergei L Kosakovsky Pond
    Department of Medicine, University of California, San Diego, CA, USA
    Methods Mol Biol 856:239-72. 2012
    ....
  6. ncbi request reprint A simple hierarchical approach to modeling distributions of substitution rates
    Sergei 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...
  7. pmc Windshield splatter analysis with the Galaxy metagenomic pipeline
    Sergei 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...
  8. pmc Evolutionary fingerprinting of genes
    Sergei L Kosakovsky Pond
    Department of Medicine, University of California, San Diego, USA
    Mol Biol Evol 27:520-36. 2010
    ....
  9. pmc An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1
    Sergei L Kosakovsky Pond
    Department of Medicine, University of California San Diego, La Jolla, California, USA
    PLoS Comput Biol 5:e1000581. 2009
    ....
  10. ncbi request reprint GARD: a genetic algorithm for recombination detection
    Sergei 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...
  11. ncbi request reprint Evolutionary model selection with a genetic algorithm: a case study using stem RNA
    Sergei 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...
  12. ncbi request reprint Automated phylogenetic detection of recombination using a genetic algorithm
    Sergei 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...
  13. pmc Correcting the bias of empirical frequency parameter estimators in codon models
    Sergei 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...
  14. pmc A random effects branch-site model for detecting episodic diversifying selection
    Sergei 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...
  15. ncbi request reprint Datamonkey: rapid detection of selective pressure on individual sites of codon alignments
    Sergei L Kosakovsky Pond
    Antiviral Research Center, University of California, San Diego, CA 92103, USA
    Bioinformatics 21:2531-3. 2005
    ..The methods range from very fast data exploration to the some of the most complex models available in public domain software, and are implemented to run in parallel on a cluster of computers...
  16. ncbi request reprint A genetic algorithm approach to detecting lineage-specific variation in selection pressure
    Sergei 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...
  17. pmc A maximum likelihood method for detecting directional evolution in protein sequences and its application to influenza A virus
    Sergei 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...
  18. pmc HIV-1 clade B pol evolution following primary infection
    George K Hightower
    Department of Medicine, University of California San Diego, La Jolla, California United States of America
    PLoS ONE 8:e68188. 2013
    ..Characterize intra-individual HIV-1 subtype B pol evolution in antiretroviral naive individuals...
  19. ncbi request reprint HyPhy: hypothesis testing using phylogenies
    Sergei 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: muse@stat.ncsu.edu SUPPLEMENTARY INFORMATION: HyPhydocumentation and tutorials are available at http://www.hyphy.org...
  20. doi request reprint Detecting signatures of selection from DNA sequences using Datamonkey
    Art 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...
  21. pmc An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope
    Art 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...
  22. pmc Persistence of transmitted drug resistance among subjects with primary human immunodeficiency virus infection
    Susan 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...
  23. pmc Adaptation to different human populations by HIV-1 revealed by codon-based analyses
    Sergei 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...
  24. pmc Comparative study of methods for detecting sequence compartmentalization in human immunodeficiency virus type 1
    Selene Zárate
    Antiviral Research Center, 150 W Washington St, Ste 100, San Diego, CA 92103, USA
    J Virol 81:6643-51. 2007
    ....
  25. pmc Clinical, virologic, and immunologic correlates of HIV-1 intraclade B dual infection among men who have sex with men
    Mary 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...
  26. ncbi request reprint Genetic attributes of cerebrospinal fluid-derived HIV-1 env
    Satish 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...
  27. pmc Using phylogeography to characterize the origins of the HIV-1 subtype F epidemic in Romania
    Sanjay 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...
  28. pmc Impact of seminal cytomegalovirus replication on HIV-1 dynamics between blood and semen
    Sara 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...
  29. pmc Parsing social network survey data from hidden populations using stochastic context-free grammars
    Art 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...
  30. pmc Coping with viral diversity in HIV vaccine design
    David C Nickle
    Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
    PLoS Comput Biol 3:e75. 2007
    ..These immunogens should elicit immune responses against high-frequency viral strains as well as against most mutant forms of the virus...
  31. pmc A Dirichlet process model for detecting positive selection in protein-coding DNA sequences
    John 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...