SIMON FROST

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint Using sexual affiliation networks to describe the sexual structure of a population
    Simon D W Frost
    UCSD Antiviral Research Center, 150 W Washington Street, Suite 100, San Diego, California 92103, USA
    Sex Transm Infect 83:i37-42. 2007
  2. pmc Respondent-driven sampling of injection drug users in two U.S.-Mexico border cities: recruitment dynamics and impact on estimates of HIV and syphilis prevalence
    Simon D W Frost
    Department of Pathology and Antiviral Research Center, University of California, San Diego, CA 92103, USA
    J Urban Health 83:i83-97. 2006
  3. pmc Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection
    Simon D W Frost
    Department of Pathology, University of California at San Diego, La Jolla, CA 92093 0679, USA
    Proc Natl Acad Sci U S A 102:18514-9. 2005
  4. 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
  5. ncbi request reprint Dynamics and evolution of HIV-1 during structured treatment interruptions
    Simon D W Frost
    Department of Pathology, School of Medicine, University of California, San Diego, USA
    AIDS Rev 4:119-27. 2002
  6. pmc Viral dynamics during structured treatment interruptions of chronic human immunodeficiency virus type 1 infection
    Simon D W Frost
    Department of Pathology, University of California, San Diego, California 92103, USA
    J Virol 76:968-79. 2002
  7. pmc Genetic drift and within-host metapopulation dynamics of HIV-1 infection
    S D Frost
    Department of Pathology, University of California, San Diego, CA 92103, USA
    Proc Natl Acad Sci U S A 98:6975-80. 2001
  8. ncbi request reprint Evidence for positive selection driving the evolution of HIV-1 env under potent antiviral therapy
    S D Frost
    Centre for HIV Research, University of Edinburgh, Scotland
    Virology 284:250-8. 2001
  9. 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
  10. pmc Using respondent-driven sampling in a hidden population at risk of HIV infection: who do HIV-positive recruiters recruit?
    Daniela Abramovitz
    Department of Medicine, University of California San Diego, La Jolla, CA, USA
    Sex Transm Dis 36:750-6. 2009

Detail Information

Publications51

  1. ncbi request reprint Using sexual affiliation networks to describe the sexual structure of a population
    Simon D W Frost
    UCSD Antiviral Research Center, 150 W Washington Street, Suite 100, San Diego, California 92103, USA
    Sex Transm Infect 83:i37-42. 2007
    ..This article reviews how data on "sexual affiliations" between people and venues may be collected, analysed, and used for surveillance and prevention of STIs...
  2. pmc Respondent-driven sampling of injection drug users in two U.S.-Mexico border cities: recruitment dynamics and impact on estimates of HIV and syphilis prevalence
    Simon D W Frost
    Department of Pathology and Antiviral Research Center, University of California, San Diego, CA 92103, USA
    J Urban Health 83:i83-97. 2006
    ..Although the frequency of HIV was low, syphilis prevalence was high, particularly in Tijuana. RDS-corrected estimates of syphilis prevalence were sensitive to model assumptions, suggesting that further validation of RDS is necessary...
  3. pmc Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection
    Simon D W Frost
    Department of Pathology, University of California at San Diego, La Jolla, CA 92093 0679, USA
    Proc Natl Acad Sci U S A 102:18514-9. 2005
    ..Our results suggest that autologous neutralizing antibody responses may play a pivotal role in the diversification of HIV-1 envelope during the early stages of infection...
  4. 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...
  5. ncbi request reprint Dynamics and evolution of HIV-1 during structured treatment interruptions
    Simon D W Frost
    Department of Pathology, School of Medicine, University of California, San Diego, USA
    AIDS Rev 4:119-27. 2002
    ..I illustrate how models can help to compare the dynamics and evolution of HIV in these different scenarios, and to assess the risks and benefits of STIs...
  6. pmc Viral dynamics during structured treatment interruptions of chronic human immunodeficiency virus type 1 infection
    Simon D W Frost
    Department of Pathology, University of California, San Diego, California 92103, USA
    J Virol 76:968-79. 2002
    ....
  7. pmc Genetic drift and within-host metapopulation dynamics of HIV-1 infection
    S D Frost
    Department of Pathology, University of California, San Diego, CA 92103, USA
    Proc Natl Acad Sci U S A 98:6975-80. 2001
    ....
  8. ncbi request reprint Evidence for positive selection driving the evolution of HIV-1 env under potent antiviral therapy
    S D Frost
    Centre for HIV Research, University of Edinburgh, Scotland
    Virology 284:250-8. 2001
    ....
  9. 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...
  10. pmc Using respondent-driven sampling in a hidden population at risk of HIV infection: who do HIV-positive recruiters recruit?
    Daniela Abramovitz
    Department of Medicine, University of California San Diego, La Jolla, CA, USA
    Sex Transm Dis 36:750-6. 2009
    ..We examined recruitment patterns of human immunodeficiency virus (HIV)-positive injection drug users (IDUs) and identified factors associated with being recruited by an HIV-positive IDU in a RDS-based study...
  11. 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...
  12. pmc Genetic basis of hypersusceptibility to protease inhibitors and low replicative capacity of human immunodeficiency virus type 1 strains in primary infection
    Andrew J Leigh Brown
    University of Edinburgh, Edinburgh, Scotland
    J Virol 78:2242-6. 2004
    ..This supports the view that variation in PR function is directly responsible for variation in fitness among strains in primary infection...
  13. ncbi request reprint Association of antiretroviral resistance genotypes with response to therapy--comparison of three models
    Marlynne Quigg
    Centre for HIV Research, Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh, UK
    Antivir Ther 7:151-7. 2002
    ....
  14. ncbi request reprint Transmission fitness of drug-resistant human immunodeficiency virus and the prevalence of resistance in the antiretroviral-treated population
    Andrew J Leigh Brown
    Department of Pathology, University of California, San Diego, California, USA
    J Infect Dis 187:683-6. 2003
    ..It revealed that resistant virus was transmitted only approximately 20% as frequently as expected from these patients. Individuals with primary resistance may become a significant source of resistant strains...
  15. pmc Evolution of the interferon alpha gene family in eutherian mammals
    Christopher H Woelk
    Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
    Gene 397:38-50. 2007
    ..Gene conversion, similar to duplication, provides a mechanism by which the protein product of a specific IFNA gene can be increased...
  16. ncbi request reprint Long-term persistence of transmitted HIV drug resistance in male genital tract secretions: implications for secondary transmission
    Davey M Smith
    University of California, San Diego, La Jolla, CA 92093 0679, USA
    J Infect Dis 196:356-60. 2007
    ..Transmitted drug-resistant HIV slowly reverts in the blood to drug-sensitive virus. The environment of the male genital tract (MGT) may result in even slower rates of reversion to drug susceptibility...
  17. 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
    ....
  18. pmc Mapping protease inhibitor resistance to human immunodeficiency virus type 1 sequence polymorphisms within patients
    Art 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...
  19. pmc Syringe possession arrests are associated with receptive syringe sharing in two Mexico-US border cities
    Robin A Pollini
    Department of Family and Preventive Medicine, School of Medicine, University of California, San Diego, CA 92093, USA
    Addiction 103:101-8. 2008
    ..To identify factors associated with receptive syringe sharing among injection drug users (IDUs) and elucidate the association between syringe possession arrests and syringe sharing...
  20. 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
    ....
  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 Herpes simplex virus type 2 acquisition during recent HIV infection does not influence plasma HIV levels
    Edward 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...
  23. 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...
  24. 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...
  25. pmc Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models
    Art 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
    ....
  26. pmc A public health model for the molecular surveillance of HIV transmission in San Diego, California
    Davey M Smith
    University of California San Diego, La Jolla, CA 92093 0679, USA
    AIDS 23:225-32. 2009
    ..Here, we investigate how molecular epidemiology can be used to identify highly related HIV networks within a population and how voluntary contact tracing of sexual partners can be used to selectively target these networks...
  27. 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...
  28. 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
    ....
  29. pmc Adaptation to human populations is revealed by within-host polymorphisms in HIV-1 and hepatitis C virus
    Art F Y Poon
    Department of Pathology, University of California San Diego, La Jolla, California, United States of America
    PLoS Pathog 3:e45. 2007
    ....
  30. ncbi request reprint Herpes simplex virus type 2 infection does not influence viral dynamics during early HIV-1 infection
    Edward R Cachay
    University of California, San Diego, La Jolla, CA 92103, USA
    J Infect Dis 195:1270-7. 2007
    ..We sought to compare baseline and longitudinal plasma HIV-1 loads between herpes simplex virus type 2 (HSV-2)-seropositive and -seronegative individuals who are enrolled in a primary HIV-1 infection cohort in San Diego, California...
  31. 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...
  32. 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...
  33. 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...
  34. pmc Pleocytosis is associated with disruption of HIV compartmentalization between blood and cerebral spinal fluid viral populations
    Davey M Smith
    University of California San Diego, La Jolla, 92093, USA
    Virology 385:204-8. 2009
    ....
  35. 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...
  36. 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...
  37. ncbi request reprint Lack of neutralizing antibody response to HIV-1 predisposes to superinfection
    Davey M Smith
    University of California San Diego, La Jolla, CA 92093 0679, USA
    Virology 355:1-5. 2006
    ..These data have considerable implications for vaccine development...
  38. ncbi request reprint Characteristics of recently HIV-infected men who use the Internet to find male sex partners and sexual practices with those partners
    Davey M Smith
    University of California San Diego, 9500 Gilman Drive 0679, La Jolla, CA 92093, USA
    J Acquir Immune Defic Syndr 43:582-7. 2006
    ....
  39. 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...
  40. 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...
  41. ncbi request reprint Human immunodeficiency virus-1 RNA levels in cerebrospinal fluid exhibit a set point in clinically stable patients not receiving antiretroviral therapy
    Ronald J Ellis
    Department of Neurosciences and HIV Neurobehavioral Research Center, University of California San Diego, San Diego, CA 92103, USA
    J Infect Dis 187:1818-21. 2003
    ....
  42. 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...
  43. ncbi request reprint Amprenavir-resistant HIV-1 exhibits lopinavir cross-resistance and reduced replication capacity
    Julia G Prado
    IrsiCaixa Foundation, Hospital Germans Trias i Pujol, Universitat Autonoma de Barcelona, Ctra de Canyet s n, 08916 Badalona, Spain
    AIDS 16:1009-17. 2002
    ..To evaluate protease inhibitor (PI) cross-resistance and reductions in replication capacity conferred by amprenavir-selected mutations...
  44. ncbi request reprint Not so different after all: a comparison of methods for detecting amino acid sites under selection
    Sergei L Kosakovsky Pond
    Antiviral Research Center, University of California San Diego, USA
    Mol Biol Evol 22:1208-22. 2005
    ..We demonstrate our methods on sequence data from the human immunodeficiency virus type 1 env and pol genes and simulated alignments...
  45. pmc Immune-driven recombination and loss of control after HIV superinfection
    Hendrik 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...
  46. pmc Phenotypic hypersusceptibility to multiple protease inhibitors and low replicative capacity in patients who are chronically infected with human immunodeficiency virus type 1
    Javier Martinez-Picado
    IrsiCaixa Foundation Hospital Germans Trias i Pujol, Ctra de Canyet, s n 08916 Badalona, Spain
    J Virol 79:5907-13. 2005
    ..The potential clinical relevance of protease inhibitor hypersusceptibility and low replication capacity to virologic response to protease inhibitor-based therapies deserves to be investigated further...
  47. ncbi request reprint Selection of drug-resistant HIV-1 mutants in response to repeated structured treatment interruptions
    Javier Martinez-Picado
    IrsiCaixa Foundation, Hospital Germans Trias i Pujol, Universitat Autonoma de Barcelona, Badalona, Spain
    AIDS 16:895-9. 2002
    ..The potential for selection of drug-resistant quasi-species remains a major concern of such a treatment strategy...
  48. ncbi request reprint Computational analysis and identification of amino acid sites in dengue E proteins relevant to development of diagnostics and vaccines
    Raja Mazumder
    Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
    Virus Genes 35:175-86. 2007
    ....
  49. pmc Viral evolution during structured treatment interruptions in chronically human immunodeficiency virus-infected individuals
    Javier Martinez-Picado
    IrsiCaixa Foundation, Hospital Germans Trias i Pujol, Universitat Autonoma de Barcelona, Badalona, Spain
    J Virol 76:12344-8. 2002
    ..Analyses of length variation and of clonal sequences demonstrated highly unpredictable evolution, which may limit the strengthening of HIV-specific immune responses by STIs because of the variability in exposure to viral antigens...
  50. ncbi request reprint Viral kinetics and hepatitis C
    Gerond Lake-Bakaar
    Hepatology 38:1588; author reply 1588-1590. 2003
  51. ncbi request reprint Hepatitis C virus and alanine aminotransferase kinetics following B-lymphocyte depletion with rituximab: evidence for a significant role of humoral immunity in the control of viremia in chronic HCV liver disease
    Gerond Lake-Bakaar
    Blood 109:845-6. 2007