Research Topics
| SIMON FROSTSummaryAffiliation: University of California Country: USA Publications
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Detail Information
Publications
Using sexual affiliation networks to describe the sexual structure of a populationSimon 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...- Respondent-driven sampling of injection drug users in two U.S.-Mexico border cities: recruitment dynamics and impact on estimates of HIV and syphilis prevalenceSimon 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... - Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infectionSimon 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... - 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... - Dynamics and evolution of HIV-1 during structured treatment interruptionsSimon 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... - Viral dynamics during structured treatment interruptions of chronic human immunodeficiency virus type 1 infectionSimon D W Frost
Department of Pathology, University of California, San Diego, California 92103, USA
J Virol 76:968-79. 2002.... - Genetic drift and within-host metapopulation dynamics of HIV-1 infectionS D Frost
Department of Pathology, University of California, San Diego, CA 92103, USA
Proc Natl Acad Sci U S A 98:6975-80. 2001.... - Evidence for positive selection driving the evolution of HIV-1 env under potent antiviral therapyS D Frost
Centre for HIV Research, University of Edinburgh, Scotland
Virology 284:250-8. 2001.... - 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... - 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... - 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... - Genetic basis of hypersusceptibility to protease inhibitors and low replicative capacity of human immunodeficiency virus type 1 strains in primary infectionAndrew 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... - Association of antiretroviral resistance genotypes with response to therapy--comparison of three modelsMarlynne Quigg
Centre for HIV Research, Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh, UK
Antivir Ther 7:151-7. 2002.... - Transmission fitness of drug-resistant human immunodeficiency virus and the prevalence of resistance in the antiretroviral-treated populationAndrew 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... - Evolution of the interferon alpha gene family in eutherian mammalsChristopher 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... - Long-term persistence of transmitted HIV drug resistance in male genital tract secretions: implications for secondary transmissionDavey 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... - 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.... - 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... - Syringe possession arrests are associated with receptive syringe sharing in two Mexico-US border citiesRobin 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... - 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.... - 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... - 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... - 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... - 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... - 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... - A public health model for the molecular surveillance of HIV transmission in San Diego, CaliforniaDavey 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... - 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... - Evolutionary fingerprinting of genesSergei L Kosakovsky Pond
Department of Medicine, University of California, San Diego, USA
Mol Biol Evol 27:520-36. 2010.... - 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.... - Herpes simplex virus type 2 infection does not influence viral dynamics during early HIV-1 infectionEdward 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... - 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... - 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 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... - Pleocytosis is associated with disruption of HIV compartmentalization between blood and cerebral spinal fluid viral populationsDavey M Smith
University of California San Diego, La Jolla, 92093, USA
Virology 385:204-8. 2009.... - 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... - 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... - Lack of neutralizing antibody response to HIV-1 predisposes to superinfectionDavey 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... - Characteristics of recently HIV-infected men who use the Internet to find male sex partners and sexual practices with those partnersDavey 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.... - 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... - 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... - Human immunodeficiency virus-1 RNA levels in cerebrospinal fluid exhibit a set point in clinically stable patients not receiving antiretroviral therapyRonald 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.... - 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... - Amprenavir-resistant HIV-1 exhibits lopinavir cross-resistance and reduced replication capacityJulia G Prado
IrsiCaixa Foundation, Hospital Germans Trias i Pujol, , Ctra. de Canyet s/n, 08916 Badalona, Spain
AIDS 16:1009-17. 2002..This study also provides data on the concordance of replication capacity measurements generated using rapid single-cycle growth and competition assays... - Not so different after all: a comparison of methods for detecting amino acid sites under selectionSergei 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... - 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... - Phenotypic hypersusceptibility to multiple protease inhibitors and low replicative capacity in patients who are chronically infected with human immunodeficiency virus type 1Javier 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... - Selection of drug-resistant HIV-1 mutants in response to repeated structured treatment interruptionsJavier 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... - Computational analysis and identification of amino acid sites in dengue E proteins relevant to development of diagnostics and vaccinesRaja Mazumder
Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
Virus Genes 35:175-86. 2007.... - Viral evolution during structured treatment interruptions in chronically human immunodeficiency virus-infected individualsJavier 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... - Viral kinetics and hepatitis CGerond Lake-Bakaar
Hepatology 38:1588; author reply 1588-1590. 2003 - 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 diseaseGerond Lake-Bakaar
Blood 109:845-6. 2007