PubMed

An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1.

Kosakovsky Pond SL, Posada D, Stawiski E, Chappey C, Poon AF, Hughes G, Fearnhill E, Gravenor MB, Leigh Brown AJ, Frost SD.

PLoS Comput Biol. 2009 Nov;5(11):e1000581. Epub 2009 Nov 26.PMID: 19956739 [PubMed - in process]Related articles

Phylogenetic Analysis of Population-Based and Deep Sequencing Data to Identify Coevolving Sites in the nef Gene of HIV-1.

Poon AF, Swenson LC, Dong WW, Deng W, Kosakovsky Pond SL, Brumme ZL, Mullins JI, Richman DD, Harrigan PR, Frost SD.

Mol Biol Evol. 2009 Dec 2. [Epub ahead of print]PMID: 19955476 [PubMed - as supplied by publisher]Related articles

Evolutionary Fingerprinting of Genes.

Kosakovsky Pond SL, Scheffler K, Gravenor MB, Poon AF, Frost SD.

Mol Biol Evol. 2009 Oct 28. [Epub ahead of print]PMID: 19864470 [PubMed - as supplied by publisher]Related articles

Phylodynamics of Infectious Disease Epidemics.

Volz EM, Kosakovsky Pond SL, Ward MJ, Leigh Brown AJ, Frost SD.

Genetics. 2009 Sep 21. [Epub ahead of print]PMID: 19797047 [PubMed - as supplied by publisher]Related articles

Parsing social network survey data from hidden populations using stochastic context-free grammars.

Poon AF, Brouwer KC, Strathdee SA, Firestone-Cruz M, Lozada RM, Pond SL, Heckathorn DD, Frost SD.

PLoS One. 2009 Sep 7;4(9):e6777.PMID: 19738904 [PubMed - in process]Related articlesFree article

Using respondent-driven sampling in a hidden population at risk of HIV infection: who do HIV-positive recruiters recruit?

Abramovitz D, Volz EM, Strathdee SA, Patterson TL, Vera A, Frost SD; Proyecto ElCuete.

Sex Transm Dis. 2009 Dec;36(12):750-6.PMID: 19704394 [PubMed - in process]Related articles

Molecular and contextual markers of hepatitis C virus and drug abuse.

Shapshak P, Somboonwit C, Drumright LN, Frost SD, Commins D, Tellinghuisen TL, Scott WK, Duncan R, McCoy C, Page JB, Giunta B, Fernandez F, Singer E, Levine A, Minagar A, Oluwadara O, Kotila T, Chiappelli F, Sinnott JT.

Mol Diagn Ther. 2009;13(3):153-79. doi: 10.2165/01250444-200913030-00002. Review.PMID: 19650670 [PubMed - indexed for MEDLINE]Related articles

Detecting signatures of selection from DNA sequences using Datamonkey.

Poon AF, Frost SD, Pond SL.

Methods Mol Biol. 2009;537:163-83.PMID: 19378144 [PubMed - indexed for MEDLINE]Related articles

Pleocytosis is associated with disruption of HIV compartmentalization between blood and cerebral spinal fluid viral populations.

Smith DM, Zárate S, Shao H, Pillai SK, Letendre SL, Wong JK, Richman DD, Frost SD, Ellis RJ; HNRC Group.

Virology. 2009 Mar 1;385(1):204-8. Epub 2008 Dec 18.PMID: 19100592 [PubMed - indexed for MEDLINE]Related articles

A public health model for the molecular surveillance of HIV transmission in San Diego, California.

Smith DM, May SJ, Tweeten S, Drumright L, Pacold ME, Kosakovsky Pond SL, Pesano RL, Lie YS, Richman DD, Frost SD, Woelk CH, Little SJ.

AIDS. 2009 Jan 14;23(2):225-32.PMID: 19098493 [PubMed - indexed for MEDLINE]Related articles

Low-level plasma HIVs in patients on prolonged suppressive highly active antiretroviral therapy are produced mostly by cells other than CD4 T-cells.

Sahu GK, Paar D, Frost SD, Smith MM, Weaver S, Cloyd MW.

J Med Virol. 2009 Jan;81(1):9-15.PMID: 19031450 [PubMed - indexed for MEDLINE]Related articles

Sexual networks and the transmission of drug-resistant HIV.

Drumright LN, Frost SD.

Curr Opin Infect Dis. 2008 Dec;21(6):644-52. Review.PMID: 18978533 [PubMed - indexed for MEDLINE]Related articles

Immune-driven recombination and loss of control after HIV superinfection.

Streeck H, Li B, Poon AF, Schneidewind A, Gladden AD, Power KA, Daskalakis D, Bazner S, Zuniga R, Brander C, Rosenberg ES, Frost SD, Altfeld M, Allen TM.

J Exp Med. 2008 Aug 4;205(8):1789-96. Epub 2008 Jul 14.PMID: 18625749 [PubMed - indexed for MEDLINE]Related articlesFree article

Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models.

Poon AF, Lewis FI, Frost SD, Kosakovsky Pond SL.

Bioinformatics. 2008 Sep 1;24(17):1949-50. Epub 2008 Jun 18.PMID: 18562270 [PubMed - indexed for MEDLINE]Related articlesFree article

A maximum likelihood method for detecting directional evolution in protein sequences and its application to influenza A virus.

Kosakovsky Pond SL, Poon AF, Leigh Brown AJ, Frost SD.

Mol Biol Evol. 2008 Sep;25(9):1809-24. Epub 2008 May 29.PMID: 18511426 [PubMed - indexed for MEDLINE]Related articlesFree article

Estimating selection pressures on HIV-1 using phylogenetic likelihood models.

Kosakovsky Pond SL, Poon AF, Zárate S, Smith DM, Little SJ, Pillai SK, Ellis RJ, Wong JK, Leigh Brown AJ, Richman DD, Frost SD.

Stat Med. 2008 Oct 15;27(23):4779-89.PMID: 18381707 [PubMed - indexed for MEDLINE]Related articlesFree article

Persistence of transmitted drug resistance among subjects with primary human immunodeficiency virus infection.

Little SJ, Frost SD, Wong JK, Smith DM, Pond SL, Ignacio CC, Parkin NT, Petropoulos CJ, Richman DD.

J Virol. 2008 Jun;82(11):5510-8. Epub 2008 Mar 19.PMID: 18353964 [PubMed - indexed for MEDLINE]Related articlesFree article

Herpes simplex virus type 2 acquisition during recent HIV infection does not influence plasma HIV levels.

Cachay ER, Frost SD, Poon AF, Looney D, Rostami SM, Pacold ME, Richman DD, Little SJ, Smith DM.

J Acquir Immune Defic Syndr. 2008 Apr 15;47(5):592-6.PMID: 18197122 [PubMed - indexed for MEDLINE]Related articlesFree article

Antibody responses in primary HIV-1 infection.

Frost SD, Trkola A, Günthard HF, Richman DD.

Curr Opin HIV AIDS. 2008 Jan;3(1):45-51.PMID: 19372943 [PubMed - as supplied by publisher]Related articles

High-risk sexual and drug using behaviors among male injection drug users who have sex with men in 2 Mexico-US border cities.

Deiss RG, Brouwer KC, Loza O, Lozada RM, Ramos R, Cruz MA, Patterson TL, Heckathorn DD, Frost SD, Strathdee SA.

Sex Transm Dis. 2008 Mar;35(3):243-9.PMID: 18046263 [PubMed - indexed for MEDLINE]Related articlesFree article

An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope.

Poon AF, Lewis FI, Pond SL, Frost SD.

PLoS Comput Biol. 2007 Nov;3(11):e231. Epub 2007 Oct 11.PMID: 18039027 [PubMed - indexed for MEDLINE]Related articlesFree article

Syringe possession arrests are associated with receptive syringe sharing in two Mexico-US border cities.

Pollini RA, Brouwer KC, Lozada RM, Ramos R, Cruz MF, Magis-Rodriguez C, Case P, Burris S, Pu M, Frost SD, Palinkas LA, Miller C, Strathdee SA.

Addiction. 2008 Jan;103(1):101-8. Epub 2007 Nov 20.PMID: 18028520 [PubMed - indexed for MEDLINE]Related articlesFree article

Mapping protease inhibitor resistance to human immunodeficiency virus type 1 sequence polymorphisms within patients.

Poon AF, Kosakovsky Pond SL, Richman DD, Frost SD.

J Virol. 2007 Dec;81(24):13598-607. Epub 2007 Oct 3.PMID: 17913806 [PubMed - indexed for MEDLINE]Related articlesFree article

Using sexual affiliation networks to describe the sexual structure of a population.

Frost SD.

Sex Transm Infect. 2007 Aug;83 Suppl 1:i37-42. Review.PMID: 17664363 [PubMed - indexed for MEDLINE]Related articles

Long-term persistence of transmitted HIV drug resistance in male genital tract secretions: implications for secondary transmission.

Smith DM, Wong JK, Shao H, Hightower GK, Mai SH, Moreno JM, Ignacio CC, Frost SD, Richman DD, Little SJ.

J Infect Dis. 2007 Aug 1;196(3):356-60. Epub 2007 Jun 19.PMID: 17597449 [PubMed - indexed for MEDLINE]Related articles

Evolution of the interferon alpha gene family in eutherian mammals.

Woelk CH, Frost SD, Richman DD, Higley PE, Kosakovsky Pond SL.

Gene. 2007 Aug 1;397(1-2):38-50. Epub 2007 Apr 3.PMID: 17512142 [PubMed - indexed for MEDLINE]Related articlesFree article

Computational analysis and identification of amino acid sites in dengue E proteins relevant to development of diagnostics and vaccines.

Mazumder R, Hu ZZ, Vinayaka CR, Sagripanti JL, Frost SD, Kosakovsky Pond SL, Wu CH.

Virus Genes. 2007 Oct;35(2):175-86. Epub 2007 May 17.PMID: 17508277 [PubMed - indexed for MEDLINE]Related articles

Comparative study of methods for detecting sequence compartmentalization in human immunodeficiency virus type 1.

Zárate S, Pond SL, Shapshak P, Frost SD.

J Virol. 2007 Jun;81(12):6643-51. Epub 2007 Apr 11.PMID: 17428864 [PubMed - indexed for MEDLINE]Related articlesFree article

Adaptation to human populations is revealed by within-host polymorphisms in HIV-1 and hepatitis C virus.

Poon AF, Kosakovsky Pond SL, Bennett P, Richman DD, Leigh Brown AJ, Frost SD.

PLoS Pathog. 2007 Mar;3(3):e45.PMID: 17397261 [PubMed - indexed for MEDLINE]Related articlesFree article

Herpes simplex virus type 2 infection does not influence viral dynamics during early HIV-1 infection.

Cachay ER, Frost SD, Richman DD, Smith DM, Little SJ.

J Infect Dis. 2007 May 1;195(9):1270-7. Epub 2007 Mar 15.PMID: 17396995 [PubMed - indexed for MEDLINE]Related articles

Evolutionary interactions between N-linked glycosylation sites in the HIV-1 envelope.

Poon AF, Lewis FI, Pond SL, Frost SD.

PLoS Comput Biol. 2007 Jan 19;3(1):e11. Epub 2006 Dec 8.PMID: 17238283 [PubMed - indexed for MEDLINE]Related articlesFree article

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.

Lake-Bakaar G, Dustin L, McKeating J, Newton K, Freeman V, Frost SD.

Blood. 2007 Jan 15;109(2):845-6. No abstract available. PMID: 17210867 [PubMed - indexed for MEDLINE]Related articlesFree article

GARD: a genetic algorithm for recombination detection.

Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SD.

Bioinformatics. 2006 Dec 15;22(24):3096-8. Epub 2006 Nov 16.PMID: 17110367 [PubMed - indexed for MEDLINE]Related articlesFree article

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.

Frost SD, Brouwer KC, Firestone Cruz MA, Ramos R, Ramos ME, Lozada RM, Magis-Rodriguez C, Strathdee SA.

J Urban Health. 2006 Nov;83(6 Suppl):i83-97.PMID: 17072761 [PubMed - indexed for MEDLINE]Related articlesFree article

Evolutionary model selection with a genetic algorithm: a case study using stem RNA.

Kosakovsky Pond SL, Mannino FV, Gravenor MB, Muse SV, Frost SD.

Mol Biol Evol. 2007 Jan;24(1):159-70. Epub 2006 Oct 12.PMID: 17038448 [PubMed - indexed for MEDLINE]Related articlesFree article

Characteristics of recently HIV-infected men who use the Internet to find male sex partners and sexual practices with those partners.

Smith DM, Drumright LN, Frost SD, Cheng WS, Espitia S, Daar ES, Little SJ, Gorbach PM.

J Acquir Immune Defic Syndr. 2006 Dec 15;43(5):582-7.PMID: 17019370 [PubMed - indexed for MEDLINE]Related articles

Lack of neutralizing antibody response to HIV-1 predisposes to superinfection.

Smith DM, Strain MC, Frost SD, Pillai SK, Wong JK, Wrin T, Liu Y, Petropolous CJ, Daar ES, Little SJ, Richman DD.

Virology. 2006 Nov 10;355(1):1-5. Epub 2006 Sep 7.PMID: 16962152 [PubMed - indexed for MEDLINE]Related articles

Automated phylogenetic detection of recombination using a genetic algorithm.

Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SD.

Mol Biol Evol. 2006 Oct;23(10):1891-901. Epub 2006 Jul 3.PMID: 16818476 [PubMed - indexed for MEDLINE]Related articlesFree article

Adaptation to different human populations by HIV-1 revealed by codon-based analyses.

Pond SL, Frost SD, Grossman Z, Gravenor MB, Richman DD, Brown AJ.

PLoS Comput Biol. 2006 Jun 23;2(6):e62. Epub 2006 Jun 23.PMID: 16789820 [PubMed - indexed for MEDLINE]Related articlesFree article

Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection.

Frost SD, Wrin T, Smith DM, Kosakovsky Pond SL, Liu Y, Paxinos E, Chappey C, Galovich J, Beauchaine J, Petropoulos CJ, Little SJ, Richman DD.

Proc Natl Acad Sci U S A. 2005 Dec 20;102(51):18514-9. Epub 2005 Dec 9.PMID: 16339909 [PubMed - indexed for MEDLINE]Related articlesFree article

Defining the role of computed tomographic pulmonary angiography in suspected pulmonary embolism.

Frost SD.

Ann Intern Med. 2005 May 3;142(9):800-1; author reply 802. No abstract available. PMID: 15867417 [PubMed - indexed for MEDLINE]Related articlesFree article

Characterization of human immunodeficiency virus type 1 (HIV-1) envelope variation and neutralizing antibody responses during transmission of HIV-1 subtype B.

Frost SD, Liu Y, Pond SL, Chappey C, Wrin T, Petropoulos CJ, Little SJ, Richman DD.

J Virol. 2005 May;79(10):6523-7.PMID: 15858036 [PubMed - indexed for MEDLINE]Related articlesFree article

Phenotypic hypersusceptibility to multiple protease inhibitors and low replicative capacity in patients who are chronically infected with human immunodeficiency virus type 1.

Martinez-Picado J, Wrin T, Frost SD, Clotet B, Ruiz L, Brown AJ, Petropoulos CJ, Parkin NT.

J Virol. 2005 May;79(10):5907-13.PMID: 15857976 [PubMed - indexed for MEDLINE]Related articlesFree article

Datamonkey: rapid detection of selective pressure on individual sites of codon alignments.

Pond SL, Frost SD.

Bioinformatics. 2005 May 15;21(10):2531-3. Epub 2005 Feb 15.PMID: 15713735 [PubMed - indexed for MEDLINE]Related articlesFree article

Not so different after all: a comparison of methods for detecting amino acid sites under selection.

Kosakovsky Pond SL, Frost SD.

Mol Biol Evol. 2005 May;22(5):1208-22. Epub 2005 Feb 9.PMID: 15703242 [PubMed - indexed for MEDLINE]Related articlesFree article

A genetic algorithm approach to detecting lineage-specific variation in selection pressure.

Pond SL, Frost SD.

Mol Biol Evol. 2005 Mar;22(3):478-85. Epub 2004 Oct 27. Erratum in: Mol Biol Evol. 2005 Apr;22(4):1157. PMID: 15509724 [PubMed - indexed for MEDLINE]Related articlesFree article

HyPhy: hypothesis testing using phylogenies.

Pond SL, Frost SD, Muse SV.

Bioinformatics. 2005 Mar 1;21(5):676-9. Epub 2004 Oct 27.PMID: 15509596 [PubMed - indexed for MEDLINE]Related articlesFree article

A simple hierarchical approach to modeling distributions of substitution rates.

Pond SL, Frost SD.

Mol Biol Evol. 2005 Feb;22(2):223-34. Epub 2004 Oct 13.PMID: 15483327 [PubMed - indexed for MEDLINE]Related articlesFree article

Genetic basis of hypersusceptibility to protease inhibitors and low replicative capacity of human immunodeficiency virus type 1 strains in primary infection.

Leigh Brown AJ, Frost SD, Good B, Daar ES, Simon V, Markowitz M, Collier AC, Connick E, Conway B, Margolick JB, Routy JP, Corbeil J, Hellmann NS, Richman DD, Little SJ.

J Virol. 2004 Mar;78(5):2242-6.PMID: 14963120 [PubMed - indexed for MEDLINE]Related articlesFree article

The preoperative evaluation: use the history and physical rather than routine testing.

Michota FA, Frost SD.

Cleve Clin J Med. 2004 Jan;71(1):63-70.PMID: 14740970 [PubMed - indexed for MEDLINE]Related articlesFree article