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S. Frost · SciRah

Researcher profile · Semantic Scholar

S. Frost

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S. Frost — researcher profile on SciRah

h-index: 52
Works: 103
Citations: 16K

Most-cited papers

Not so different after all: a comparison of methods for detecting amino acid sites under selection.
Sergei L. Kosakovsky Pond, S. Frost
2005Molecular biology and evolution2,238 citations Open access
Semantic Scholar
Datamonkey: rapid detection of selective pressure on individual sites of codon alignments
Sergei L Kosakovsky Pond, S. Frost
2005Bioinform.1,384 citations Open access
Semantic Scholar
Automated phylogenetic detection of recombination using a genetic algorithm.
Sergei L. Kosakovsky Pond, D. Posada, M. Gravenor, C. Woelk +1 more
2006Molecular biology and evolution945 citations Open access
Semantic Scholar
HyPhy 2.5 - a customizable platform for evolutionary hypothesis testing using phylogenies.
Sergei L. Kosakovsky Pond, A. Poon, Ryan Velazquez, S. Weaver +10 more
2019Molecular biology and evolution678 citations Open access
Semantic Scholar
A random effects branch-site model for detecting episodic diversifying selection.
Sergei L. Kosakovsky Pond, B. Murrell, M. Fourment, S. Frost +2 more
2011Molecular biology and evolution436 citations Open access
Semantic Scholar
Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection.
S. Frost, T. Wrin, Davey M. Smith, Sergei L. Kosakovsky Pond +8 more
2005Proceedings of the National Academy of Sciences of the United States of America382 citations Open access
Semantic Scholar
GARD: a genetic algorithm for recombination detection
Sergei L. Kosakovsky Pond, D. Posada, M. Gravenor, Christopher H. Woelk +1 more
2006Bioinform.294 citations Open access
Semantic Scholar
Evaluation of Respondent-Driven Sampling
N. McCreesh, S. Frost, J. Seeley, Joseph Katongole +10 more
2012Epidemiology280 citations Open access
Semantic Scholar
An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1
Sergei L. Kosakovsky Pond, D. Posada, Eric W. Stawiski, C. Chappey +6 more
2009PLoS Comput. Biol.257 citations Open access
Semantic Scholar
Phylodynamics of Infectious Disease Epidemics
Erik M. Volz, Sergei L. Kosakovsky Pond, M. Ward, A. Leigh Brown +1 more
2009Genetics249 citations Open access
Semantic Scholar
Adaptation to Different Human Populations by HIV-1 Revealed by Codon-Based Analyses
Sergei L Kosakovsky Pond, S. Frost, Z. Grossman, M. Gravenor +2 more
2006PLoS Comput. Biol.238 citations Open access
Semantic Scholar
Persistence of Transmitted Drug Resistance among Subjects with Primary Human Immunodeficiency Virus Infection
S. Little, S. Frost, J. Wong, Davey M. Smith +5 more
2008Journal of Virology224 citations Open access
Semantic Scholar
A genetic algorithm approach to detecting lineage-specific variation in selection pressure.
Sergei L Kosakovsky Pond, S. Frost
2005Molecular biology and evolution211 citations Open access
Semantic Scholar
Characterization of Human Immunodeficiency Virus Type 1 (HIV-1) Envelope Variation and Neutralizing Antibody Responses during Transmission of HIV-1 Subtype B
S. Frost, Yang Liu, Sergei L Kosakovsky Pond, C. Chappey +4 more
2005Journal of Virology203 citations Open access
Semantic Scholar
Transmission fitness of drug-resistant human immunodeficiency virus and the prevalence of resistance in the antiretroviral-treated population.
A. Leigh Brown, S. Frost, W. C. Mathews, Keith Dawson +4 more
2003Journal of Infectious Diseases176 citations
Semantic Scholar
Residual human immunodeficiency virus (HIV) Type 1 RNA and DNA in lymph nodes and HIV RNA in genital secretions and in cerebrospinal fluid after suppression of viremia for 2 years.
H. Günthard, D. Havlir, S. Fiscus, Zhi-Qiang Zhang +16 more
2001Journal of Infectious Diseases160 citations Open access
Semantic Scholar
HIV dynamics and T-cell immunity after three structured treatment interruptions in chronic HIV-1 infection
L. Ruiz, G. Carcelain, J. Martinez-Picado, S. Frost +7 more
2001AIDS (London)158 citations Open access
Semantic Scholar
Genetic drift and within-host metapopulation dynamics of HIV-1 infection
S. Frost, M. Dumaurier, S. Wain-Hobson, A. Leigh Brown
2001Proceedings of the National Academy of Sciences of the United States of America140 citations Open access
Semantic Scholar
Immune-driven recombination and loss of control after HIV superinfection
H. Streeck, Bin Li, A. Poon, A. Schneidewind +10 more
2008Journal of Experimental Medicine138 citations Open access
Semantic Scholar
CCL3L1-CCR5 genotype influences durability of immune recovery during antiretroviral therapy of HIV-1–infected individuals
S. Ahuja, Hemant Kulkarni, G. Catano, B. Agan +15 more
2008Nature Medicine129 citations Open access
Semantic Scholar
A Public Health Model for the Molecular Surveillance of HIV Transmission in San Diego, California
Davey M. Smith, S. May, S. Tweeten, L. Drumright +8 more
2009AIDS (London)122 citations Open access
Semantic Scholar
Amprenavir-resistant HIV-1 exhibits lopinavir cross-resistance and reduced replication capacity
J. Prado, T. Wrin, Jeff Beauchaine, L. Ruiz +5 more
2002AIDS (London)121 citations Open access
Semantic Scholar
An Evolutionary-Network Model Reveals Stratified Interactions in the V3 Loop of the HIV-1 Envelope
A. Poon, F. Lewis, Sergei L Kosakovsky Pond, S. Frost
2007PLoS Comput. Biol.118 citations Open access
Semantic Scholar
Lack of neutralizing antibody response to HIV-1 predisposes to superinfection.
Davey M. Smith, M. Strain, S. Frost, S. Pillai +7 more
2006Virology114 citations Open access
Semantic Scholar
A maximum likelihood method for detecting directional evolution in protein sequences and its application to influenza A virus.
Sergei L. Kosakovsky Pond, A. Poon, A. Leigh Brown, S. Frost
2008Molecular biology and evolution112 citations Open access
Semantic Scholar
Simple Epidemiological Dynamics Explain Phylogenetic Clustering of HIV from Patients with Recent Infection
Erik M. Volz, J. Koopman, M. Ward, A. Leigh Brown +1 more
2012PLoS Comput. Biol.111 citations Open access
Semantic Scholar
Comparative Study of Methods for Detecting Sequence Compartmentalization in Human Immunodeficiency Virus Type 1
S. Zárate, Sergei L Kosakovsky Pond, P. Shapshak, S. Frost
2007Journal of Virology108 citations Open access
Semantic Scholar
Selection of drug-resistant HIV-1 mutants in response to repeated structured treatment interruptions
J. Martinez-Picado, Kristina Morales-Lopetegi, T. Wrin, J. Prado +4 more
2002AIDS (London)105 citations Open access
Semantic Scholar
Evolution of Lamivudine Resistance in Human Immunodeficiency Virus Type 1-Infected Individuals: the Relative Roles of Drift and Selection
S. Frost, M. Nijhuis, R. Schuurman, C. Boucher +1 more
2000Journal of Virology99 citations Open access
Semantic Scholar
A Dirichlet process model for detecting positive selection in protein-coding DNA sequences.
J. Huelsenbeck, Sonia Jain, S. Frost, Sergei L Kosakovsky Pond
2006Proceedings of the National Academy of Sciences of the United States of America93 citations
Semantic Scholar
Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models
A. Poon, F. Lewis, S. Frost, Sergei L Kosakovsky Pond
2008Bioinform.91 citations Open access
Semantic Scholar
Detecting signatures of selection from DNA sequences using Datamonkey.
A. Poon, S. Frost, Sergei L Kosakovsky Pond
2009Methods in molecular biology89 citations
Semantic Scholar
Hepatitis C Infection, Cryoglobulinemia, and Vasculitic Neuropathy. Treatment With Interferon Alfa
S. Khella, S. Frost, G. Hermann, L. Leventhal +3 more
1995Neurology81 citations
Semantic Scholar
Respondent driven sampling—where we are and where should we be going?
Richard G. White, A. Lansky, Sharad Goel, David P. Wilson +3 more
2012Sexually Transmitted Infections79 citations Open access
Semantic Scholar
Evolutionary Interactions between N-Linked Glycosylation Sites in the HIV-1 Envelope
A. Poon, F. Lewis, Sergei L Kosakovsky Pond, S. Frost
2006PLoS Comput. Biol.79 citations Open access
Semantic Scholar
Evolution of the interferon alpha gene family in eutherian mammals.
C. Woelk, S. Frost, D. Richman, Prentice E Higley +1 more
2007Gene78 citations Open access
Semantic Scholar
Long-term persistence of transmitted HIV drug resistance in male genital tract secretions: implications for secondary transmission.
Davey M. Smith, J. Wong, Hai-Feng Shao, G. Hightower +6 more
2007Journal of Infectious Diseases76 citations Open access
Semantic Scholar
Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1.
A. Poon, L. Swenson, W. Dong, W. Deng +6 more
2010Molecular biology and evolution73 citations Open access
Semantic Scholar
Evolutionary fingerprinting of genes.
Sergei L Kosakovsky Pond, K. Scheffler, M. Gravenor, A. Poon +1 more
2010Molecular biology and evolution70 citations Open access
Semantic Scholar
Viral Dynamics during Structured Treatment Interruptions of Chronic Human Immunodeficiency Virus Type 1 Infection
S. Frost, J. Martinez-Picado, L. Ruiz, B. Clotet +1 more
2002Journal of Virology69 citations Open access
Semantic Scholar
Pneumococcal within-host diversity during colonization, transmission and treatment
G. Tonkin-Hill, C. Ling, C. Chaguza, S. Salter +11 more
2022bioRxiv68 citations Open access
Semantic Scholar
Low-level Plasma HIVs in Patients on Prolonged Suppressive Highly Active Antiretroviral Therapy Are Produced Mostly by Cells Other Than CD4 T-cells
G. K. Sahu, D. Paár, S. Frost, Melissa M. Smith +2 more
2009Journal of Medical Virology68 citations Open access
Semantic Scholar
A simple hierarchical approach to modeling distributions of substitution rates.
Sergei L Kosakovsky Pond, S. Frost
2005Molecular biology and evolution65 citations Open access
Semantic Scholar
Adaptation to Human Populations Is Revealed by Within-Host Polymorphisms in HIV-1 and Hepatitis C Virus
Art F. Y. Poon, Sergei L. Kosakovsky Pond, Phil Bennett, D. Richman +2 more
2007PLoS Pathogens64 citations Open access
Semantic Scholar
Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison
O. Ratmann, Emma B. Hodcroft, M. Pickles, A. Cori +20 more
2016Molecular biology and evolution63 citations Open access
Semantic Scholar
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.
G. Lake-Bakaar, L. Dustin, J. McKeating, K. Newton +2 more
2007Blood62 citations Open access
Semantic Scholar
Using sexual affiliation networks to describe the sexual structure of a population
S. Frost
2007Sexually Transmitted Infections58 citations
Semantic Scholar
Neutral Theory and Rapidly Evolving Viral Pathogens
S. Frost, B. Magalis, Sergei L. Kosakovsky Pond
2018Molecular biology and evolution56 citations Open access
Semantic Scholar
Estimating selection pressures on alignments of coding sequences Analyses using HyPhy
Sergei L Kosakovsky Pond, S. Frost
200754 citations
Semantic Scholar
Assessment of a multiplex PCR and Nanopore-based method for dengue virus sequencing in Indonesia
Samuel C. B. Stubbs, B. Blacklaws, B. Yohan, F. Yudhaputri +8 more
2020Virology Journal50 citations Open access
Semantic Scholar

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