S. Frost

发表

Selection of drug-resistant HIV-1 mutants in response to repeated structured treatment interruptions

B. Clotet, J. Martinez-Picado, K. Morales-Lopetegi, 2002, AIDS.

HIV dynamics and T-cell immunity after three structured treatment interruptions in chronic HIV-1 infection

R. Paredes, B. Clotet, J. Martinez-Picado, 2001, AIDS.

Viral Dynamics during Structured Treatment Interruptions of Chronic Human Immunodeficiency Virus Type 1 Infection

B. Clotet, J. Martinez-Picado, S. Frost, 2002, Journal of Virology.

Dynamics and evolution of HIV-1 during structured treatment interruptions.

S. Frost, 2002, AIDS reviews.

Amprenavir-resistant HIV-1 exhibits lopinavir cross-resistance and reduced replication capacity

B. Clotet, J. Martinez-Picado, T. Wrin, 2002, AIDS.

Phylodynamics of Infectious Disease Epidemics

Sergei L. Kosakovsky Pond, E. Volz, S. Frost, 2009, Genetics.

Evidence for positive selection driving the evolution of HIV-1 env under potent antiviral therapy.

D. Richman, H. Günthard, S. Frost, 2001, Virology.

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

Sergei L. Kosakovsky Pond, S. Frost, 2005, Molecular biology and evolution.

A random effects branch-site model for detecting episodic diversifying selection.

Sergei L. Kosakovsky Pond, S. Frost, B. Murrell, 2011, Molecular biology and evolution.

Analysis of a capture-recapture estimator for the size of populations with heterogenous catchability, and its evaluation on RDS data from rural Uganda

Richard G. White, S. Frost, Y. Berchenko, 2011, 1111.1714.

Capture-recapture methods and respondent-driven sampling: their potential and limitations

S. Frost, Y. Berchenko, 2011, Sexually Transmitted Infections.

AN EMPIRICAL EVALUATION OF RESPONDENT-DRIVEN SAMPLING

Richard G. White, R. Hayes, J. Seeley, 2011 .

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

Sergei L. Kosakovsky Pond, S. Frost, A. Leigh Brown, 2008, Molecular biology and evolution.

Evolution of the interferon alpha gene family in eutherian mammals.

Sergei L. Kosakovsky Pond, D. Richman, S. Frost, 2007, Gene.

Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1.

Sergei L. Kosakovsky Pond, J. Mullins, D. Richman, 2010, Molecular biology and evolution.

Assigning and visualizing germline genes in antibody repertoires

S. Frost, B. Murrell, G. Silverman, 2015, Philosophical Transactions of the Royal Society B: Biological Sciences.

Genetic drift and within-host metapopulation dynamics of HIV-1 infection

S. Frost, S. Wain-Hobson, M. Dumaurier, 2001, Proceedings of the National Academy of Sciences of the United States of America.

Mapping Protease Inhibitor Resistance to Human Immunodeficiency Virus Type 1 Sequence Polymorphisms within Patients

Sergei L. Kosakovsky Pond, D. Richman, S. Frost, 2007, Journal of Virology.

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

S. Frost, 2007, Sexually Transmitted Infections.

Genotype-Specific Evolution of Hepatitis E Virus

Bethany L. Dearlove, S. Frost, Adam B. Brayne, 2017, Journal of Virology.

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

Sergei L. Kosakovsky Pond, Sergei L Kosakovsky Pond, Michael B Gravenor, 2007, Molecular biology and evolution.

OutbreakTools: A new platform for disease outbreak analysis using the R software

Samuel Soubeyrand, Michael Höhle, Thibaut Jombart, 2014, Epidemics.

A Dirichlet process model for detecting positive selection in protein-coding DNA sequences.

John P Huelsenbeck, Sonia Jain, J. Huelsenbeck, 2006, Proceedings of the National Academy of Sciences of the United States of America.

Evolution of Envelope Sequences of Human Immunodeficiency Virus Type 1 in Cellular Reservoirs in the Setting of Potent Antiviral Therapy

Alan S. Perelson, Douglas D. Richman, Simon D. W. Frost, 1999, Journal of Virology.

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.

D. Richman, H. Günthard, S. Frost, 2001, The Journal of infectious diseases.

HyPhy 2.5 - a customizable platform for evolutionary hypothesis testing using phylogenies.

Stephanie J. Spielman, Sergei L. Kosakovsky Pond, A. Nekrutenko, 2019, Molecular biology and evolution.

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

Sergei L. Kosakovsky Pond, Simon D. W. Frost, S. Frost, 2005, Molecular biology and evolution.

Evaluation of Respondent-driven Sampling Original Article

Richard G. White, R. Hayes, J. Seeley, 2015 .

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

Cathy H. Wu, Sergei L. Kosakovsky Pond, C. R. Vinayaka, 2007, Virus Genes.

OP-MOLB160219 185..203

Richard H. Liang, David A. Rasmussen, Bethany L. Dearlove, 2016 .

Neutral Theory and Rapidly Evolving Viral Pathogens

Sergei L. Kosakovsky Pond, S. Frost, B. R. Magalis, 2018, Molecular biology and evolution.

Comparative Study of Methods for Detecting Sequence Compartmentalization in Human Immunodeficiency Virus Type 1 Samples of Viral Populations Are Collected Either by Examining Brain Tissue from Infected Individuals Post Mortem or by Drawing Samples From

S. Frost, P. Shapshak, Sergei L Kosakovsky Pond, 2006 .

An investig-ation into the epidemiology of chikungunya virus across neglected regions of Indonesia

S. Frost, R. T. Sasmono, A. Powers, 2020, PLoS neglected tropical diseases.

Improving ILI Surveillance using Hospital Staff Influenza-like Absence (ILA)

D. Fleming, S. Frost, A. Elliot, 2013, Online Journal of Public Health Informatics.

Phylogenetic Characterisation of Crimean-Congo Hemorrhagic Fever Virus Detected in African Blue Ticks Feeding on Cattle in a Ugandan Abattoir

S. Frost, R. Hewson, P. Waiswa, 2021 .

Distinct Dengue Disease Epidemiology, Clinical, and Diagnosis Features in Western, Central, and Eastern Regions of Indonesia, 2017–2019

S. Frost, R. T. Sasmono, K. Myint, 2020, Frontiers in Medicine.

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.

S. Frost, J. McKeating, V. Freeman, 2007, Blood.

Comparative Study of Methods for Detecting Sequence Compartmentalization in Human Immunodeﬁciency Virus Type 1 (cid:1)

S. Frost, P. Shapshak, Sergei L Kosakovsky Pond, 2007 .

Edinburgh Research Explorer Evolution of lamivudine resistance in human immunodeficiency virus type 1-infected individuals

S. Frost, C. Boucher, M. Nijhuis, 2018 .

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

D. Richman, S. Frost, Sergei L Kosakovsky Pond, 2018 .

The Depth of CTL Epitope Coverage Correlates with Strength of Selection in Gag p17 for Subtype B but not Subtype C

D. Richman, S. Frost, Davey M. Smith, 2008 .

Hepatitis C Infection, Cryoglobulinemia, and Vasculitic Neuropathy. Treatment With Interferon Alfa

S. Frost, L. Leventhal, S. Scherer, 1995, Neurology.

Bat pluripotent stem cells reveal unique entanglement between host and viruses

Graham M. Hughes, R. Young, S. Puechmaille, 2022, bioRxiv.

Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology

Sergei L. Kosakovsky Pond, Simon D. W. Frost, Art F. Y. Poon, 2010, Bioinform..

HyPhy: hypothesis testing using phylogenies

Sergei L. Kosakovsky Pond, Simon D. W. Frost, Sergei L. Kosakovsky Pond, 2005, Bioinform..

GARD: a genetic algorithm for recombination detection

Sergei L. Kosakovsky Pond, David Posada, Michael B. Gravenor, 2006, Bioinform..

Persistence of Transmitted Drug Resistance among Subjects with Primary Human Immunodeficiency Virus Infection

D. Richman, S. Little, S. Frost, 2008, Journal of Virology.

Transmission fitness of drug-resistant human immunodeficiency virus and the prevalence of resistance in the antiretroviral-treated population.

Simon D W Frost, D. Richman, S. Little, 2003, The Journal of infectious diseases.

CCL3L1-CCR5 genotype influences durability of immune recovery during antiretroviral therapy of HIV-1–infected individuals

D. Richman, S. Little, S. Frost, 2008, Nature Medicine.

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

Sergei L. Kosakovsky Pond, Simon D. W. Frost, S. Frost, 2005, Bioinform..

Automated phylogenetic detection of recombination using a genetic algorithm.

David Posada, Sergei L. Kosakovsky Pond, Sergei L Kosakovsky Pond, 2006, Molecular biology and evolution.

The Phylogenetic Handbook: Estimating selection pressures on alignments of coding sequences

Sergei L. Kosakovsky Pond, Simon D. W. Frost, Art F. Y. Poon, 2009 .

Estimating selection pressures on alignments of coding sequences Analyses using HyPhy

Sergei L. Kosakovsky Pond, S. Frost, Sergei L Kosakovsky Pond, 2007 .

Evolutionary fingerprinting of genes.

Konrad Scheffler, Art F Y Poon, Michael B Gravenor, 2010, Molecular biology and evolution.

Adaptation to Different Human Populations by HIV-1 Revealed by Codon-Based Analyses

Sergei L. Kosakovsky Pond, Douglas D. Richman, Michael B. Gravenor, 2006, PLoS Comput. Biol..

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

Sergei L. Kosakovsky Pond, David Posada, Michael B. Gravenor, 2009, PLoS Comput. Biol..

Mitochondrial Disease Caused by a Novel Homozygous Mutation (Gly106del) in the SCO1 Gene

S. Frost, M. Petersen, I. Pedersen, 2019, Neonatology.

Phylogenetic analysis of GBV-C/hepatitis G virus.

N. Cuceanu, P. Simmonds, S. Frost, 2000, The Journal of general virology.

Evolutionary Interactions between N-Linked Glycosylation Sites in the HIV-1 Envelope

Sergei L. Kosakovsky Pond, Simon D. W. Frost, Art F. Y. Poon, 2006, PLoS Comput. Biol..

Phylogenetic Characterization of Crimean-Congo Hemorrhagic Fever Virus Detected in African Blue Ticks Feeding on Cattle in a Ugandan Abattoir

S. Frost, R. Hewson, D. Allen, 2021, Microorganisms.

A simple hierarchical approach to modeling distributions of substitution rates.

Simon D W Frost, S. Frost, Sergei L Kosakovsky Pond, 2005, Molecular biology and evolution.

Antibody responses in primary HIV-1 infection

A. Trkola, D. Richman, H. Günthard, 2008, Current opinion in HIV and AIDS.

Adaptation to Human Populations Is Revealed by Within-Host Polymorphisms in HIV-1 and Hepatitis C Virus

Sergei L. Kosakovsky Pond, D. Richman, S. Frost, 2007, PLoS pathogens.

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

Yang Liu, Terri Wrin, Sergei L. Kosakovsky Pond, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Detecting signatures of selection from DNA sequences using Datamonkey.

S. Frost, A. Poon, Sergei L Kosakovsky Pond, 2009, Methods in molecular biology.

Estimating selection pressures on HIV‐1 using phylogenetic likelihood models

Sergei L. Kosakovsky Pond, D. Richman, S. Little, 2008, Statistics in medicine.

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

Sergei L. Kosakovsky Pond, Simon D. W. Frost, Art F. Y. Poon, 2008, Bioinform..

An Evolutionary-Network Model Reveals Stratified Interactions in the V3 Loop of the HIV-1 Envelope

Sergei L. Kosakovsky Pond, Simon D. W. Frost, Art F. Y. Poon, 2007, PLoS Comput. Biol..

Evolution of Lamivudine Resistance in Human Immunodeficiency Virus Type 1-Infected Individuals: the Relative Roles of Drift and Selection

S. Frost, C. Boucher, M. Nijhuis, 2000, Journal of Virology.

Immune-driven recombination and loss of control after HIV superinfection

Todd M. Allen, E. Rosenberg, M. Altfeld, 2008, The Journal of experimental medicine.

Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison

Tanja Stadler, Michael Pickles, Denise Kühnert, 2016, Molecular biology and evolution.

Surveys, Serologies, and Sequences Reveal History of Iatrogenic Transmission of HIV-1

S. Frost, S. Kwofie, 2016, The Journal of infectious diseases.

Can Non-lytic CD8+ T Cells Drive HIV-1 Escape?

Becca Asquith, Roland R. Regoes, Simon D. W. Frost, 2013, PLoS pathogens.

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

Christopher H Woelk, Lydia Drumright, D. Richman, 2009, AIDS.

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

D. Richman, S. Little, T. Wrin, 2006, Virology.

Characterization of Human Immunodeficiency Virus Type 1 (HIV-1) Envelope Variation and Neutralizing Antibody Responses during Transmission of HIV-1 Subtype B

Yang Liu, Terri Wrin, Colombe Chappey, 2005, Journal of Virology.

Assessment of a multiplex PCR and Nanopore-based method for dengue virus sequencing in Indonesia

S. Frost, R. T. Sasmono, B. Blacklaws, 2020, Virology Journal.

A Nanopore-based method for generating complete coding region sequences of dengue virus in resource-limited settings

Sam Stubbs, Barbara Blacklaws, Benediktus Yohan, 2018, bioRxiv.

Human immunodeficiency virus-1 RNA levels in cerebrospinal fluid exhibit a set point in clinically stable patients not receiving antiretroviral therapy.

S. Frost, R. Ellis, J. McCutchan, 2003, The Journal of infectious diseases.

Respondent Driven Sampling: Determinants of Recruitment and a Method to Improve Point Estimation

Nicky McCreesh, Simon D. W. Frost, Richard J. Hayes, 2013, PloS one.

Evaluation of Respondent-driven Sampling

Andrew J Copas, Nicky McCreesh, Pam Sonnenberg, 2012, Epidemiology.

Evaluation of the role of location and distance in recruitment in respondent-driven sampling

Richard G. White, L. Johnston, R. Hayes, 2011, International journal of health geographics.

Association of Antiretroviral Resistance Genotypes with Response to Therapy – Comparison of Three Models

C. Leen, S. Frost, D. Clutterbuck, 2001, Antiviral therapy.

Pneumococcal within-host diversity during colonization, transmission and treatment

J. Corander, S. Bentley, S. Frost, 2022, bioRxiv.

Transmitted Drug Resistance in the CFAR Network of Integrated Clinical Systems Cohort: Prevalence and Effects on Pre-Therapy CD4 and Viral Load

R. Haubrich, S. Frost, S. Boswell, 2011, PloS one.

Phenotypic Hypersusceptibility to Multiple Protease Inhibitors and Low Replicative Capacity in Patients Who Are Chronically Infected with Human Immunodeficiency Virus Type 1

Christos J. Petropoulos, Terri Wrin, Simon D. W. Frost, 2005, Journal of Virology.

Characteristics of Recently HIV-Infected Men Who Use the Internet to Find Male Sex Partners and Sexual Practices With Those Partners

S. Little, S. Frost, E. Daar, 2006, Journal of acquired immune deficiency syndromes.

Respondent driven sampling—where we are and where should we be going?

Sharad Goel, Richard G. White, Richard G White, 2012, Sexually Transmitted Infections.

The Immune System as an Inducible Defense

S. Frost, 2021 .

Sequence analysis GARD : a genetic algorithm for recombination detection

S. Frost, D. Posada, M. Gravenor, 2006 .

Genetic Basis of Hypersusceptibility to Protease Inhibitors and Low Replicative Capacity of Human Immunodeficiency Virus Type 1 Strains in Primary Infection

J. Corbeil, J. Margolick, D. Richman, 2004, Journal of Virology.

Quasispecies dynamics and the emergence of drug resistance during zidovudine therapy of HIV infection

S. Frost, A. McLean, A R McLean, 1994, AIDS.

Viral Evolution during Structured Treatment Interruptions in Chronically Human Immunodeficiency Virus-Infected Individuals

B. Clotet, J. Martinez-Picado, K. Morales-Lopetegi, 2002, Journal of Virology.

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

Simon D W Frost, D. Richman, S. Little, 2007, The Journal of infectious diseases.

Six challenges in measuring contact networks for use in modelling.

K Eames, S Bansal, S Frost, 2015, Epidemics.

Assessing the use of hospital staff influenza-like absence (ILA) for enhancing hospital preparedness and national surveillance

S. Frost, R. Pebody, A. Elliot, 2015, BMC Infectious Diseases.

Herpes Simplex Virus Type 2 Acquisition During Recent HIV Infection Does Not Influence Plasma HIV Levels

D. Richman, S. Little, S. Frost, 2008, Journal of acquired immune deficiency syndromes.

Germinal centre destruction as a major pathway of HIV pathogenesis.

S. Frost, A. McLean, A R McLean, 1994, Journal of acquired immune deficiency syndromes.

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

S. Frost, S. Weaver, M. Cloyd, 2009, Journal of medical virology.

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

D. Richman, S. Frost, R. Ellis, 2009, Virology.

Viral kinetics and hepatitis C

S. Frost, G. Lake‐Bakaar, 2003, Hepatology.

Simple Epidemiological Dynamics Explain Phylogenetic Clustering of HIV from Patients with Recent Infection

Erik M. Volz, Simon D. W. Frost, James S. Koopman, 2012, PLoS Comput. Biol..

Bioinformatics Applications Note Sequence Analysis Datamonkey 2010: a Suite of Phylogenetic Analysis Tools for Evolutionary Biology

S. Frost, A. Poon, Sergei L Kosakovsky Pond, 2022 .

Evolution of lamivudine resistance in human immunodeficiency virus type 1-infected individuals

S. Frost, C. Boucher, M. Nijhuis, 2016 .

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

D. Richman, S. Little, S. Frost, 2007, The Journal of infectious diseases.

Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology

S. Frost, A. Poon, Sergei L Kosakovsky Pond, 2010, Bioinform..

Genotype-Specific Evolution of Hepatitis E Virus

Bethany L. Dearlove, S. Frost, Adam B. Brayne, 2017, Journal of Virology.

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

S. Frost, F. Lewis, A. Poon, 2008, Bioinform..

GARD: a genetic algorithm for recombination detection

S. Frost, S. L. K. Pond, David Posada, 2006, Bioinform..

UC Office of the President Recent Work Title Assigning and visualizing germline genes in antibody repertoires Permalink

S. Frost, B. Murrell, G. Silverman, 2015 .

Comparative Study of Methods for Detecting Sequence Compartmentalization in Human Immunodeficiency Virus Type 1

S. Frost, P. Shapshak, Sergei L Kosakovsky Pond, 2007, Journal of Virology.

BIOINFORMATICS APPLICATIONS

Sergei L. Kosakovsky Pond, S. Frost, S. Muse, 2022 .

Adaptation to Human Populations Is Revealed by Within-Host Polymorphisms in HIV-1 and Hepatitis C Virus

S. Frost, A. Leigh Brown, S. K. Kosakovsky Pond, 2007, PLoS pathogens.

Phenotypic Hypersusceptibility to Multiple Protease Inhibitors and Low Replicative Capacity in Patients Who Are Chronically Infected with Human Immunodeficiency Virus Type 1

B. Clotet, J. Martinez-Picado, T. Wrin, 2005, Journal of Virology.

Lymphocyte dynamics, apoptosis and HIV infection.

S. Frost, C. Michie, 1996, Trends in microbiology.