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List of works by Simon Frost

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

scholarly article

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

scientific article published on 27 October 2004

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

scientific article published on 29 May 2008

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

scientific article published on January 2009

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

scientific article published on 13 June 2011

A simple hierarchical approach to modeling distributions of substitution rates.

scientific article published on 13 October 2004

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

scientific article (publication date: March 2007)

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

scientific article

An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1

scientific article

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

scientific article

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

scientific article published on 21 December 2020

Antibody responses in primary HIV-1 infection.

scientific article published on January 2008

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

scientific article

Assigning and visualizing germline genes in antibody repertoires

scientific article

Association of antiretroviral resistance genotypes with response to therapy--comparison of three models

scientific article published on 01 September 2002

Automated phylogenetic detection of recombination using a genetic algorithm

scientific article published on 3 July 2006

BIOMEDICINE: Badgers and Bovine TB: Conflicts Between Conservation and Health

scientific article published in Science

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

scientific article published on 30 March 2008

Can non-lytic CD8+ T cells drive HIV-1 escape?

scientific article

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

scientific article published on June 1, 2011

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

scientific article (publication date: October 2010)

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

scientific article (publication date: 15 May 2005)

Detecting signatures of selection from DNA sequences using Datamonkey.

scientific article

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

scientific article

Eight challenges in phylodynamic inference.

scientific article

Epidemiological bridging by injection drug use drives an early HIV epidemic

scientific article published in September 2010

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

scientific article published on October 2008

Evaluation of respondent-driven sampling.

scientific article published on January 2012

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

scientific article published on 18 October 2011

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

scientific article published in June 2001

Evolution of envelope sequences of human immunodeficiency virus type 1 in cellular reservoirs in the setting of potent antiviral therapy.

scientific article

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

scientific article

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

scientific article published on 12 October 2006

Fast hierarchical Bayesian analysis of population structure

scientific article published on 01 June 2019

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

scientific article published on 29 May 2001

Genomic characterization of two novel HIV-1 second-generation recombinant forms among men who have sex with men in Beijing, China

scientific article

Germinal centre destruction as a major pathway of HIV pathogenesis

scientific article published in March 1994

Gillespie.jl: Stochastic Simulation Algorithm in Julia

scientific article published on 30 July 2016

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

article

HIV prevalence and demographic determinants of unprotected anal sex and HIV testing among men who have sex with men in Beirut, Lebanon

scientific article

HIV seroprevalence, self-reported STIs and associated risk factors among men who have sex with men: a cross-sectional study in Rwanda, 2015.

scientific article

HIV-1 Transmission Clustering and Phylodynamics Highlight the Important Role of Young Men Who Have Sex with Men

article

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

scientific article published on March 2008

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

scientific article published on 15 May 2003

HyPhy: hypothesis testing using phylogenies

scientific article (publication date: 27 October 2004)

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

scientific article published on 14 July 2008

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

scientific article

Individual and network factors associated with prevalent hepatitis C infection among rural Appalachian injection drug users

scientific article published on 15 November 2012

Inferring the source of transmission with phylogenetic data

scientific article (publication date: 2013)

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

scientific article published on 7 September 2006

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

scientific article published on 19 June 2007

Lymphocyte dynamics, apoptosis and HIV infection.

scientific article published on February 1996

Mapping antigenic variation in HIV-1 envelope.

scientific article published on 19 September 2013

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

scientific article

Modeling infectious disease dynamics in the complex landscape of global health

scientific article published on 13 March 2015

Modelling tree shape and structure in viral phylodynamics.

scientific article published on 04 February 2013

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

scientific article published on January 2009

Molecular evolution analysis of the human immunodeficiency virus type 1 envelope in simian/human immunodeficiency virus-infected macaques: implications for challenge dose selection.

scientific article published on 27 July 2011

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

scientific article (publication date: June 2014)

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

scientific article published on 19 March 2008

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

scientific article

Phylogenetic analysis of GBV-C/hepatitis G virus.

scientific article published in March 2000

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

scientific article

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

scientific article published in March 1994

Rapid social network assessment for predicting HIV and STI risk among men attending bars and clubs in San Diego, California.

scientific article published on 21 October 2010

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

scientific article published on October 2012

Respondent driven sampling: determinants of recruitment and a method to improve point estimation

scientific article

RhierBAPS: An R implementation of the population clustering algorithm hierBAPS

scientific article published on 30 July 2018

Sampling through time and phylodynamic inference with coalescent and birth-death models

scientific article

Six challenges in measuring contact networks for use in modelling.

scientific article

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

scientific article published on 18 June 2008

Stability of immunophenotypic lymphoid markers in fixed canine peripheral blood for flow cytometric analysis

scientific article published on 28 January 2014

The changing molecular epidemiology of HIV in the Philippines.

scientific article published on 05 June 2017

The role of venues in structuring HIV, sexually transmitted infections, and risk networks among men who have sex with men.

scientific article published on 7 February 2018

Transmitted drug resistance in the CFAR network of integrated clinical systems cohort: prevalence and effects on pre-therapy CD4 and viral load

scientific article

Understanding drivers of phylogenetic clustering in molecular epidemiological studies of HIV.

scientific article published on 13 October 2014

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

scientific article published on August 2007

Viral kinetics and hepatitis C.

scientific article published in December 2003

Viral phylodynamics and the search for an 'effective number of infections'.

scientific article

genieR: An R package for inference of demographic history of phylogenies

scientific article published on 05 January 2019

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