Social and Genetic Networks of HIV-1 Transmission in New York City

The International Dimension of the U.S. HIV Transmission Network and Onward Transmission of HIV Recently Imported into the United States

(2016) Joel O. Wertheim et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

Near real-time monitoring of HIV transmission hotspots from routine HIV genotyping: an implementation case study

(2016) Art F Y Poon et al.   Lancet HIV

Molecular analysis allows inference into HIV transmission among young men who have sex with men in the United States

(2015) Y. Omar Whiteside et al.   AIDS

Using Molecular HIV Surveillance Data to Understand Transmission Between Subpopulations in the United States

(2015) Alexandra M. Oster et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES

Phylogenetic Studies of Transmission Dynamics in Generalized HIV Epidemics

(2014) Ann M. Dennis et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES

The Impact of Clinical, Demographic and Risk Factors on Rates of HIV Transmission: A Population-based Phylogenetic Analysis in British Columbia, Canada

(2014) Art F. Y. Poon et al.   JOURNAL OF INFECTIOUS DISEASES

Yersinia pestis and the Plague of Justinian 541–543 AD: a genomic analysis

(2014) David M Wagner et al.   LANCET INFECTIOUS DISEASES

Evolutionary Origins of Human Herpes Simplex Viruses 1 and 2

(2014) Joel O. Wertheim et al.   MOLECULAR BIOLOGY AND EVOLUTION

Timing and Order of Transmission Events Is Not Directly Reflected in a Pathogen Phylogeny

(2014) Ethan Romero-Severson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Using HIV Networks to Inform Real Time Prevention Interventions

(2014) Susan J. Little et al.   PLoS One

The early spread and epidemic ignition of HIV-1 in human populations

(2014) N. R. Faria et al.   SCIENCE

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

(2014) S. K. Gire et al.   SCIENCE

The Role of Viral Introductions in Sustaining Community-Based HIV Epidemics in Rural Uganda: Evidence from Spatial Clustering, Phylogenetics, and Egocentric Transmission Models

(2014) Mary K. Grabowski et al.   PLOS MEDICINE

Automated analysis of phylogenetic clusters

(2013) Manon Ragonnet-Cronin et al.   BMC BIOINFORMATICS

Social Network–Based Recruitment Successfully Reveals HIV-1 Transmission Networks Among High-Risk Individuals in El Salvador

(2013) Ann M. Dennis et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES

The Global Transmission Network of HIV-1

(2013) Joel O. Wertheim et al.   JOURNAL OF INFECTIOUS DISEASES

HIV-1 Clade B pol Evolution following Primary Infection

(2013) George K. Hightower et al.   PLoS One

Characterizing HIV Transmission Networks Across the United States

(2012) Jeannette L. Aldous et al.   CLINICAL INFECTIOUS DISEASES

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

(2012) Erik M. Volz et al.   PLoS Computational Biology

Transmission Network Parameters Estimated From HIV Sequences for a Nationwide Epidemic

(2011) Andrew J. Leigh Brown et al.   JOURNAL OF INFECTIOUS DISEASES

Purifying Selection Can Obscure the Ancient Age of Viral Lineages

(2011) Joel O. Wertheim et al.   MOLECULAR BIOLOGY AND EVOLUTION

Viral Linkage in HIV-1 Seroconverters and Their Partners in an HIV-1 Prevention Clinical Trial

(2011) Mary S. Campbell et al.   PLoS One

Transmission Patterns of HIV and Hepatitis C Virus among Networks of People Who Inject Drugs

(2011) Richard Pilon et al.   PLoS One

Using HIV Transmission Networks to Investigate Community Effects in HIV Prevention Trials

(2011) Joel O. Wertheim et al.   PLoS One

Determinants of HIV-1 transmission in men who have sex with men: a combined clinical, epidemiological and phylogenetic approach

(2010) Martin Fisher et al.   AIDS

Prevalence of transmitted drug resistance associated mutations and HIV-1 subtypes in new HIV-1 diagnoses, U.S.–2006

(2010) William H Wheeler et al.   AIDS

HIV Incidence Estimation Using the BED Capture Enzyme Immunoassay

(2010) Till Bärnighausen et al.   EPIDEMIOLOGY

Molecular Epidemiology Reveals Long‐Term Changes in HIV Type 1 Subtype B Transmission in Switzerland

(2010) Roger D. Kouyos et al.   JOURNAL OF INFECTIOUS DISEASES

Genome-Scale Phylogenetic Analyses of Chikungunya Virus Reveal Independent Emergences of Recent Epidemics and Various Evolutionary Rates

(2010) S. M. Volk et al.   JOURNAL OF VIROLOGY

Transmission networks of HIV-1 among men having sex with men in the Netherlands

(2009) Daniela Bezemer et al.   AIDS

Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic

(2009) Gavin J. D. Smith et al.   NATURE

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

(2009) Sergei L. Kosakovsky Pond et al.   PLoS Computational Biology

Molecular Phylodynamics of the Heterosexual HIV Epidemic in the United Kingdom

(2009) Gareth J. Hughes et al.   PLoS Pathogens

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

(2008) Davey M Smith et al.   AIDS

Estimation of HIV Incidence in the United States

(2008) H. Irene Hall   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960

(2008) Michael Worobey et al.   NATURE

Episodic Sexual Transmission of HIV Revealed by Molecular Phylodynamics

(2008) Fraser Lewis et al.   PLOS MEDICINE