J. Herbeck

P. Drain, K. Freedberg, I. Bassett, 2018, The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease.

Combination HIV prevention and the battle of the sexes

C. Fraser, D. Pillay, P. Kellam, 2015 .

Oral abstracts of the 21st International AIDS Conference 18–22 July 2016, Durban, South Africa

Michael I. Jordan, Donald A. Jackson, J. G. Ndirangu, 2016, Journal of the International AIDS Society.

PANGEA-HIV: phylogenetics for generalised epidemics in Africa.

C. Fraser, D. Pillay, P. Kellam, 2015, Lancet. Infectious Diseases (Print).

Peer-mediated HIV assisted partner services to identify and link to care HIV-positive and HCV-positive people who inject drugs: a cohort study protocol

B. Chohan, J. Herbeck, T. de Oliveira, 2021, BMJ Open.

Evolution of HIV virulence in response to widespread scale up of antiretroviral therapy: a modeling study

G. Gottlieb, S. Goodreau, J. Mittler, 2016, bioRxiv.

Community viral load as an index of HIV transmission potential.

J. Herbeck, F. Tanser, 2016, The lancet. HIV.

Simultaneous quantitation of multiple contraceptive hormones in human serum by LC-MS/MS.

J. Baeten, R. Heffron, J. Herbeck, 2018, Contraception.

industrial and developing countries with the shared goal of ending the HIV/AIDS pandemic.

C. Fraser, D. Pillay, P. Kellam, 2015 .

Polymorphisms and HLA Allele Associations Founder Effects in the Assessment of HIV

D. Heckerman, T. Miura, B. Walker, 2008 .

CD39/Adenosine Pathway Is Involved in AIDS Progression

O. Delaneau, J. Mullins, H. Schuitemaker, 2011, PLoS pathogens.

Longitudinal Trends in the Prevalence of Detectable HIV Viremia: Population-Based Evidence From Rural KwaZulu-Natal, South Africa

T. Bärnighausen, D. Pillay, A. Phillips, 2018, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

Codon Usage Patterns in Cytochrome Oxidase I Across Multiple Insect Orders

John Novembre, Joshua T. Herbeck, J. Novembre, 2003, Journal of Molecular Evolution.

Polymorphisms of large effect explain the majority of the host genetic contribution to variation of HIV-1 virus load

D. Goldstein, J. Goedert, M. Carrington, 2015, Proceedings of the National Academy of Sciences.

Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly endosymbiont Wigglesworthia.

D. Wall, J. Herbeck, J. Wernegreen, 2003, Microbiology.

Converging on a general model of protein evolution.

Dennis P Wall, Joshua T Herbeck, D. Wall, 2005, Trends in biotechnology.

Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, Uganda

Ann M. Dennis, C. Fraser, J. Seeley, 2020, The lancet. HIV.

Association Study of Common Genetic Variants and HIV-1 Acquisition in 6,300 Infected Cases and 7,200 Controls

Paul J. McLaren, Jacques Fellay, David B. Goldstein, 2013, PLoS pathogens.

Is the virulence of HIV changing? A meta-analysis of trends in prognostic markers of HIV disease progression and transmission

G. Gottlieb, J. Mullins, H. Günthard, 2012, AIDS.

Multistage genomewide association study identifies a locus at 1q41 associated with rate of HIV-1 disease progression to clinical AIDS.

J. Goedert, J. Margolick, S. O’Brien, 2010, The Journal of infectious diseases.

Participation in methadone programs improves antiretroviral uptake and HIV viral suppression among people who inject drugs in Kenya.

B. Chohan, J. Herbeck, A. Monroe-Wise, 2021, Journal of substance abuse treatment.

Short Communication: Phylogenetic Evidence of HIV-1 Transmission Between Adult and Adolescent Men Who Have Sex with Men.

J. Herbeck, K. Thomas, Elizabeth R. Wolf, 2016, AIDS research and human retroviruses.

Human Immunodeficiency Virus Type 1 env Evolves toward Ancestral States upon Transmission to a New Host

D. Nickle, G. Gottlieb, G. Learn, 2006, Journal of Virology.

A Strong Case for Viral Genetic Factors in HIV Virulence

Joshua T. Herbeck, Christophe Fraser, C. Fraser, 2011, Viruses.

Viral evolution and escape during acute HIV-1 infection.

Todd M. Allen, James I Mullins, Todd M Allen, 2010, The Journal of infectious diseases.

Sexual role and HIV-1 set point viral load among men who have sex with men

J. Margolick, G. Gottlieb, S. Goodreau, 2018, Epidemics.

Demographic Processes Affect HIV-1 Evolution in Primary Infection before the Onset of Selective Processes

Joshua T. Herbeck, Wenjie Deng, Morgane Rolland, 2011, Journal of Virology.

RV144 vaccine imprinting constrained HIV-1 evolution following breakthrough infection

Jerome H. Kim, J. Mullins, Hongjun Bai, 2021, Virus evolution.

Lack of Evidence for Changing Virulence of HIV-1 in North America

J. Margolick, J. Phair, G. Gottlieb, 2008, PloS one.

HIV-1 infections with multiple founders are associated with higher viral loads than infections with single founders

Jerome H. Kim, J. Mullins, S. Self, 2015, Nature Medicine.

An HIV Epidemic Model Based on Viral Load Dynamics: Value in Assessing Empirical Trends in HIV Virulence and Community Viral Load

Joshua T. Herbeck, John E. Mittler, Geoffrey S. Gottlieb, 2014, PLoS Comput. Biol..

Evolution during primary HIV infection does not require adaptive immune selection

J. Schiffer, J. Herbeck, D. Reeves, 2020, Proceedings of the National Academy of Sciences.

Screening Low-Frequency SNPS From Genome-Wide Association Study Reveals a New Risk Allele for Progression to AIDS

O. Delaneau, J. Mullins, C. Winkler, 2011, Journal of acquired immune deficiency syndromes.

Prevalence and genetic diversity of HIV type 1 subtypes A and D in women attending antenatal clinics in Uganda.

J. Mullins, P. Kaleebu, J. Herbeck, 2007, AIDS research and human retroviruses.

Multiple-cohort genetic association study reveals CXCR6 as a new chemokine receptor involved in long-term nonprogression to AIDS.

O. Delaneau, J. Goedert, J. Phair, 2010, The Journal of infectious diseases.

A conservative test of genetic drift in the endosymbiotic bacterium Buchnera: slightly deleterious mutations in the chaperonin groEL.

D. J. Funk, J. Herbeck, P. Degnan, 2003, Genetics.

p21WAF1/CIP1 RNA Expression in Highly HIV-1 Exposed, Uninfected Individuals

J. Margolick, J. Mullins, R. Detels, 2015, PloS one.

UvA-DARE ( Digital Academic Repository ) CD 39 / Adenosine Pathway Is Involved in AIDS Progression

O. Delaneau, J. Mullins, H. Schuitemaker, 2011 .

Risk compensation after HIV-1 vaccination may accelerate viral adaptation and reduce cost-effectiveness: a modeling study

G. Gottlieb, S. Goodreau, J. Mittler, 2020, Scientific Reports.

Community and Provider Perspectives on Molecular HIV Surveillance and Cluster Detection and Response for HIV Prevention: Qualitative Findings From King County, Washington

R. Lechtenberg, S. Buskin, J. Herbeck, 2021, The Journal of the Association of Nurses in AIDS Care : JANAC.

Detection and Response to an HIV Cluster: People Living Homeless and Using Drugs in Seattle, Washington.

R. Lechtenberg, M. Golden, S. Buskin, 2021, American journal of preventive medicine.

A public health approach to monitoring HIV with resistance to HIV pre-exposure prophylaxis

R. Lechtenberg, M. Golden, S. Buskin, 2022, PloS one.

Fidelity of SNP Array Genotyping Using Epstein Barr Virus-Transformed B-Lymphocyte Cell Lines: Implications for Genome-Wide Association Studies

Joshua T. Herbeck, Geoffrey S. Gottlieb, Roger Detels, 2009, PloS one.

HIV transmission patterns among transgender women, their cisgender male partners, and cisgender MSM in Lima, Peru: A molecular epidemiologic and phylodynamic analysis

J. Mullins, S. Reisner, J. Herbeck, 2021, Lancet Regional Health. Americas.

Evidence of Local HIV Transmission in the African Community of King County, Washington

M. Golden, S. Buskin, J. Herbeck, 2017, Journal of Immigrant and Minority Health.

Molecular Epidemiology of Individuals Experiencing Unstable Housing or Living Homeless at HIV Diagnosis: Analysis of HIV Surveillance Data in King County, Washington

R. Lechtenberg, M. Golden, S. Buskin, 2022, AIDS and Behavior.

Test-and-treat coverage and HIV virulence evolution among men who have sex with men

G. Gottlieb, S. Goodreau, J. Mittler, 2021, Virus evolution.

Characteristics associated with HIV and hepatitis C seroprevalence among sexual and injecting partners of HIV positive persons who inject drugs in Nairobi and coastal Kenya

B. Chohan, J. Herbeck, A. Monroe-Wise, 2022, BMC Infectious Diseases.

Presenting Plasma HIV RNA Level and Rate of CD 4 T-Cell Decline To the

D. Nickle, G. Gottlieb, N. Kiviat, 2007 .

High percentage of undiagnosed HIV cases within a hyperendemic South African community: a population-based study

T. Bärnighausen, J. Herbeck, T. de Oliveira, 2017, Journal of Epidemiology & Community Health.

Why does age at HIV infection correlate with set point viral load? An evolutionary hypothesis

G. Gottlieb, S. Goodreau, J. Mittler, 2022, Epidemics.

Transmission of HIV-1 drug resistance mutations within partner-pairs: A cross-sectional study of a primary HIV infection cohort

Ingrid A. Beck, J. Mullins, J. Herbeck, 2018, PLoS medicine.

SARS-CoV-2 antibody prevalence, correlates, and access to harm reduction services among people who inject drugs living with and without HIV and their partners in Kenya

Khai Hoan Tram, B. Chohan, J. Herbeck, 2023, Harm Reduction Journal.

Presenting plasma HIV RNA level and rate of CD4 T-cell decline.

D. Nickle, G. Gottlieb, J. Mullins, 2007, Journal of the American Medical Association (JAMA).

Age and CD4+ T cell counts are inversely associated with HIV drug resistance mutations in treatment naive female sex workers

L. McKinnon, J. Kimani, J. Herbeck, 2023, Medicine.

Lessons learned from community engagement regarding phylodynamic research with molecular HIV surveillance data

J. Herbeck, R. Kerani, D. Tordoff, 2023, Journal of the International AIDS Society.

Large benefits to youth-focused HIV treatment-as-prevention efforts in generalized heterosexual populations: An agent-based simulation model

Steven M Goodreau, John E Mittler, James T Murphy, 2019, PLoS Comput. Biol..

Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis

Ann M. Dennis, C. Fraser, J. Seeley, 2019, Nature Communications.

Optimized phylogenetic clustering of HIV-1 sequence data for public health applications

M. Kalish, J. Herbeck, A. Poon, 2022, bioRxiv.

SARS-CoV-2 antibody prevalence, correlates, and access to harm reduction services among people who inject drugs living with and without HIV and their partners in Kenya

Khai Hoan Tram, B. Chohan, J. Herbeck, 2023, Harm Reduction Journal.

Multistage genomewide association study identifies a locus at 1q41 associated with rate of HIV-1 disease progression to clinical AIDS.

J. Goedert, J. Margolick, S. O’Brien, 2010, Journal of Infectious Diseases.

Polymorphisms of large effect explain the majority of the host genetic contribution to variation of HIV-1 virus load

D. Goldstein, J. Goedert, M. Carrington, 2015, Proceedings of the National Academy of Sciences.

Africa-specific human genetic variation near CHD1L associates with HIV-1 load

Andrew R. Bassett, J. Goedert, A. Trkola, 2023, Nature.

Alcohol use among people who inject drugs living with HIV in Kenya is associated with needle sharing, more new sex partners, and lower engagement in HIV care

B. Chohan, J. Herbeck, A. Monroe-Wise, 2023, AIDS and Behavior.

Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic

Ann M. Dennis, C. Fraser, P. Kaleebu, 2016, Scientific Reports.

HIV-1 over time: fitness loss or robustness gain?

D. Nickle, G. Gottlieb, J. Mullins, 2007, Nature Reviews Microbiology.

Combining traditional and molecular epidemiology methods to quantify local HIV transmission among foreign-born residents

R. Lechtenberg, M. Golden, S. Buskin, 2020, AIDS.

Prevalence and correlates of violence among sexual and injecting partners of people who inject drugs living with HIV in Kenya: a cross-sectional study

J. Herbeck, A. Monroe-Wise, C. Farquhar, 2023, Harm Reduction Journal.

Phylogenetic Studies of Transmission Dynamics in Generalized HIV Epidemics: An Essential Tool Where the Burden is Greatest?

Ann M. Dennis, C. Fraser, D. Pillay, 2014, Journal of acquired immune deficiency syndromes.

Genetic clusters and transmission in transgender women.

J. Herbeck, Tiago Gräf, 2019, The lancet. HIV.