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List of works by Joshua Herbeck

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

scientific article

A strong case for viral genetic factors in HIV virulence

scientific article

A transmission-virulence evolutionary trade-off explains attenuation of HIV-1 in Uganda

scientific article

An HIV epidemic model based on viral load dynamics: value in assessing empirical trends in HIV virulence and community viral load

scientific article

Association study of common genetic variants and HIV-1 acquisition in 6,300 infected cases and 7,200 controls

scientific article

CD39/adenosine pathway is involved in AIDS progression

scientific article

Characterization of Molecular Cluster Detection and Evaluation of Cluster Investigation Criteria Using Machine Learning Methods and Statewide Surveillance Data in Washington State

scientific article published on 26 January 2020

Codon usage patterns in cytochrome oxidase I across multiple insect orders

scientific article published in June 2003

Combining traditional and molecular epidemiology methods to quantify local HIV transmission among foreign-born residents of King County, Washington

scientific article published on 10 December 2020

Community viral load as an index of HIV transmission potential

scientific article

Converging on a general model of protein evolution

scientific article published on 01 October 2005

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

scientific article published on May 18, 2011

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

scientific article published on 9 July 2016

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

scientific article published in July 2016

Evolutionary patterns of codon usage in the chloroplast gene rbcL.

scientific article

Fidelity of SNP array genotyping using Epstein Barr virus-transformed B-lymphocyte cell lines: implications for genome-wide association studies

scientific article

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

scientific article published in Science

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

scientific article published in September 2003

Genetic Cluster Analysis for HIV Prevention.

scientific article published on 19 February 2018

Genetic clusters and transmission in transgender women

scientific article published on 11 February 2019

Genome-wide association study identifies single nucleotide polymorphism in DYRK1A associated with replication of HIV-1 in monocyte-derived macrophages

scientific article

HIV population-level adaptation can rapidly diminish the impact of a partially effective vaccine.

scientific article

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

scientific article

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

article

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

scientific article published on 24 November 2017

High-Sequence Diversity and Rapid Virus Turnover Contribute to Higher Rates of Coreceptor Switching in Treatment-Experienced Subjects with HIV-1 Viremia

scientific article published on 7 September 2016

Human immunodeficiency virus type 1 env evolves toward ancestral states upon transmission to a new host.

scientific article

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

scientific article

Lack of evidence for changing virulence of HIV-1 in North America.

scientific article

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

scientific article published on 17 December 2019

Longitudinal trends in the prevalence of detectable HIV viremia: Population-based evidence from rural KwaZulu-Natal, South Africa

scientific article published on 25 November 2017

Models to predict the public health impact of vaccine resistance: A systematic review

scientific article published on 12 July 2019

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

scientific article published on September 2010

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

scientific article

Nonhomogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the enterobacteriales (gamma-Proteobacteria)

scientific article published on 03 November 2004

P07-06. HIV-1 transmission and early evolution: whole genome analysis

article

PANGEA-HIV: phylogenetics for generalised epidemics in Africa

scientific article published on March 2015

Phylogenetic studies of transmission dynamics in generalized HIV epidemics: an essential tool where the burden is greatest?

scientific article

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

scientific article

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

scientific article published in February 2007

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

scientific article published on May 2007

Relational concurrency, stages of infection, and the evolution of HIV set point viral load

article

Screening low-frequency SNPS from genome-wide association study reveals a new risk allele for progression to AIDS

scientific article

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

scientific article

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

scientific article published on 20 October 2016

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

scientific article published on 30 January 2018

The changing virulence of HIV

scientific article published on 18 November 2014

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

scientific article

Urinary LAM grade, culture positivity, and mortality among HIV-infected South African out-patients

scientific article published in November 2018

Viral Evolution and Escape during Acute HIV‐1 Infection ⬇️

scientific article published on October 15, 2010

What Proportion of Hiv-Infected Foreign-Born Individuals in The U.S. Have Been Infected After Immigrating to The U.S.?

scientific article published on 15 November 2017

p21(WAF1/CIP1) RNA expression in highly HIV-1 exposed, uninfected individuals

scientific article

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