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Joshua Herbeck

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Buskin SE, Lechtenberg RJ, Slaughter FA, Herbeck JT, Kerani RP, Golden MR, Dombrowski JC. (2022). A public health approach to monitoring HIV with resistance to HIV pre-exposure prophylaxis. PloS one, 17(8)

Goodreau SM, Stansfield SE, Mittler JE, Murphy JT, Abernethy NF, Gottlieb GS, Reid MC, Burke JC, Pollock ED, Herbeck JT. (2022). Why does age at HIV infection correlate with set point viral load? An evolutionary hypothesis. Epidemics, (41)

Tordoff DM, Kerani RP, Glick SN, Hood J, Golden MR, Lechtenberg R, Buskin S, Herbeck JT. (2022). Molecular Epidemiology of Individuals Experiencing Unstable Housing or Living Homeless at HIV Diagnosis: Analysis of HIV Surveillance Data in King County, Washington. AIDS and behavior

Sambai BC, Kingston H, Monroe-Wise A, Mbogo L, Juma E, Ludwig-Barron N, Guthrie BL, Bukusi D, Chohan BH, Scott J, Bosire R, Dunbar M, Macharia P, Masyuko S, Sinkele W, Herbeck JT, Farquhar C. (2022). 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. BMC infectious diseases, 22(1)

Tseng AS, Sambai B, Monroe-Wise A, Mbogo LW, Ludwig-Barron NT, Masyuko SJ, Chohan BH, Scott JD, Sinkele W, Herbeck JT, Farquhar C, Guthrie BL. (2022). Assisted partner services for people who inject drugs: Index characteristics associated with untreated HIV in partners. Journal of acquired immune deficiency syndromes (1999)

Swan DA, Rolland M, Herbeck JT, Schiffer JT, Reeves DB. (2022). Evolution during primary HIV infection does not require adaptive immune selection. Proceedings of the National Academy of Sciences of the United States of America, 119(7)

Long JE, Tordoff DM, Reisner SL, Dasgupta S, Mayer KH, Mullins JI, Lama JR, Herbeck JT, Duerr A. (2022). HIV transmission patterns among transgender women, their cisgender male partners, and cisgender MSM in Lima, Peru: A molecular epidemiologic and phylodynamic analysis. Lancet Regional Health. Americas, (6)

Peebles K, Mittler JE, Goodreau SM, Murphy JT, Reid MC, Abernethy N, Gottlieb GS, Barnabas RV, Herbeck JT. (2021). Risk compensation after HIV-1 vaccination may accelerate viral adaptation and reduce cost-effectiveness: a modeling study. Scientific reports, 11(1)

Monroe-Wise A, Mbogo L, Guthrie B, Bukusi D, Sambai B, Chohan B, Scott J, Cherutich P, Musyoki H, Bosire R, Dunbar M, Macharia P, Masyuko S, Wilkinson E, De Oliveira T, Ludwig-Barron N, Sinkele B, Herbeck J, Farquhar C. (2021). 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. BMJ open, 11(4)

Buskin SE, Erly SJ, Glick SN, Lechtenberg RJ, Kerani RP, Herbeck JT, Dombrowski JC, Bennett AB, Slaughter FA, Barry MP, Neme S, Quinnan-Hostein L, Bryan A, Golden MR. (2021). Detection and Response to an HIV Cluster: People Living Homeless and Using Drugs in Seattle, Washington. American journal of preventive medicine, 61(5S1)

Lewitus E, Sanders-Buell E, Bose M, O'Sullivan AM, Poltavee K, Li Y, Bai H, Mdluli T, Donofrio G, Slike B, Zhao H, Wong K, Chen L, Miller S, Lee J, Ahani B, Lepore S, Muhammad S, Grande R, Tran U, Dussupt V, Mendez-Rivera L, Nitayaphan S, Kaewkungwal J, Pitisuttithum P, Rerks-Ngarm S, O'Connell RJ, Janes H, Gilbert PB, Gramzinski R, Vasan S, Robb ML, Michael NL, Krebs SJ, Herbeck JT, Edlefsen PT, Mullins JI, Kim JH, Tovanabutra S, Rolland M. (2021). RV144 vaccine imprinting constrained HIV-1 evolution following breakthrough infection. Virus evolution, 7(2)

Mbogo LW, Sambai B, Monroe-Wise A, Ludwig-Barron NT, Guthrie BL, Bukusi D, Chohan B, Macharia P, Dunbar M, Juma E, Sinkele W, Gitau E, Tseng AS, Bosire R, Masyuko S, Musyoki H, Temu TM, Herbeck J, Farquhar C. (2021). Participation in methadone programs improves antiretroviral uptake and HIV viral suppression among people who inject drugs in Kenya. Journal of substance abuse treatment

Stansfield SE, Herbeck JT, Gottlieb GS, Abernethy NF, Murphy JT, Mittler JE, Goodreau SM. (2021). Test-and-treat coverage and HIV virulence evolution among men who have sex with men. Virus evolution, 7(1)

Tordoff DM, Greninger AL, Roychoudhury P, Shrestha L, Xie H, Jerome KR, Breit N, Huang ML, Famulare M, Herbeck JT. (2021). Phylogenetic estimates of SARS-CoV-2 introductions into Washington State. Lancet Regional Health. Americas, (1)

Erly SJ, Herbeck JT, Kerani RP, Reuer JR. (2020). Characterization of Molecular Cluster Detection and Evaluation of Cluster Investigation Criteria Using Machine Learning Methods and Statewide Surveillance Data in Washington State. Viruses, 12(2)

Tordoff DM, Buskin S, Lechtenberg R, Golden MR, Kerani RP, Herbeck JT. (2020). Combining traditional and molecular epidemiology methods to quantify local HIV transmission among foreign-born residents of King County, Washington. AIDS (London, England)

Reid MC, Peebles K, Stansfield SE, Goodreau SM, Abernethy N, Gottlieb GS, Mittler JE, Herbeck JT. (2019). Models to predict the public health impact of vaccine resistance: A systematic review. Vaccine, 37(35)

Gräf T, Herbeck JT. (2019). Genetic clusters and transmission in transgender women. The lancet. HIV, 6(3)

Mittler JE, Murphy JT, Stansfield SE, Peebles K, Gottlieb GS, Abernethy NF, Reid MC, Goodreau SM, Herbeck JT. (2019). Large benefits to youth-focused HIV treatment-as-prevention efforts in generalized heterosexual populations: An agent-based simulation model. PLoS computational biology, 15(12)

Grabowski MK, Herbeck JT, Poon AFY. (2018). Genetic Cluster Analysis for HIV Prevention. Current HIV/AIDS reports, 15(2)

Stansfield SE, Mittler JE, Gottlieb GS, Murphy JT, Hamilton DT, Detels R, Wolinsky SM, Jacobson LP, Margolick JB, Rinaldo CR, Herbeck JT, Goodreau SM. (2019). Sexual role and HIV-1 set point viral load among men who have sex with men. Epidemics, (26)

Blue SW, Winchell AJ, Kaucher AV, Lieberman RA, Gilles CT, Pyra MN, Heffron R, Hou X, Coombs RW, Nanda K, Davis NL, Kourtis AP, Herbeck JT, Baeten JM, Lingappa JR, Erikson DW. (2018). Simultaneous quantitation of multiple contraceptive hormones in human serum by LC-MS/MS. Contraception, 97(4)

Stekler JD, Milne R, Payant R, Beck I, Herbeck J, Maust B, Deng W, Tapia K, Holte S, Maenza J, Stevens CE, Mullins JI, Collier AC, Frenkel LM. (2018). Transmission of HIV-1 drug resistance mutations within partner-pairs: A cross-sectional study of a primary HIV infection cohort. PLoS medicine, 15(3)

Goodreau SM, Stansfield SE, Murphy JT, Peebles KC, Gottlieb GS, Abernethy NF, Herbeck JT, Mittler JE. (2018). Relational concurrency, stages of infection, and the evolution of HIV set point viral load. Virus evolution, 4(2)

Vandormael A, de Oliveira T, Tanser F, Bärnighausen T, Herbeck JT. (2018). High percentage of undiagnosed HIV cases within a hyperendemic South African community: a population-based study. Journal of epidemiology and community health, 72(2)

Herbeck JT, Peebles K, Edlefsen PT, Rolland M, Murphy JT, Gottlieb GS, Abernethy N, Mullins JI, Mittler JE, Goodreau SM. (2018). HIV population-level adaptation can rapidly diminish the impact of a partially effective vaccine. Vaccine, 36(4)

Herbeck JT, Kerani RP, Poon AFY. (2018). What Proportion of HIV-Infected Foreign-Born Individuals in the United States Have Been Infected After Immigrating to the United States?. Journal of acquired immune deficiency syndromes (1999), 77(4)

Vandormael A, Bärnighausen T, Herbeck J, Tomita A, Phillips A, Pillay D, de Oliveira T, Tanser F. (2018). Longitudinal Trends in the Prevalence of Detectable HIV Viremia: Population-Based Evidence From Rural KwaZulu-Natal, South Africa. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 66(8)

Kerani RP, Herbeck JT, Buskin SE, Dombrowksi JC, Bennett A, Barash E, Barbee LA, Golden MR. (2017). Evidence of Local HIV Transmission in the African Community of King County, Washington. Journal of immigrant and minority health, 19(4)

Nedellec R, Herbeck JT, Hunt PW, Deeks SG, Mullins JI, Anton ED, Reeves JD, Mosier DE. (2017). High-Sequence Diversity and Rapid Virus Turnover Contribute to Higher Rates of Coreceptor Switching in Treatment-Experienced Subjects with HIV-1 Viremia. AIDS research and human retroviruses, 33(3)

Blanquart F, Grabowski MK, Herbeck J, Nalugoda F, Serwadda D, Eller MA, Robb ML, Gray R, Kigozi G, Laeyendecker O, Lythgoe KA, Nakigozi G, Quinn TC, Reynolds SJ, Wawer MJ, Fraser C. (2016). A transmission-virulence evolutionary trade-off explains attenuation of HIV-1 in Uganda. Elife, (5)

Wolf E, Herbeck JT, Van Rompaey S, Kitahata M, Thomas K, Pepper G, Frenkel L. (2017). Short Communication: Phylogenetic Evidence of HIV-1 Transmission Between Adult and Adolescent Men Who Have Sex with Men. AIDS research and human retroviruses, 33(4)

Herbeck JT, Mittler JE, Gottlieb GS, Goodreau SM, Murphy JT, Cori A, Pickles M, Fraser C. (2016). Evolution of HIV virulence in response to widespread scale up of antiretroviral therapy: a modeling study. Virus evolution, 2(2)

Herbeck J, Tanser F. (2016). Community viral load as an index of HIV transmission potential. The lancet. HIV, 3(4)

Herbeck J, Ghorai S, Chen L, Rinaldo CR, Margolick JB, Detels R, Jacobson L, Wolinsky S, Mullins JI. (2015). p21(WAF1/CIP1) RNA expression in highly HIV-1 exposed, uninfected individuals. PLoS One, 10(3)

Janes H, Herbeck JT, Tovanabutra S, Thomas R, Frahm N, Duerr A, Hural J, Corey L, Self SG, Buchbinder SP, McElrath MJ, O'Connell RJ, Paris RM, Rerks-Ngarm S, Nitayaphan S, Pitisuttihum P, Kaewkungwal J, Robb ML, Michael NL, Mullins JI, Kim JH, Gilbert PB, Rolland M. (2015). HIV-1 infections with multiple founders are associated with higher viral loads than infections with single founders. Nature medicine, 21(10)

Herbeck J, Celum C. (2014). The changing virulence of HIV. The lancet. HIV, 1(3)

Herbeck JT, Mittler JE, Gottlieb GS, Mullins JI. (2014). An HIV epidemic model based on viral load dynamics: value in assessing empirical trends in HIV virulence and community viral load. PLoS computational biology, 10(6)

Herbeck JT, Rolland M, Liu Y, McLaughlin S, McNevin J, Zhao H, Wong K, Stoddard JN, Raugi D, Sorensen S, Genowati I, Birditt B, McKay A, Diem K, Maust BS, Deng W, Collier AC, Stekler JD, McElrath MJ, Mullins JI. (2011). Demographic processes affect HIV-1 evolution in primary infection before the onset of selective processes. Journal of virology, 85(15)

Herbeck JT, Müller V, Maust BS, Ledergerber B, Torti C, Di Giambenedetto S, Gras L, Günthard HF, Jacobson LP, Mullins JI, Gottlieb GS. (2012). Is the virulence of HIV changing? A meta-analysis of trends in prognostic markers of HIV disease progression and transmission. AIDS (London, England), 26(2)

Müller V, Fraser C, Herbeck JT. (2011). A strong case for viral genetic factors in HIV virulence. Viruses, 3(3)

Herbeck JT, Gottlieb GS, Winkler CA, Nelson GW, An P, Maust BS, Wong KG, Troyer JL, Goedert JJ, Kessing BD, Detels R, Wolinsky SM, Martinson J, Buchbinder S, Kirk GD, Jacobson LP, Margolick JB, Kaslow RA, O'Brien SJ, Mullins JI. (2010). Multistage genomewide association study identifies a locus at 1q41 associated with rate of HIV-1 disease progression to clinical AIDS. The Journal of infectious diseases, 201(4)

Herbeck JT, Gottlieb GS, Wong K, Detels R, Phair JP, Rinaldo CR, Jacobson LP, Margolick JB, Mullins JI. (2009). Fidelity of SNP array genotyping using Epstein Barr virus-transformed B-lymphocyte cell lines: implications for genome-wide association studies. PLoS One, 4(9)

Herbeck JT, Gottlieb GS, Li X, Hu Z, Detels R, Phair J, Rinaldo C, Jacobson LP, Margolick JB, Mullins JI. (2008). Lack of evidence for changing virulence of HIV-1 in North America. PLoS One, 3(2)

Rolland M, Brander C, Nickle DC, Herbeck JT, Gottlieb GS, Campbell MS, Maust BS, Mullins JI. (2007). HIV-1 over time: fitness loss or robustness gain?. Nature reviews. Microbiology, 5(9)

Herbeck JT, Lyagoba F, Moore SW, Shindo N, Biryahwaho B, Kaleebu P, Mullins JI. (2007). Prevalence and genetic diversity of HIV type 1 subtypes A and D in women attending antenatal clinics in Uganda. AIDS research and human retroviruses, 23(5)

Herbeck JT, Nickle DC, Learn GH, Gottlieb GS, Curlin ME, Heath L, Mullins JI. (2006). Human immunodeficiency virus type 1 env evolves toward ancestral states upon transmission to a new host. Journal of virology, 80(4)

Herbeck JT, Wall DP. (2005). Converging on a general model of protein evolution. Trends in biotechnology, 23(10)

Herbeck JT, Degnan PH, Wernegreen JJ. (2005). Nonhomogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the enterobacteriales (gamma-Proteobacteria). Molecular biology and evolution, 22(3)

Herbeck JT, Wall DP, Wernegreen JJ. (2003). Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly endosymbiont Wigglesworthia. Microbiology (Reading, England), 149(Pt 9)

Wall DP, Herbeck JT. (2003). Evolutionary patterns of codon usage in the chloroplast gene rbcL. Journal of molecular evolution, 56(6)

Herbeck JT, Novembre J. (2003). Codon usage patterns in cytochrome oxidase I across multiple insect orders. Journal of molecular evolution, 56(6)

Herbeck JT, Funk DJ, Degnan PH, Wernegreen JJ. (2003). A conservative test of genetic drift in the endosymbiotic bacterium Buchnera: slightly deleterious mutations in the chaperonin groEL. Genetics, 165(4)

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