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Items: 1 to 50 of 52

1.
2.

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

Mittler JE, Murphy JT, Stansfield SE, Peebles K, Gottlieb GS, Abernethy NF, Reid MC, Goodreau SM, Herbeck JT.

PLoS Comput Biol. 2019 Dec 17;15(12):e1007561. doi: 10.1371/journal.pcbi.1007561. eCollection 2019 Dec.

3.

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

Reid MC, Peebles K, Stansfield SE, Goodreau SM, Abernethy N, Gottlieb GS, Mittler JE, Herbeck JT.

Vaccine. 2019 Aug 14;37(35):4886-4895. doi: 10.1016/j.vaccine.2019.07.013. Epub 2019 Jul 12. Review.

PMID:
31307874
4.

Genetic clusters and transmission in transgender women.

Gräf T, Herbeck JT.

Lancet HIV. 2019 Mar;6(3):e143-e144. doi: 10.1016/S2352-3018(18)30365-5. Epub 2019 Feb 11. No abstract available.

PMID:
30765314
5.

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

Goodreau SM, Stansfield SE, Murphy JT, Peebles KC, Gottlieb GS, Abernethy NF, Herbeck JT, Mittler JE.

Virus Evol. 2018 Nov 21;4(2):vey032. doi: 10.1093/ve/vey032. eCollection 2018 Jul.

6.

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

Kubiak RW, Herbeck JT, Coleman SM, Ross D, Freedberg K, Bassett IV, Drain PK.

Int J Tuberc Lung Dis. 2018 Nov 1;22(11):1366-1373. doi: 10.5588/ijtld.18.0099.

7.

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

Stansfield SE, Mittler JE, Gottlieb GS, Murphy JT, Hamilton DT, Detels R, Wolinsky SM, Jacobson LP, Margolick JB, Rinaldo CR, Herbeck JT, Goodreau SM.

Epidemics. 2019 Mar;26:68-76. doi: 10.1016/j.epidem.2018.08.006. Epub 2018 Aug 30.

8.

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

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.

PLoS Med. 2018 Mar 27;15(3):e1002537. doi: 10.1371/journal.pmed.1002537. eCollection 2018 Mar.

9.

Genetic Cluster Analysis for HIV Prevention.

Grabowski MK, Herbeck JT, Poon AFY.

Curr HIV/AIDS Rep. 2018 Apr;15(2):182-189. doi: 10.1007/s11904-018-0384-1. Review.

10.

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

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.

Contraception. 2018 Apr;97(4):363-369. doi: 10.1016/j.contraception.2018.01.015. Epub 2018 Jan 31.

11.

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

Herbeck JT, Peebles K, Edlefsen PT, Rolland M, Murphy JT, Gottlieb GS, Abernethy N, Mullins JI, Mittler JE, Goodreau SM.

Vaccine. 2018 Jan 25;36(4):514-520. doi: 10.1016/j.vaccine.2017.12.004. Epub 2017 Dec 11.

12.

What Proportion of HIV-Infected Foreign-Born Individuals in the United States Have Been Infected After Immigrating to the United States?

Herbeck JT, Kerani RP, Poon AFY.

J Acquir Immune Defic Syndr. 2018 Apr 1;77(4):e35-e36. doi: 10.1097/QAI.0000000000001594. No abstract available.

13.

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

Vandormael A, Bärnighausen T, Herbeck J, Tomita A, Phillips A, Pillay D, de Oliveira T, Tanser F.

Clin Infect Dis. 2018 Apr 3;66(8):1254-1260. doi: 10.1093/cid/cix976.

14.

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

Vandormael A, de Oliveira T, Tanser F, Bärnighausen T, Herbeck JT.

J Epidemiol Community Health. 2018 Feb;72(2):168-172. doi: 10.1136/jech-2017-209713. Epub 2017 Nov 24.

15.

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

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.

Elife. 2016 Nov 5;5. pii: e20492. doi: 10.7554/eLife.20492.

16.

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

Wolf E, Herbeck JT, Van Rompaey S, Kitahata M, Thomas K, Pepper G, Frenkel L.

AIDS Res Hum Retroviruses. 2017 Apr;33(4):318-322. doi: 10.1089/AID.2016.0061. Epub 2016 Nov 1.

17.

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

Herbeck JT, Mittler JE, Gottlieb GS, Goodreau SM, Murphy JT, Cori A, Pickles M, Fraser C.

Virus Evol. 2016 Oct 3;2(2):vew028. doi: 10.1093/ve/vew028. eCollection 2016 Jul.

18.

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

Nedellec R, Herbeck JT, Hunt PW, Deeks SG, Mullins JI, Anton ED, Reeves JD, Mosier DE.

AIDS Res Hum Retroviruses. 2017 Mar;33(3):234-245. doi: 10.1089/AID.2016.0153. Epub 2016 Oct 12.

19.

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

Kerani RP, Herbeck JT, Buskin SE, Dombrowksi JC, Bennett A, Barash E, Barbee LA, Golden MR.

J Immigr Minor Health. 2017 Aug;19(4):891-896. doi: 10.1007/s10903-016-0458-3.

20.

Community viral load as an index of HIV transmission potential.

Herbeck J, Tanser F.

Lancet HIV. 2016 Apr;3(4):e152-4. doi: 10.1016/S2352-3018(16)00036-9. Epub 2016 Mar 11. No abstract available.

PMID:
27036988
21.

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

McLaren PJ, Coulonges C, Bartha I, Lenz TL, Deutsch AJ, Bashirova A, Buchbinder S, Carrington MN, Cossarizza A, Dalmau J, De Luca A, Goedert JJ, Gurdasani D, Haas DW, Herbeck JT, Johnson EO, Kirk GD, Lambotte O, Luo M, Mallal S, van Manen D, Martinez-Picado J, Meyer L, Miro JM, Mullins JI, Obel N, Poli G, Sandhu MS, Schuitemaker H, Shea PR, Theodorou I, Walker BD, Weintrob AC, Winkler CA, Wolinsky SM, Raychaudhuri S, Goldstein DB, Telenti A, de Bakker PI, Zagury JF, Fellay J.

Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):14658-63. doi: 10.1073/pnas.1514867112. Epub 2015 Nov 9.

22.

The changing virulence of HIV.

Herbeck J, Celum C.

Lancet HIV. 2014 Dec;1(3):e99-e100. doi: 10.1016/S2352-3018(14)00004-6. Epub 2014 Nov 18. No abstract available.

PMID:
26424124
23.

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

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.

Nat Med. 2015 Oct;21(10):1139-41. doi: 10.1038/nm.3932. Epub 2015 Aug 31.

24.

PANGEA-HIV: phylogenetics for generalised epidemics in Africa.

Pillay D, Herbeck J, Cohen MS, de Oliveira T, Fraser C, Ratmann O, Brown AL, Kellam P; PANGEA-HIV Consortium.

Lancet Infect Dis. 2015 Mar;15(3):259-61. doi: 10.1016/S1473-3099(15)70036-8. No abstract available.

25.

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

Herbeck J, Ghorai S, Chen L, Rinaldo CR, Margolick JB, Detels R, Jacobson L, Wolinsky S, Mullins JI.

PLoS One. 2015 Mar 6;10(3):e0119218. doi: 10.1371/journal.pone.0119218. eCollection 2015.

26.

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

Dennis AM, Herbeck JT, Brown AL, Kellam P, de Oliveira T, Pillay D, Fraser C, Cohen MS.

J Acquir Immune Defic Syndr. 2014 Oct 1;67(2):181-95. doi: 10.1097/QAI.0000000000000271. Review.

27.

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

Herbeck JT, Mittler JE, Gottlieb GS, Mullins JI.

PLoS Comput Biol. 2014 Jun 19;10(6):e1003673. doi: 10.1371/journal.pcbi.1003673. eCollection 2014 Jun.

28.

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

McLaren PJ, Coulonges C, Ripke S, van den Berg L, Buchbinder S, Carrington M, Cossarizza A, Dalmau J, Deeks SG, Delaneau O, De Luca A, Goedert JJ, Haas D, Herbeck JT, Kathiresan S, Kirk GD, Lambotte O, Luo M, Mallal S, van Manen D, Martinez-Picado J, Meyer L, Miro JM, Mullins JI, Obel N, O'Brien SJ, Pereyra F, Plummer FA, Poli G, Qi Y, Rucart P, Sandhu MS, Shea PR, Schuitemaker H, Theodorou I, Vannberg F, Veldink J, Walker BD, Weintrob A, Winkler CA, Wolinsky S, Telenti A, Goldstein DB, de Bakker PI, Zagury JF, Fellay J.

PLoS Pathog. 2013;9(7):e1003515. doi: 10.1371/journal.ppat.1003515. Epub 2013 Jul 25.

29.

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

Herbeck JT, Müller V, Maust BS, Ledergerber B, Torti C, Di Giambenedetto S, Gras L, Günthard HF, Jacobson LP, Mullins JI, Gottlieb GS.

AIDS. 2012 Jan 14;26(2):193-205. doi: 10.1097/QAD.0b013e32834db418.

30.

A strong case for viral genetic factors in HIV virulence.

Müller V, Fraser C, Herbeck JT.

Viruses. 2011 Mar;3(3):204-16. doi: 10.3390/v3030204. Epub 2011 Mar 8.

31.

CD39/adenosine pathway is involved in AIDS progression.

Nikolova M, Carriere M, Jenabian MA, Limou S, Younas M, Kök A, Huë S, Seddiki N, Hulin A, Delaneau O, Schuitemaker H, Herbeck JT, Mullins JI, Muhtarova M, Bensussan A, Zagury JF, Lelievre JD, Lévy Y.

PLoS Pathog. 2011 Jul;7(7):e1002110. doi: 10.1371/journal.ppat.1002110. Epub 2011 Jul 7.

32.

Demographic processes affect HIV-1 evolution in primary infection before the onset of selective processes.

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.

J Virol. 2011 Aug;85(15):7523-34. doi: 10.1128/JVI.02697-10. Epub 2011 May 18.

33.

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

Bol SM, Moerland PD, Limou S, van Remmerden Y, Coulonges C, van Manen D, Herbeck JT, Fellay J, Sieberer M, Sietzema JG, van 't Slot R, Martinson J, Zagury JF, Schuitemaker H, van 't Wout AB.

PLoS One. 2011 Feb 25;6(2):e17190. doi: 10.1371/journal.pone.0017190.

34.

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

Le Clerc S, Coulonges C, Delaneau O, Van Manen D, Herbeck JT, Limou S, An P, Martinson JJ, Spadoni JL, Therwath A, Veldink JH, van den Berg LH, Taing L, Labib T, Mellak S, Montes M, Delfraissy JF, Schächter F, Winkler C, Froguel P, Mullins JI, Schuitemaker H, Zagury JF.

J Acquir Immune Defic Syndr. 2011 Mar 1;56(3):279-84. doi: 10.1097/QAI.0b013e318204982b.

35.

Viral evolution and escape during acute HIV-1 infection.

Boutwell CL, Rolland MM, Herbeck JT, Mullins JI, Allen TM.

J Infect Dis. 2010 Oct 15;202 Suppl 2:S309-14. doi: 10.1086/655653. Review.

36.

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

Limou S, Coulonges C, Herbeck JT, van Manen D, An P, Le Clerc S, Delaneau O, Diop G, Taing L, Montes M, van't Wout AB, Gottlieb GS, Therwath A, Rouzioux C, Delfraissy JF, Lelièvre JD, Lévy Y, Hercberg S, Dina C, Phair J, Donfield S, Goedert JJ, Buchbinder S, Estaquier J, Schächter F, Gut I, Froguel P, Mullins JI, Schuitemaker H, Winkler C, Zagury JF.

J Infect Dis. 2010 Sep 15;202(6):908-15. doi: 10.1086/655782.

37.

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

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.

J Infect Dis. 2010 Feb 15;201(4):618-26. doi: 10.1086/649842.

38.

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

Herbeck JT, Gottlieb GS, Wong K, Detels R, Phair JP, Rinaldo CR, Jacobson LP, Margolick JB, Mullins JI.

PLoS One. 2009 Sep 4;4(9):e6915. doi: 10.1371/journal.pone.0006915.

39.

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

Herbeck JT, Gottlieb GS, Li X, Hu Z, Detels R, Phair J, Rinaldo C, Jacobson LP, Margolick JB, Mullins JI.

PLoS One. 2008 Feb 6;3(2):e1525. doi: 10.1371/journal.pone.0001525.

40.

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

Rolland M, Brander C, Nickle DC, Herbeck JT, Gottlieb GS, Campbell MS, Maust BS, Mullins JI.

Nat Rev Microbiol. 2007 Sep;5(9):C1. No abstract available.

PMID:
17703224
41.

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

Herbeck JT, Lyagoba F, Moore SW, Shindo N, Biryahwaho B, Kaleebu P, Mullins JI.

AIDS Res Hum Retroviruses. 2007 May;23(5):755-60.

PMID:
17531003
42.

Founder effects in the assessment of HIV polymorphisms and HLA allele associations.

Bhattacharya T, Daniels M, Heckerman D, Foley B, Frahm N, Kadie C, Carlson J, Yusim K, McMahon B, Gaschen B, Mallal S, Mullins JI, Nickle DC, Herbeck J, Rousseau C, Learn GH, Miura T, Brander C, Walker B, Korber B.

Science. 2007 Mar 16;315(5818):1583-6.

43.

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

Gottlieb GS, Hawes SE, Nickle DC, Herbeck JT, Kiviat NB, Mullins JI, Sow PS.

JAMA. 2007 Feb 28;297(8):805; author reply 806-7. No abstract available.

PMID:
17327518
44.

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

Herbeck JT, Nickle DC, Learn GH, Gottlieb GS, Curlin ME, Heath L, Mullins JI.

J Virol. 2006 Feb;80(4):1637-44.

45.

Converging on a general model of protein evolution.

Herbeck JT, Wall DP.

Trends Biotechnol. 2005 Oct;23(10):485-7.

PMID:
16054255
46.

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

Herbeck JT, Degnan PH, Wernegreen JJ.

Mol Biol Evol. 2005 Mar;22(3):520-32. Epub 2004 Nov 3. Erratum in: Mol Biol Evol. 2005 Apr;22(4):1158.

PMID:
15525700
47.
48.

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

Herbeck JT, Wall DP, Wernegreen JJ.

Microbiology. 2003 Sep;149(Pt 9):2585-2596. doi: 10.1099/mic.0.26381-0.

PMID:
12949182
49.

Codon usage patterns in cytochrome oxidase I across multiple insect orders.

Herbeck JT, Novembre J.

J Mol Evol. 2003 Jun;56(6):691-701.

PMID:
12911032
50.

Evolutionary patterns of codon usage in the chloroplast gene rbcL.

Wall DP, Herbeck JT.

J Mol Evol. 2003 Jun;56(6):673-88; discussion 689-90.

PMID:
12911031

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