Publications

2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 and before

2023

Smith DM, Schafer JR, Tullius B, Witkam L, Paust S. Natural killer cells for antiviral therapy. Sci Transl Med. 2023 Jan 4;15(677):eabl5278. doi: 10.1126/scitranslmed.abl5278. Epub 2023 Jan 4. Review. PubMed PMID: 36599006.
Carlin AF, Clark AE, Chaillon A, Garretson AF, Bray W, Porrachia M, Santos AT, Rana TM, Smith DM. Virologic and Immunologic Characterization of Coronavirus Disease 2019 Recrudescence After Nirmatrelvir/Ritonavir Treatment. Clin Infect Dis. 2023 Feb 8;76(3):e530-e532. doi: 10.1093/cid/ciac496. PubMed PMID: 35723411; PubMed Central PMCID: PMC9278181.

2022

Davey M. Smith, Jolie R. Schafer, Brian Tullius, Laura Witkam, Silke Paust. NK cells for antiviral therapy. Sci Transl Med. In press. 2022.
Choudhary MC, Chew KW, Deo R, Flynn JP, Regan J, Crain CR, Moser C, Hughes MD, Ritz J, Ribeiro RM, Ke R, Dragavon JA, Javan AC, Nirula A, Klekotka P, Greninger AL, Fletcher CV, Daar ES, Wohl DA, Eron JJ, Currier JS, Parikh UM, Sieg SF, Perelson AS, Coombs RW, Smith DM, Li JZ. Emergence of SARS-CoV-2 escape mutations during Bamlanivimab therapy in a phase II randomized clinical trial. Nat Microbiol. 2022 Nov;7(11):1906-1917. doi: 10.1038/s41564-022-01254-1. Epub 2022 Oct 26. PubMed PMID: 36289399; PubMed Central PMCID: PMC9675946.
Riggs PK, Chaillon A, Jiang G, Letendre SL, Tang Y, Taylor J, Kaytes A, Smith DM, Dubé K, Gianella S. Lessons for Understanding Central Nervous System HIV Reservoirs from the Last Gift Program. Curr HIV/AIDS Rep. 2022 Oct 19:1–14. doi: 10.1007/s11904-022-00628-8. Epub ahead of print. PMID: 36260191; PMCID: PMC9580451.
Smith DM, Li JZ, Moser C, Yeh E, Currier JS, Chew KW, Hughes MD; ACTIV-2/A5401 Study Team. Recurrence of Symptoms Following a 2-Day Symptom Free Period in Patients With COVID-19. JAMA Netw Open. 2022 Oct 3;5(10):e2238867. doi: 10.1001/jamanetworkopen.2022.38867. PMID: 36301549; PMCID: PMC9614575.
Deo R, Choudhary MC, Moser C, Ritz J, Daar ES, Wohl DA, Greninger AL, Eron JJ, Currier JS, Hughes MD, Smith DM, Chew KW, Li JZ; ACTIV-2/A5401 Study Team. Viral and Symptom Rebound in Untreated COVID-19 Infection. medRxiv [Preprint]. 2022 Aug 2:2022.08.01.22278278. doi: 10.1101/2022.08.01.22278278. PMID: 35982660; PMCID: PMC9387151.
Mehta SR, Smith DM, Boukadida C, Chaillon A. Comparative Dynamics of Delta and Omicron SARS-CoV-2 Variants across and between California and Mexico. Viruses. 2022 Jul 8;14(7):1494. doi: 10.3390/v14071494. PMID: 35891473; PMCID: PMC9317407.
Boucau J, Chew KW, Choudhary M, Deo R, Regan J, Flynn JP, Crain CR, Hughes MD, Ritz J, Moser C, Dragavon JA, Javan AC, Nirula A, Klekotka P, Greninger AL, Coombs RW, Fischer WA 2nd, Daar ES, Wohl DA, Eron JJ, Currier JS, Smith DM, Li JZ, Barczak AK; ACTIV-2/A5401 Study Team. Monoclonal antibody treatment drives rapid culture conversion in SARS-CoV-2 infection. medRxiv [Preprint]. 2021 Dec 30:2021.12.25.21268211. Update in: Cell Rep Med. 2022 Jun 20;:100678. PMID: 35018382; PMCID: PMC8750705.
Shapiro AE, Bender Ignacio RA, Whitney BM, Delaney JA, Nance RM, Bamford L, Wooten D, Keruly JC, Burkholder G, Napravnik S, Mayer KH, Webel AR, Kim HN, Van Rompaey SE, Christopoulos K, Jacobson J, Karris M, Smith D, Johnson MO, Willig A, Eron JJ, Hunt P, Moore RD, Saag MS, Mathews WC, Crane HM, Cachay ER, Kitahata MM; CFAR Network of Integrated Clinical Systems. Factors Associated With Severity of COVID-19 Disease in a Multicenter Cohort of People With HIV in the United States, March-December 2020. J Acquir Immune Defic Syndr. 2022 Aug 1;90(4):369-376. doi: 10.1097/QAI.0000000000002989. PMID: 35364600.
Lessard D, Dubé K, Bilodeau M, Keeler P, Margolese S, Rosenes R, Sinyavskaya L, Durand M, Benko E, Kovacs C, Guerlotté C, Tharao W, Arnold K, Masching R, Taylor D, Sousa J, Ostrowski M, Taylor J, Kaytes A, Smith D, Gianella S, Chomont N, Angel JB, Routy JP, Cohen ÉA, Lebouché B, Costiniuk CT. Willingness of Older Canadians with HIV to Participate in HIV Cure Research Near and After the End of Life: A Mixed-Method Study. AIDS Res Hum Retroviruses. 2022 Aug;38(8):670-682. doi: 10.1089/AID.2022.0006. Epub 2022 Jul 28. PMID: 35778845.
Birabaharan M, Kaelber DC, Pettus JH, Smith DM. Risk of new-onset type 2 diabetes in 600 055 people after COVID-19: A cohort study. Diabetes Obes Metab. 2022 Jun;24(6):1176-1179. doi: 10.1111/dom.14659. Epub 2022 Feb 15. PMID: 35112782; PMCID: PMC9035030.
Kanazawa J, Rawlings SA, Hendrickx S, Gianella S, Concha-Garcia S, Taylor J, Kaytes A, Patel H, Ndukwe S, Little SJ, Smith D, Dubé K. Lessons learned from the Last Gift study: ethical and practical challenges faced while conducting HIV cure-related research at the end of life. J Med Ethics. 2022 Jun 22:medethics-2021-107512. Epub ahead of print. PMID: 35732421.
Ding X, Chaillon A, Pan X, Zhang J, Zhong P, He L, Chen W, Fan Q, Jiang J, Luo M, Xia Y, Guo Z, Smith DM. Characterizing genetic transmission networks among newly diagnosed HIV-1 infected individuals in eastern China: 2012-2016. PLoS One. 2022 Jun 16;17(6):e0269973. PMID: 35709166; PMCID: PMC9202869.
Carlin AF, Clark AE, Chaillon A, Garretson AF, Bray W, Porrachia M, Santos AT, Rana TM, Smith DM. Virologic and Immunologic Characterization of COVID-19 Recrudescence after Nirmatrelvir/Ritonavir Treatment. Clin Infect Dis. 2022 Jun 20:ciac496. doi: 10.1093/cid/ciac496. Epub ahead of print. PMID: 35723411; PMCID: PMC9278181.
He WT, Musharrafieh R, Song G, Dueker K, Tse LV, Martinez DR, Schäfer A, Callaghan S, Yong P, Beutler N, Torres JL, Volk RM, Zhou P, Yuan M, Liu H, Anzanello F, Capozzola T, Parren M, Garcia E, Rawlings SA, Smith DM, Wilson IA, Safonova Y, Ward AB, Rogers TF, Baric RS, Gralinski LE, Burton DR, Andrabi R. Targeted isolation of diverse human protective broadly neutralizing antibodies against SARS-like viruses. Nat Immunol. 2022 Jun;23(6):960-970. doi: 10.1038/s41590-022-01222-1. Epub 2022 Jun 2. PMID: 35654851.
Wang C, Schlub TE, Yu WH, Tan CS, Stefic K, Gianella S, Smith DM, Lauffenburger DA, Chaillon A, Julg B. Landscape of Human Immunodeficiency Virus Neutralization Susceptibilities Across Tissue Reservoirs. Clin Infect Dis. 2022 Oct 12;75(8):1342-1350. doi: 10.1093/cid/ciac164. PMID: 35234862.
Pusterla N, Chaillon A, Ignacio C, Smith DM, Barnum S, Lawton KOY, Smith G, Pickering B. SARS-CoV-2 Seroconversion in an Adult Horse with Direct Contact to a COVID-19 Individual. Viruses. 2022 May 14;14(5):1047. doi: 10.3390/v14051047. PMID: 35632788.
Carlin AF, Clark AE, Chaillon A, Garretson AF, Bray W, Porrachi M, Santos AT, Smith DM. Virologic and Immunologic Characterization of COVID-19 Recrudescence after Nirmatrelvir/Ritonavir Treatment. Res Sq [Preprint]. 2022 May 18:rs.3.rs-1662783. doi: 10.21203/rs.3.rs-1662783/v1. Update in: Clin Infect Dis. 2022 Jun 20;: PMID: 35611335; PMCID: PMC9128786.
Birabaharan M, Strunk A, Kaelber DC, Smith DM, Martin TCS. Sex differences in type 2 diabetes mellitus prevalence among persons with HIV. AIDS. 2022 Mar 1;36(3):383-389. doi: 10.1097/QAD.0000000000003127. PMID: 34750292; PMCID: PMC8795484.
Zhou P, Yuan M, Song G, Beutler N, Shaabani N, Huang D, He WT, Zhu X, Callaghan S, Yong P, Anzanello F, Peng L, Ricketts J, Parren M, Garcia E, Rawlings SA, Smith DM, Nemazee D, Teijaro JR, Rogers TF, Wilson IA, Burton DR, Andrabi R. A human antibody reveals a conserved site on beta-coronavirus spike proteins and confers protection against SARS-CoV-2 infection. Sci Transl Med. 2022 Mar 23;14(637):eabi9215. doi: 10.1126/scitranslmed.abi9215. Epub 2022 Mar 23. PMID: 35133175.
Yu ED, Wang E, Garrigan E, Goodwin B, Sutherland A, Tarke A, Chang J, Gálvez RI, Mateus J, Ramirez SI, Rawlings SA, Smith DM, Filaci G, Frazier A, Weiskopf D, Dan JM, Crotty S, Grifoni A, Sette A, da Silva Antunes R. Development of a T cell-based immunodiagnostic system to effectively distinguish SARS-CoV-2 infection and COVID-19 vaccination status. Cell Host Microbe. 2022;30(3):388-99.e3. Epub 20220208. doi: 10.1016/j.chom.2022.02.003. PubMed PMID: 35172129.

2021

He WT, Musharrafieh R, Song G, Dueker K, Tse LV, Martinez DR, Schäfer A, Callaghan S, Yong P, Beutler N, Torres JL, Volk RM, Zhou P, Yuan M, Liu H, Anzanello F, Capozzola T, Parren M, Garcia E, Rawlings SA, Smith DM, Wilson IA, Safonova Y, Ward AB, Rogers TF, Baric RS, Gralinski LE, Burton DR, Andrabi R. Targeted isolation of panels of diverse human protective broadly neutralizing antibodies against SARS-like viruses. bioRxiv [Preprint]. 2022 Feb 8:2021.09.08.459480. doi: 10.1101/2021.09.08.459480. Update in: Nat Immunol. 2022 Jun;23(6):960-970. PMID: 35169804.
Dubé K, Kanazawa J, Dee L, Taylor J, Sauceda JA, Gianella S, Smith D, Deeks SG, Peluso MJ. Considerations for designing and implementing combination HIV cure trials: findings from a qualitative in-depth interview study in the United States. AIDS Res Ther. 2021;18(1):75. Epub 20211018. PubMed PMID: 34663375.
Huff S, Kummetha IR, Tiwari SK, Huante MB, Clark AE, Wang S, Bray W, Smith D, Carlin AF, Endsley M, Rana TM. Discovery and Mechanism of SARS-CoV-2 Main Protease Inhibitors. J Med Chem. 2021. Epub 20210927. PubMed PMID: 34570513.
Kanazawa J, Gianella S, Concha-Garcia S, Taylor J, Kaytes A, Christensen C, Patel H, Ndukwe S, Rawlings S, Hendrickx S, Little S, Brown B, Smith D, Dubé K. Ethical and practical considerations for interventional HIV cure-related research at the end-of-life: A qualitative study with key stakeholders in the United States. PLoS One. 2021;16(7):e0254148. PubMed PMID: 34270612.
Rawlings SA, Chaillon A, Smith D, Gianella S. Scale up rapid research autopsies for tissue immunology. Nature. 2021;595(7867):352. PubMed PMID: 34257439.
Zhang T, Gupta A, Frederick D, Layman L, Smith DM, Gianella S, Kieffer C. 3D Visualization of Immune Cell Populations in HIV-Infected Tissues via Clearing, Immunostaining, Confocal, and Light Sheet Fluorescence Microscopy. J Vis Exp. 2021(171):e62441. PubMed PMID: 34028448.
Javadi SS, Mathur K, Concha-Garcia S, Patel H, Perry KE, Lo M, Taylor J, Kaytes A, Little S, Gianella S, Smith D, Dubé K. Attitudes and perceptions of next-of-kin/loved ones toward end-of-life HIV cure-related research: A qualitative focus group study in Southern California. PLoS One. 2021 May 7;16(5):e0250882. doi: 10.1371/journal.pone.0250882. PMID: PMCID: PMC8104928.
Tarke A, Sidney J, Methot N, Yu ED, Zhang Y, Dan JM, Goodwin B, Rubiro P, Sutherland A, Wang E, Frazier A, Ramirez SI, Rawlings SA, Smith DM, da Silva Antunes R, Peters B, Scheuermann RH, Weiskopf D, Crotty S, Grifoni A, Sette A. Impact of SARS-CoV-2 variants on the total CD4(+) and CD8(+) T cell reactivity in infected or vaccinated individuals. Cell Rep Med. 2021:100355. PubMed PMID: 34230917.
Rawlings SA, Scott B, Layman L, Naranatt P, Heltsley R, Ignacio C, Porrachia M, Gianella S, Smith D, Chaillon A. Can’t Work From Home: Pooled Nucleic Acid Testing of Laboratory Workers During the COVID-19 Pandemic. Open Forum Infect Dis. 2021;8(7):ofab129. doi: 10.1093/ofid/ofab129. PubMed PMID: 34327248.
Song G, He WT, Callaghan S, Anzanello F, Huang D, Ricketts J, Torres JL, Beutler N, Peng L, Vargas S, Cassell J, Parren M, Yang L, Ignacio C, Smith DM, Voss JE, Nemazee D, Ward AB, Rogers T, Burton DR, Andrabi R. Cross-reactive serum and memory B cell responses to spike protein in SARS-CoV-2 and endemic coronavirus infection. Nature. 2021 doi: 10.1101/2020.09.22.308965. PubMed PMID: 32995770.
Chaillon A, Smith DM. Phylogenetic analyses of SARS-CoV-2 B.1.1.7 lineage suggest a single origin followed by multiple exportation events versus convergent evolution. Clin Infect Dis. 2021. Epub 2021/03/28. doi: 10.1093/cid/ciab265. PubMed PMID: 33772259.
Gallardo CM, Wang S, Montiel-Garcia DJ, Little SJ, Smith DM, Routh AL, Torbett BE. MrHAMER yields highly accurate single molecule viral sequences enabling analysis of intra-host evolution. Nucleic Acids Res. 2021:2021.01.27.428469. Epub 2021/04/14. doi: 10.1093/nar/gkab231. PubMed PMID: 33849057.
Little SJ, Chen T, Wang R, Anderson C, Kosakovsky Pond S, Nakazawa M, Mathews WC, DeGruttola V, Smith DM. Effective HIV Molecular Surveillance Requires Identification of Incident Cases of Infection. Clin Infect Dis. 2021. Epub 2021/02/16. doi: 10.1093/cid/ciab140. PubMed PMID: 33588434.
Ajmera V, Thompson WK, Smith DM, Malhotra A, Mehta RL, Tolia V, Yin J, Sriram K, Insel PA, Collier S, Richards L, Loomba R. RAMIC: Design of a randomized, double-blind, placebo-controlled trial to evaluate the efficacy of ramipril in patients with COVID-19. Contemp Clin Trials. 2021;103:106330. Epub 2021/02/26. doi: 10.1016/j.cct.2021.106330. PubMed PMID: 33631357.
Tarke A, Sidney J, Kidd CK, Dan JM, Ramirez SI, Yu ED, Mateus J, da Silva Antunes R, Moore E, Rubiro P, Methot N, Phillips E, Mallal S, Frazier A, Rawlings SA, Greenbaum JA, Peters B, Smith DM, Crotty S, Weiskopf D, Grifoni A, Sette A. Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases. Cell Rep Med. 2021 Feb 16;2(2):100204. doi: 10.1016/j.xcrm.2021.100204. Epub 2021 Jan 26. PMID: 33521695.
Dan JM, Mateus J, Kato Y, Hastie KM, Yu ED, Faliti CE, Grifoni A, Ramirez SI, Haupt S, Frazier A, Nakao C, Rayaprolu V, Rawlings SA, Peters B, Krammer F, Simon V, Saphire EO, Smith DM, Weiskopf D, Sette A, Crotty S. Immunological memory to SARS-CoV-2 assessed for up to 8 months after infection. Science. 2021. Epub 2021/01/08. doi: 10.1126/science.abf4063. PubMed PMID: 33408181.
Moshiri N, Smith DM, Mirarab S. HIV Care Prioritization using Phylogenetic Branch Length. J Acquir Immune Defic Syndr. 2020;Publish Ahead of Print. Epub 2021/01/05. doi: 10.1097/qai.0000000000002612. PubMed PMID: 33394616.

2020

Perry KE, Taylor J, Patel H, Javadi SS, Mathur K, Kaytes A, Concha-Garcia S, Little S, Smith D, Gianella S, Dubé K. “[It] is now my responsibility to fulfill that wish:” Clinical and rapid autopsy staff members’ experiences and perceptions of HIV reservoir research at the end of life. PLoS One. 2020;15(11):e0242420. Epub 2020/11/19. doi: 10.1371/journal.pone.0242420. PubMed PMID: 33206710.
Jean Louis F, Domercant JW, Ignacio C, Gianella S, Galbaud G, Leonard M, Smith DM, Chaillon A. High Prevalence of HIV-1 Drug Resistance and Dynamics of Transmission Among High-Risk Populations in Port-au-Prince, Haiti. J Acquir Immune Defic Syndr. 2020;85(4):416-22. Epub 2020/11/03. doi: 10.1097/qai.0000000000002475. PubMed PMID: 33136738.
Saag MS, Gandhi RT, Hoy JF, Landovitz RJ, Thompson MA, Sax PE, Smith DM, Benson CA, Buchbinder SP, Del Rio C, Eron JJ, Jr., Fätkenheuer G, Günthard HF, Molina JM, Jacobsen DM, Volberding PA. Antiretroviral Drugs for Treatment and Prevention of HIV Infection in Adults: 2020 Recommendations of the International Antiviral Society-USA Panel. Jama. 2020;324(16):1651-69. Epub 2020/10/15. doi: 10.1001/jama.2020.17025. PubMed PMID: 33052386.
Rydyznski Moderbacher C, Ramirez SI, Dan JM, Grifoni A, Hastie KM, Weiskopf D, Belanger S, Abbott RK, Kim C, Choi J, Kato Y, Crotty EG, Kim C, Rawlings SA, Mateus J, Tse LPV, Frazier A, Baric R, Peters B, Greenbaum J, Ollmann Saphire E, Smith DM, Sette A, Crotty S. Antigen-Specific Adaptive Immunity to SARS-CoV-2 in Acute COVID-19 and Associations with Age and Disease Severity. Cell. 2020;183(4):996-1012.e19. Epub 2020/10/05. doi: 10.1016/j.cell.2020.09.038. PubMed PMID: 33010815.
Ayers JW, Althouse BM, Poliak A, Leas EC, Nobles AL, Dredze M, Smith D. Quantifying Public Interest in Police Reforms by Mining Internet Search Data Following George Floyd’s Death. J Med Internet Res. 2020;22(10):e22574. Epub 2020/10/22. doi: 10.2196/22574. PubMed PMID: 33084578.
Vrancken B, Mehta SR, Ávila-Ríos S, García-Morales C, Tapia-Trejo D, Reyes-Terán G, Navarro-Álvarez S, Little SJ, Hoenigl M, Pines HA, Patterson T, Strathdee SA, Smith DM, Dellicour S, Chaillon A. Dynamics and Dispersal of Local HIV Epidemics Within San Diego and Across The San Diego-Tijuana Border. Clin Infect Dis. 2020. Epub 2020/10/21. doi: 10.1093/cid/ciaa1588. PubMed PMID: 33079188.
Strathdee SA, Martin NK, Pitpitan EV, Stockman JK, Smith DM. What the HIV Pandemic Experience Can Teach the United States About the COVID-19 Response. J Acquir Immune Defic Syndr. 2021;86(1):1-10. Epub 2020/10/08. doi: 10.1097/qai.0000000000002520. PubMed PMID: 33027152.
Sahoo D, Katkar GD, Khandelwal S, Behroozikhah M, Claire A, Castillo V, Tindle C, Fuller M, Taheri S, Rogers TF, Beutler N, Ramirez SI, Rawlings SA, Pretorius V, Smith DM, Burton DR, Crotty Alexander LE, Duran J, Crotty S, Dan JM, Das S, Ghosh P. AI-guided discovery of the invariant host response to viral pandemics. bioRxiv. 2020. Epub 2020/10/01. doi: 10.1101/2020.09.21.305698. PubMed PMID: 32995790.
Wang S, Li W, Hui H, Tiwari SK, Zhang Q, Croker BA, Rawlings S, Smith D, Carlin AF, Rana TM. Cholesterol 25-Hydroxylase inhibits SARS-CoV-2 and coronaviruses by depleting membrane cholesterol. EMBO J. 2020:e2020106057. Epub 2020/09/19. doi:10.15252/embj.2020106057. PubMed PMID: 32944968.
Rawlings SA, Ignacio C, Porrachia M, Du P, Smith DM, Chaillon A. No Evidence of SARS-CoV-2 Seminal Shedding Despite SARS-CoV-2 Persistence in the Upper Respiratory Tract. Open Forum Infect Dis. 2020;7(8):ofaa325. Published 2020 Aug 7. doi:10.1093/ofid/ofaa325
Rogers T, Zhao F, Huang D, Beutler N, Burns A, He W, Limbo O, Smith C, Song G, Woehl J, Yang L, Abbott R, Callaghan S, Garcia E, Hurtado J, Parren M, Peng L, Ramirez S, Ricketts J, Ricciardi M, Rawlings S, Wu N, Yuan M, Smith D, Nemazee D, Teijaro J, Voss J, Wilson I, Andrabi R, Briney B, Landais E, Sok D, Jardine J, Burton D. Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model. 2020. Science Mag. doi: 10.1126/science.abc7520.
Burbelo P, Riedo F, Morishima C, Rawlings S, Smith D, Das S, Strich J, Chertow D, Davey Jr R, Cohen J. Sensitivity in Detection of Antibodies to Nucleocapsid and Spike Proteins of Severe Acute Respiratory Syndrome Coronavirus 2 in Patients With Coronavirus Disease. 2019. The Journal of Infectious Diseases. doi: 10.1093/infdis/jiaa273.
Grifoni A, Weiskopf D, Ramirez S, Mateus J, Dan J, Moderbacher C, Rawlings S, Sutherland A, Premkumar L, Jadi R, Marrama D, de Silva A, Frazier A, Carlin A, Greenbaum J, Peters B, Krammer F, Smith D, Crotty S, Sette A. Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals. Cell. 2020. doi: 10.1016/j.cell.2020.05.015.
Zai J, Liu H, Lu Z, Chaillon A, Smith D, Li Y, Li X. Tracing the transmission dynamics of HIV-1 CRF55_01B. Sci Rep. 2020;10(1):5098. Epub 2020/03/22. doi: 10.1038/s41598-020-61870-x. PubMed PMID: 32198405; PMCID: PMC7083841.
Martin TCS, Chaillon A, Graves SK, Lin T, Gianella S, Smith DM, Little SJ, Hoenigl M. Genetic Network Analysis to Assess the Risk of Human Immunodeficiency Virus Transmission Among Men Who Have Sex With Men Seeking Partners on the Internet. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2020;70(5):925-32. Epub 2019/04/07. doi: 10.1093/cid/ciz278. PubMed PMID: 30953067.

2019

Boobalan J, Dinesha TR, Gomathi S, Elakkiya E, Pradeep A, Chitra D, Murugavel KG, Balakrishnan P, Shantha S, Solomon SS, Kumarasamy N, Smith DM, Saravanan S. Pooled nucleic acid testing strategy for monitoring HIV-1 treatment in resource limited settings. J Clin Virol. 2019;117:56-60. Epub 2019/06/19. doi: 10.1016/j.jcv.2019.05.012. PubMed PMID: 31212189.
Wooten D, Smith D. Response to: Is Burnout Infectious? Understanding Drivers of Burnout and Job Satisfaction Among Academic Infectious Diseases Physicians. Open Forum Infect Dis. 2019;6(10):ofz378. Epub 2019/10/30. doi: 10.1093/ofid/ofz378. PubMed PMID: 31660342; PubMed Central PMCID: PMCPMC6786503.
Hoenigl M, Little SJ, Stockman JK, Skaathun B, Grelotti D, Weibel N, Smith DM. 1961. GrindrTM on Screen Activity on iPhones Correlates with HIV Risk and Substance Use in Men Who Have Sex with Men, San Diego. Open Forum Infectious Diseases. 2019;6(Supplement_2):S63-S4. doi: 10.1093/ofid/ofz359.138.
Gianella S, Moser C, Vitomirov A, McKhann A, Layman L, Scott B, Caballero G, Lada S, Bosch RJ, Hoenigl M, Lurain N, Landay A, Lederman MM, Hunt PW, Smith D. Presence of asymptomatic CMV and EBV DNA in blood of persons with HIV starting antiretroviral therapy are associated with non-AIDS clinical events. AIDS (London, England). 2020:10.1097/QAD.0000000000002484. Epub 2020/02/01. doi: 10.1097/QAD.0000000000002484. PubMed PMID: 32004204.
Hoenigl M, Little SJ, Grelotti D, Skaathun B, Wagner GA, Weibel N, Stockman JK, Smith DM. GrindrTM Users Take more Risks, but are more Open to HIV Pre-Exposure Prophylaxis: Could this Dating App Provide Platform for HIV Prevention Outreach? Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2019:ciz1093. Epub 2019/11/05. doi: 10.1093/cid/ciz1093. PubMed PMID: 31677383.
Chaillon A, Gianella S, Dellicour S, Rawlings SA, Schlub TE, Faria De Oliveira M, Ignacio C, Porrachia M, Vrancken B, Smith DM. HIV persists throughout deep tissues with repopulation from multiple anatomical sources. J Clin Invest. 2020:134815. Epub 2020/01/08. doi: 10.1172/JCI134815. PubMed PMID: 31910162.
Chaillon A, Hoenigl M, Freitas L, Feldman H, Tilghman W, Wang L, Smith D, Little S, Mehta SR. Optimizing Screening for HIV. Open Forum Infectious Diseases. 2020;7(2). doi: 10.1093/ofid/ofaa024.
Leas EC, Nobles AL, Caputi TL, Dredze M, Smith DM, Ayers JW. Trends in Internet Searches for Cannabidiol (CBD) in the United States. JAMA Netw Open. 2019;2(10):e1913853. Epub 2019/10/24. doi: 10.1001/jamanetworkopen.2019.13853. PubMed PMID: 31642924; PubMed Central PMCID: PMC6820034.
Chaillon A, Mehta SR, Hoenigl M, Solomon SS, Vickerman P, Hickman M, Skaathun B, Martin NK. Cost-effectiveness and budgetary impact of HCV treatment with direct-acting antivirals in India including the risk of reinfection. PLoS One. 2019;14(6):e0217964. Epub 2019/06/07. doi: 10.1371/journal.pone.0217964. PubMed PMID: 31170246; PubMed Central PMCID: PMC6553784.
Nobles AL, Leas EC, Althouse BM, Dredze M, Longhurst CA, Smith DM, Ayers JW. Requests for Diagnoses of Sexually Transmitted Diseases on a Social Media Platform. JAMA. 2019;322(17):1712-3. Epub 2019/11/07. doi: 10.1001/jama.2019.14390. PubMed PMID: 31688875; PubMed Central PMCID: PMC6865226.
Hani L, Chaillon A, Nere ML, Ruffin N, Alameddine J, Salmona M, Lopez Zaragoza JL, Smith DM, Schwartz O, Lelievre JD, Delaugerre C, Levy Y, Seddiki N. Proliferative memory SAMHD1low CD4+ T cells harbour high levels of HIV-1 with compartmentalized viral populations. PLoS pathogens. 2019;15(6):e1007868. Epub 2019/06/21. doi: 10.1371/journal.ppat.1007868. PubMed PMID: 31220191; PubMed Central PMCID: PMC6605680.
Chaillon A, Delaugerre C, Brenner B, Armero A, Capitant C, Nere ML, Leturque N, Pialoux G, Cua E, Tremblay C, Smith DM, Goujard C, Meyer L, Molina JM, Chaix ML. In-depth Sampling of High- risk Populations to Characterize HIV Transmission Epidemics Among Young MSM Using PrEP in France and Quebec. Open forum infectious diseases. 2019;6(3):ofz080. Epub 2019/03/23. doi: 10.1093/ofid/ofz080. PubMed PMID: 30899768; PubMed Central PMCID: PMC6422434.
LaMere SA, Chaillon A, Huynh C, Smith DM, Gianella S. Challenges in Quantifying Cytosine Methylation in the HIV Provirus. mBio. 2019;10(1). Epub 2019/01/24. doi: 10.1128/mBio.02268- 18. PubMed PMID: 30670613; PubMed Central PMCID: PMC6343035.
Smith D, Huynh C, Moore AJ, Frick A, Anderson C, Porrachia M, Scott B, Stous S, Schooley R, Little S, Santos AT. Herd Immunity Likely Protected the Men Who Have Sex With Men in the Recent Hepatitis A Outbreak in San Diego, California. Clinical infectious diseases: an official publication of the Infectious Diseases Society of America. 2019;68(7):1228-30. Epub 2018/07/28. doi: 10.1093/cid/ciy592. PubMed PMID: 30052941.
Chaillon A, Sun X, Cachay ER, Looney D, Wyles D, Garfein RS, Martin TCS, Jain S, Mehta SR, Smith DM, Little SJ, Martin NK. Primary Incidence of Hepatitis C Virus Infection Among HIV- Infected Men Who Have Sex With Men in San Diego, 2000-2015. Open forum infectious diseases. 2019;6(4):ofz160. Epub 2019/05/02. doi: 10.1093/ofid/ofz160. PubMed PMID: 31041355; PubMed Central PMCID: PMC6483132.
Beck S, Zhu Z, Oliveira MF, Smith DM, Rich JN, Bernatchez JA, Siqueira-Neto JL. Mechanism of Action of Methotrexate Against Zika Virus. Viruses. 2019;11(4). Epub 2019/04/13. doi: 10.3390/v11040338. PubMed PMID: 30974762; PubMed Central PMCID: PMC6521145.
Pines HA, Patrick R, Smith DM, Harvey-Vera A, Blumenthal JS, Rangel G, Semple SJ, Patterson TL. HIV Prevention Method Preferences Within Sexual Partnerships Reported by HIV-Negative MSM and TW in Tijuana, Mexico. AIDS and behavior. 2019. Epub 2019/04/05. doi: 10.1007/s10461-019-02492-x. PubMed PMID: 30945030.
de Almeida SM, Oliveira MF, Chaillon A, Rotta I, Ribeiro CE, de Pereira AP, Smith D, Letendre S, Ellis RJ. Transient and asymptomatic meningitis in human immunodeficiency virus-1 subtype C: a case study of genetic compartmentalization and biomarker dynamics. Journal of neurovirology. 2018;24(6):786-96. Epub 2018/09/09. doi: 10.1007/s13365-018-0672-y. PubMed PMID: 30194587; PubMed Central PMCID: PMC6279585.
Saag MS, Gunthard HF, Smith DM. Baseline Genotype Testing to Assess Drug Resistance Before Beginning HIV Treatment-Reply. Jama. 2018;320(20):2154. Epub 2018/11/28. doi: 10.1001/jama.2018.15946. PubMed PMID: 30480722; PubMed Central PMCID: PMC6415747.
Wertheim JO, Murrell B, Mehta SR, Forgione LA, Kosakovsky Pond SL, Smith DM, Torian LV. Growth of HIV-1 Molecular Transmission Clusters in New York City. The Journal of infectious diseases. 2018;218(12):1943-53. Epub 2018/07/17. doi: 10.1093/infdis/jiy431. PubMed PMID: 30010850; PMCID: PMC6217720.
Saag MS, Benson CA, Gandhi RT, Hoy JF, Landovitz RJ, Mugavero MJ, Sax PE, Smith DM, Thompson MA, Buchbinder SP, Del Rio C, Eron JJ, Jr., Fatkenheuer G, Gunthard HF, Molina JM, Jacobsen DM, Volberding PA. Antiretroviral Drugs for Treatment and Prevention of HIV Infection in Adults: 2018 Recommendations of the International Antiviral Society-USA Panel. JAMA. 2018;320(4):379-96. Epub 2018/07/26. doi: 10.1001/jama.2018.8431. PubMed PMID: 30043070.
Prakash K, Gianella S, Dubé K, Taylor J, Lee G, Smith DM. Willingness to participate in HIV research at the end of life (EOL). PLoS One. 2018 Jul 23; 13(7):e0199670. doi: 10.1371/journal.pone.0199670. PMID: 30036365. PMC6056048.
Christensen-Quick A, Chaillon A, Yek C, Zanini F, Jordan P, Ignacio C, Caballero G, Gianella S, Smith D. Influenza Vaccination Can Broadly Activate the HIV Reservoir During Antiretroviral Therapy. J Acquir Immune Defic Syndr. 2018 Nov 1; 79(3):e104-e107. doi: 10.1097/QAI.0000000000001829. PMID: 30085954. PMC6185804.
Namazi G, Fajnzylber JM, Aga E, Bosch RJ, Acosta EP, Sharaf R, Hartogensis W, Jacobson JM, Connick E, Volberding P, Skiest D, Margolis D, Sneller MC, Little SJ, Gianella S, Smith DM, Kuritzkes DR, Gulick RM, Mellors JW, Mehraj V, Gandhi RT, Mitsuyasu R, Schooley RT, Henry K, Tebas P, Deeks SG, Chun TW, Collier AC, Routy JP, Hecht FM, Walker BD, Li JZ. The Control of HIV After Antiretroviral Medication Pause (CHAMP) Study: Posttreatment Controllers Identified From 14 Clinical Studies. J Infect Dis. 2018 Nov 5; 218(12):1954-1963. doi: 10.1093/infdis/jiy479. PMID: 30085241. PMC6217727.
Dubé K, Gianella S, Concha-Garcia S, Little SJ, Kaytes A, Taylor J, Mathur K, Javadi S, Nathan A, Patel H, Luter S, Philpott-Jones S, Brown B, Smith D. Ethical considerations for HIV cure- related research at the end of life. BMC Med Ethics. 2018 Oct 20; 19(1):83. doi: 10.1186/s12910- 018-0321-2. PMID: 30342507; PMC6196016.
Carlin AF, Wen J, Vizcarra EA, McCauley M, Chaillon A, Akrami K, Kim C, Ngono AE, Lara- Marquez ML, Smith DM, Glass CK, Schooley RT, Benner C, Shresta S. A longitudinal systems immunologic investigation of acute Zika virus infection in an individual infected while traveling to Caracas, Venezuela. PLoS Negl Trop Dis. 2018 Dec 31; 12(12):e0007053. doi: 10.1371/journal.pntd.0007053. PMID: 30596671; PMC6329527.
Avila-Rios S, Garcia-Morales C, Valenzuela-Lara M, Chaillon A, Tapia-Trejo D, Perez-Garcia M, Lopez-Sanchez DM, Maza-Sanchez L, Del Arenal-Sanchez SJ, Paz-Juarez HE, Quiroz-Morales VS, Mehta SR, Smith DM, Leon-Juarez EA, Magis-Rodriguez C, Reyes-Teran G. HIV-1 drug resistance before initiation or re-initiation of first-line ART in eight regions of Mexico: a sub- nationally representative survey. The Journal of antimicrobial chemotherapy. 2019;74(4):1044-55. Epub 2019/01/01. doi: 10.1093/jac/dky512. PubMed PMID: 30597094.

2018

Lofano G, Gorman MJ, Yousif AS, Yu WH, Fox JM, Dugast AS, Ackerman ME, Suscovich TJ, Weiner J, Barouch D, Streeck H, Little S, Smith D, Richman D, Lauffenburger D, Walker BD, Diand MS, Alter G. Antigen-specific antibody Fc glycosylation enhances humoral immunity via the recruitment of complement. Science immunology. 2018;3(26). Epub 2018/08/19. doi: 10.1126/sciimmunol.aat7796. PubMed PMID: 30120121; PubMed Central PMCID: PMC6298214.
Sadanand S, Das J, Chung AW, Schoen MK, Lane S, Suscovich TJ, Streeck H, Smith DM, Little SJ, Lauffenburger DA, Richman DD, Alter G. Temporal variation in HIV-specific IgG subclass antibodies during acute infection differentiates spontaneous controllers from chronic progressors. AIDS. 2018 Feb 20;32(4):443-450. doi: 10.1097/QAD.0000000000001716. PMID: 29239894, PMC5983383.
Mehta SR, Chaillon A, Gaines TL, Gonzalez-Zuniga PE, Stockman JK, Almanza-Reyes H, Chavez JR, Vera A, Wagner KD, Patterson TL, Scott B, Smith DM, Strathdee SA. Impact of Public Safety Policies on Human Immunodeficiency Virus Transmission Dynamics in Tijuana, Mexico. Clin Infect Dis. 2018 Feb 10;66(5):758-764. doi: 10.1093/cid/cix884. PMID: 29045592, PMC5848227.
Gianella S, Sonya Haw J, Blumenthal J, Sullivan B, Smith D. The Importance of Human Immunodeficiency Virus Research for Transgender and Gender-Nonbinary Individuals. Clin Infect Dis. 2018 Apr 17;66(9):1460-1466. doi: 10.1093/cid/cix990. PMID: 29126186, PMC5905620.
Xu M, Moresco JJ, Chang M, Mukim A, Smith D, Diedrich JK, Yates JR 3rd, Jones KA. SHMT2 and the BRCC36/BRISC deubiquitinase regulate HIV-1 Tat K63-ubiquitylation and destruction by autophagy. PLoS Pathog. 2018 May 23;14(5):e1007071. doi: 10.1371/journal.ppat.1007071. PMID: 29791506.
Dinesha TR, Boobalan J, Sivamalar S, Solomon SS, Poongulali S, Pradeep A, Murugavel KG, Balakrishnan P, Smith DM, Saravanan S. HIV, Hepatitis B Virus, and Hepatitis C Virus Prevalence Among High-Risk Populations in South India. AIDS Res Hum Retroviruses. 2018 Apr; 34(4):327-328. doi: 10.1089/AID.2017.0253. PMID: 29161880, PMC5899286.
Dinesha TR, Boobalan J, Sivamalar S, Subashini D, Solomon SS, Murugavel KG, Balakrishnan P, Smith DM, Saravanan S. Occult HBV infection in HIV-infected adults and evaluation of pooled NAT for HBV. J Viral Hepat. 2018 Jun; 25(6):718-723. doi: 10.1111/jvh.12858. PMID: 29316078, PMC5980682

2017

Salas-Espinoza KJ, Menchaca-Diaz R, Patterson TL, Urada LA, Smith D, Strathdee SA, Pitpitan EV. HIV Prevalence and Risk Behaviors in Male to Female (MTF) Transgender Persons in Tijuana, Mexico. AIDS Behav. 2017 Dec; 21(12):3271-3278. doi: 10.1007/s10461-017-1931-2. PMID: 29032411 PMCID: PMC5736304.
Caputi TL, Smith D, Ayers JW. Suicide Risk Behaviors Among Sexual Minority Adolescents in the United States, 2015. JAMA. 2017 Dec 19;318(23):2349-2351. doi: 10.1001/jama.2017.16908. PMID: 29260214.
Chaillon A, Gianella S, Lada SM, Perez-Santiago J, Jordan P, Ignacio C, Karris M, Richman DD, Mehta SR, Little SJ, Wertheim JO, Smith DM. Size, Composition and Evolution of HIV DNA Populations during Early Antiretroviral Therapy and Intensification with Maraviroc. J Virol. 2018 Jan 17; 92(3). pii: e01589-17. doi: 10.1128/JVI.01589-17. PMID: 29142136 PMC5774877
Chaillon A, Sun X, Cachay ER, Looney D, Wyles DL, Garfein RL, Anderson CM, Martin TC, Jain S, Mehta SR, Smith DM, Little SJ, Martin NK. Increasing Primary Incidence of Hepatitis C Among HIV-Infected Men Who Have Sex with Men in San Diego; a Pooled Analysis of Two Large Clinics from 2000-2015. Hepatology, 66:72A-73A, 2017.
Schooley RT, Biswas B, Schooley RT, Biswas B, Gill JJ, Hernandez-Morales A, Lancaster J, Lessor L, Barr JJ, Reed SL, Rohwer F, Benler S, Segall AM, Taplitz R, Smith DM, Kerr K, Kumaraswamy M, Nizet V, Lin L, McCauley MD, Strathdee SA, Benson CA, Pope RK, Leroux BM, Picel AC, Mateczun AJ, Cilwa KE, Regeimbal JM, Estrella LA, Wolfe DM, Henry MS, Quinones J, Salka S, Bishop-Lilly KA, Young R, Hamilton T. Development and Use of Personalized Bacteriophage-Based Therapeutic Cocktails To Treat a Patient with a Disseminated Resistant Acinetobacter baumannii Infection. Antimicrob Agents Chemother. 2017 Sep 22;61(10). pii: e00954-17. doi: 10.1128/AAC.00954-17. PMID: 28807909 PMCID: PMC5610518. Errratum in Antimicrobial agents and chemotherapy. 2018;62(12). Epub 2018/11/28. doi: 10.1128/aac.02221- 18. PubMed PMID: 30478181; PubMed Central PMCID: PMC6256779.
Oom AL, Smith D, Akrami K. Identification of putative unique immunogenic ZIKV and DENV1-4 peptides for diagnostic cellular based tests. Sci Rep. 2017 Jul 24; 7(1):6218. doi: 10.1038/s41598-017-05980-z. PMID: 28740150; PMC5524841.
Chaillon A, Nakazawa M, Wertheim JO, Little SJ, Smith DM, Mehta SR, Gianella S. No Substantial Evidence for Sexual Transmission of Minority HIV Drug Resistance Mutations in Men Who Have Sex with Men. J Virol. 2017 Aug 9. pii: JVI.00769-17. doi: 10.1128/JVI.00769-17. PMID: 28794047. PMC5640831
Pérez-Santiago J, Ramirez-Gaona M, Holm-Kennedy R, Smith DM, Fierer J. Bacteremia and Skin Infections in Four Patients Caused by Helicobacter-Like Organisms. Open Forum Infect Dis. 2017;4(3):ofx074. Published 2017 Aug 3. doi:10.1093/ofid/ofx074. PMID: 31338379; PMCID: PMC6636245.
Pérez-Santiago J, Ramirez-Gaona M, Holm-Kennedy R, Smith DM, Fierer J. Bacteremia and Skin Infections in Four Patients Caused by Helicobacter-Like Organisms. Open Forum Infectious Diseases, Volume 4, Issue 3, 1 July 2017, ofx074, doi: 10.1093/ofid/ofx074.
de Almeida SM, Rotta I, Ribeiro CE, Oliveira MF, Chaillon A, de Pereira AP, Cunha AP, Zonta M, Bents JF, Raboni SM, Smith D, Letendre S, Ellis RJ. Dynamic of CSF and serum biomarkers in HIV-1 subtype C encephalitis with CNS genetic compartmentalization-case study. J Neurovirol. 2017 Jun; 23(3):460-473. doi: 10.1007/s13365-017-0518-z. PMID: 28247269; PMC5441962.
Landais E, Murrell B, Briney B, Murrell S, Rantalainen K, Berndsen ZT, Ramos A, Wickramasinghe L, Smith ML, Eren K, de Val N, Wu M, Cappelletti A, Umotoy J, Lie Y, Wrin T, Algate P, Chan-Hui PY, Karita E; IAVI Protocol C Investigators; IAVI African HIV Research Network, Ward AB, Wilson IA, Burton DR, Smith D, Pond SLK, Poignard P. HIV Envelope Glycoform Heterogeneity and Localized Diversity Govern the Initiation and Maturation of a V2 Apex Broadly Neutralizing Antibody Lineage. Immunity. 2017 Nov 21;47(5):990-1003.e9. doi: 10.1016/j.immuni.2017.11.002. PMID: 29166592; PMCID: PMC5736302.
Wertheim JO, Kosakovsky Pond SL, Forgione LA, Mehta SR, Murrell B, Shah S, Smith DM, Scheffler K, Torian LV. Social and Genetic Networks of HIV-1 Transmission in New York City. PLoS Pathog. 2017; 13(1):e1006000. doi: 10.1371/journal.ppat.1006000. PubMed PMID: 28068413; PMC5221827
Ahn MY, Wertheim JO, Kim WJ, Kim SW, Lee JS, Ann HW, Jeon Y, Ahn JY, Song JE, Oh DH, Kim YC, Kim EJ, Jung IY, Kim MH, Jeong W, Jeong SJ, Ku NS, Kim JM, Smith DM, Choi JY. Short Communication: HIV-1 Transmission Networks Across South Korea. AIDS Res Hum Retroviruses. 2017 Aug; 33(8):827-831. doi: 10.1089/aid.2016.0212. PMID: 28346838; PMC5564048.
Choi JY, Pond SLK, Anderson CM, Richman DD, Smith DM. Molecular Features of the V1-V4 Coding Region of Sexually Transmitted Human Immunodeficiency Virus Type 1. J Infect Dis. 2017; 215(10):1506-13. doi: 10.1093/infdis/jix184. PMID: 28419276. PMCID in process.
Wagner GA, Landais E, Caballero G, Phung P, Kosakovsky Pond SL, Poignard P, Richman DD, Little SJ, Smith DM. Intrasubtype B HIV-1 Superinfection Correlates with Delayed Neutralizing Antibody Response. J Virol. 2017 Aug 10; 91(17). pii: e00475-17. doi: 10.1128/JVI.00475-17. PMID: 28615205; PMC5553187.
Chaillon A, Smith DM, Vanpouille C, Lisco A, Jordan P, Caballero G, Vargas M, Gianella S, Mehta SR. HIV Trafficking Between Blood and Semen During Early Untreated HIV Infection. J Acquir Immune Defic Syndr. 2017; 74(1):95-102. doi: 10.1097/QAI.0000000000001156. PMID: 27548440; PMC5140710.
Gianella S, Taylor J, Brown TR, Kaytes A, Achim CL, Moore DJ, Little SJ, Ellis RJ, Smith DM. Can research at the end of life be a useful tool to advance HIV cure? AIDS. 2017; 31(1):1-4. doi: 10.1097/QAD.0000000000001300. PMID: 27755112; PMCID: PMC5137789.
Green N, Hoenigl M, Chaillon A, Anderson CM, Kosakovsky Pond SL, Smith DM, Little SJ. Partner services in adults with acute and early HIV infection. AIDS. 2017; 31(2):287-93. doi: 10.1097/QAD.0000000000001308. PMID: 27831950; PMCID: PMC5177524.
Chaillon A, Essat A, Frange P, Smith DM, Delaugerre C, Barin F, Ghosn J, Pialoux G, Robineau O, Rouzioux C, Goujard C, Meyer L, Chaix ML, on behalf the APCS. Spatiotemporal dynamics of HIV-1 transmission in France (1999-2014) and impact of targeted prevention strategies. Retrovirology. 2017; 14(1):15. doi: 10.1186/s12977-017-0339-4. PubMed PMID: 28222757; PMCID: PMC5322782.
Vesa J, Chaillon A, Wagner GA, Anderson CM, Richman DD, Smith DM, Little SJ. Increased HIV- 1 superinfection risk in carriers of specific human leukocyte antigen alleles. AIDS. 2017 May 15; 31(8):1149-1158. doi: 10.1097/QAD.0000000000001445. PMID: 28244954; PMCID: PMC5559224.
Glinka ER, Smith DM, Johns ST. Now is the Time to Study the Timing of Influenza Vaccine. HIV Med, HIV Med. 2018 Mar; 19(3):e53. doi: 10.1111/hiv.12486. PMID: 28116796. (PMCID not applicable)
Oliveira MF, Chaillon A, Nakazawa M, Vargas M, Letendre SL, Strain MC, Ellis RJ, Morris S, Little SJ, Smith DM, Gianella S. Early Antiretroviral Therapy Is Associated with Lower HIV DNA Molecular Diversity and Lower Inflammation in Cerebrospinal Fluid but Does Not Prevent the Establishment of Compartmentalized HIV DNA Populations. PLoS Pathog. 2017 Jan 3; 13(1):e1006112. doi: 10.1371/journal.ppat.1006112. eCollection 2017 Jan. PMID: 28046096; PMCID: PMC5266327.
Morris SR, Zhao M, Smith DM, Vargas MV, Little SJ, Gianella S. Longitudinal Viral Dynamics in Semen During Early HIV Infection. Clin Infect Dis. 2017 Feb 15; 64(4):428-434. doi: 10.1093/cid/ciw784. PMID: 28174909; PMCID: PMC5849030.
Chen X, Ye M, Pang W, Smith DM, Zhang C, Zheng YT. First Appearance of HIV-1 CRF07_BC and CRF08_BC Outside China. AIDS Res Hum Retroviruses. 2017 Jan; 33(1):74-76. doi: 10.1089/AID.2016.0169. PMID: 27392826. (PMCID not applicable)
Hu Y, Wan Z, Zhou YH, Smith D, Zheng YT, Zhang C. Identification of Two New HIV-1 Circulating Recombinant Forms (CRF87_cpx and CRF88_BC) from Reported Unique Recombinant Forms in Asia. AIDS Res Hum Retroviruses. 2017 Apr; 33(4):353-358. doi: 10.1089/AID.2016.0252. PMID: 27762598; PMCID: PMC5372766.
Chen X, Ye M, Duo L, Pang W, Smith D, Zhang C, Zheng YT. First description of two new HIV-1 recombinant forms CRF82_cpx and CRF83_cpx among drug users in Northern Myanmar. Virulence. 2017 Jul 4; 8(5):497-503. doi: 10.1080/21505594.2016.1226722. PMID: 27574950; PMCID: PMC5538334.
Saravanan S, Kausalya B, Gomathi S, Sivamalar S, Pachamuthu B, Selvamuthu P, Pradeep A, Sunil S, Mothi SN, Smith DM, Kantor R. Etravirine and Rilpivirine Drug Resistance Among HIV-1 Subtype C Infected Children Failing Non-Nucleoside Reverse Transcriptase Inhibitor-Based Regimens in South India. AIDS Res Hum Retroviruses. 2017 Jun; 33(6):567-574. doi: 10.1089/AID.2016.0133. PubMed PMID: 27869478. PubMed Central PMCID: PMC5695734.
Carter C, Akrami K, Hall D, Smith D, Aronoff-Spencer E. Lyophilized visually readable loop- mediated isothermal reverse transcriptase nucleic acid amplification test for detection Ebola Zaire RNA. J Virol Methods. 2017 Jun;244:32-38. DOI: 10.1016/j.jviromet.2017.02.013. PMID: 28242293, PMCID: PMC5568651.

2016

Landais E, Murrell B, Briney B, de Val N, Murrell S, Laird M, Ramos A, Wickramasinghe L, Wrin T, Paul Algate P, Chan-Hui P-Y, Smith D, Wilson I, Ward A, Burton D, Kosakovsky-Pond S, Poignard P. Common Env Escape Drives the Maturation of V2-apex Targeting bnAbs in HIV-1 Infected Individuals. AIDS Res Human Retroviruses, 32:120-120, 2016.
Chaillon A, Martin NK, Martin TC, Wyles DL, Smith DM, Mehta SR, Ballard C, Colwell B, Torriani F, Hill L, Mathews C, Hicks C, Cachay ER. Elevated HCV reinfection incidence after successful treatment among HIV-infected men who have sex with men in San Diego. Hepatology, 64: 367A- 367A, 2016.
Zhao J, Chen L, Chaillon A, Zheng C, Cai W, Yang Z, Li G, Gan Y, Wang X, Hu Y, Zhong P, Zhang C, Smith DM. The dynamics of the HIV epidemic among men who have sex with men (MSM) from 2005 to 2012 in Shenzhen, China. Sci Rep. 2016 Jun 29; 6:28703. doi: 10.1038/srep28703. PMID: 27352965; PMCID: PMC4926087.
Pérez-Santiago J, Schrier RD, de Oliveira MF, Gianella S, Var SR, Day TR, Ramirez-Gaona M, Suben JD, Murrell B, Massanella M, Cherner M, Smith DM, Ellis RJ, Letendre SL, Mehta SR. Cell-free mitochondrial DNA in CSF is associated with early viral rebound, inflammation, and severity of neurocognitive deficits in HIV infection. J Neurovirol. 2016 Apr; 22(2):191-200. doi: 10.1007/s13365-015-0384-5. Epub 2015 Oct 1. PMID: 26428514; PMCID: PMC4862614.
Gianella S, Anderson CM, Var SR, Oliveira MF, Lada SM, Vargas MV, Massanella M, Little SJ, Richman DD, Strain MC, Pérez-Santiago J, Smith DM. Replication of Human Herpesviruses Is Associated with Higher HIV DNA Levels during Antiretroviral Therapy Started at Early Phases of HIV Infection. J Virol. 2016 Mar 28; 90(8):3944-52. doi: 10.1128/JVI.02638-15. PMID: 26842469; PMC4810527.
Ann HW, Jun S, Shin NY, Han S, Ahn JY, Ahn MY, Jeon YD, Jung IY, Kim MH, Jeong WY, Ku NS, Kim JM, Smith DM, Choi JY. Characteristics of Resting-State Functional Connectivity in HIV- Associated Neurocognitive Disorder. PLoS One. 2016 Apr 22; 11(4):e0153493. doi: 10.1371/journal.pone.0153493. eCollection 2016. PubMed PMID: 27104345; PubMed Central PMCID: PMC4841538.
Mehta SR, Murrell B, Anderson CM, Kosakovsky Pond SL, Wertheim JO, Young JA, Freitas L, Richman DD, Mathews WC, Scheffler K, Little SJ, Smith DM. Using HIV Sequence and Epidemiologic Data to Assess the Effect of Self-referral Testing for Acute HIV Infection on Incident Diagnoses in San Diego, California. Clin Infect Dis. 2016 Jul 1; 63(1):101-107. doi: 10.1093/cid/ciw161. PMID: 27174704; PMC4901863.
Wagner GA, Chaillon A, Liu S, Franklin DR Jr, Caballero G, Kosakovsky Pond SL, Vaida F, Heaton RK, Letendre SL, Grant I, Richman DD, Smith DM. HIV-associated neurocognitive disorder is associated with HIV-1 dual infection. AIDS. 2016 Nov 13; 30(17):2591-2597. DOI: 10.1097/QAD.0000000000001237. PMID: 27536983; PMC5083206.
Günthard HF, Saag MS, Benson CA, del Rio C, Eron JJ, Gallant JE, Hoy JF, Mugavero MJ, Sax PE, Thompson MA, Gandhi RT, Landovitz RJ, Smith DM, Jacobsen DM, Volberding PA. Antiretroviral Drugs for Treatment and Prevention of HIV Infection in Adults: 2016 Recommendations of the International Antiviral Society-USA Panel. JAMA. 2016 Jul 12; 316(2):191-210. doi: 10.1001/jama.2016.8900. PMID: 27404187; PMC5012643.
Karris MY, Umlauf A, Vaida F, Richman D, Little S, Smith D. A randomized controlled clinical trial on the impact of CCR5 blockade with maraviroc in early infection on T-cell dynamics. Medicine (Baltimore). 2016 Nov; 95(44):e5315. DOI: 10.1097/MD.0000000000005315. PMID: 27858912; PMC5591160.
de Almeida SM, Rotta I, Ribeiro CE, Smith D, Wang R, Judicello J, Potter M, Vaida F, Letendre S, Ellis RJ; HNRC Group. Blood-CSF barrier and compartmentalization of CNS cellular immune response in HIV infection. J Neuroimmunol. 2016 Dec 15; 301:41-48. doi: 10.1016/j.jneuroim.2016.10.009. PMID: 27836178; PMC5148696.
Hoenigl M, Pérez-Santiago J, Nakazawa M, de Oliveira MF, Zhang Y, Finkelman MA, Letendre S, Smith D, Gianella S. (1→3)-β-d-Glucan: A Biomarker for Microbial Translocation in Individuals with Acute or Early HIV Infection? Front Immunol. 2016 Oct 3; 7:404. DOI: 10.3389/fimmu.2016.00404. PMID: 27752257; PMC5046804.
Smith DM, Nakazawa M, Freeman ML, Anderson CM, Oliveira MF, Little SJ, Gianella S. Asymptomatic CMV Replication During Early Human Immunodeficiency Virus (HIV) Infection Is Associated With Lower CD4/CD8 Ratio During HIV Treatment. Clin Infect Dis. 2016 Dec 1; 63(11):1517-1524. Epub 2016 Sep 6. DOI: 10.1093/cid/ciw612. PMID: 27601222; PMC5106612.
Bharti AR, McCutchan A, Deutsch R, Smith DM, Ellis RJ, Cherner M, Woods SP, Heaton RK, Grant I, Letendre SL. Latent Toxoplasma Infection and Higher Toxoplasma gondii Immunoglobulin G Levels Are Associated With Worse Neurocognitive Functioning in HIV-Infected Adults. Clin Infect Dis. 2016 Dec 15; 63(12):1655-1660. Epub 2016 Oct 28. DOI: 10.1093/cid/ciw655. PMID: 27794019; PMC5146725.
Geiger R, Smith DM, Little SJ, Mehta SR. Validation of the GeneXpert® CT/NG Assay for use with Male Pharyngeal and Rectal Swabs. Austin J HIV AIDS Res. 2016; 3(1). pii: 1021. PMID: 27536736; PMC4985020.
Hoenigl M, Chaillon A, Mehta SR, Smith DM, Graff-Zivin J, Little SJ. Screening for acute HIV infection in community-based settings: Cost-effectiveness and impact on transmissions. J Infect. 2016 Nov; 73(5):476-484. doi: 10.1016/j.jinf.2016.07.019. PMID: 27521468; PMC5143169.
Gianella S, Kosakovsky Pond SL, Oliveira MF, Scheffler K, Strain MC, De la Torre A, Letendre S, Smith DM, Ellis RJ. Compartmentalized HIV rebound in the central nervous system after interruption of antiretroviral therapy. Virus Evol. 2016 Aug 3; 2(2):vew020. eCollection 2016 Jul. DOI: 10.1093/ve/vew020. PMID: 27774305; PMC5072458.
Laird Smith M, Murrell B, Eren K, Ignacio C, Landais E, Weaver S, Phung P, Ludka C, Hepler L, Caballero G, Pollner T, Guo Y, Richman D, Poignard P, Paxinos EE, Kosakovsky Pond SL, Smith DM. Rapid Sequencing of Complete env Genes from Primary HIV-1 Samples. Virus Evol. 2016;2(2):vew018. Epub 2016/07/08. doi: 10.1093/ve/vew018. PubMed PMID: 29492273; PubMed Central PMCID: PMC5822884.
de Almeida SM, Rotta I, Jiang Y, Li X, Raboni SM, Ribeiro CE, Smith D, Potter M, Vaida F, Letendre S, Ellis RJ; HNRC Group. Biomarkers of chemotaxis and inflammation in cerebrospinal fluid and serum in individuals with HIV-1 subtype C versus B. J Neurovirol. 2016 Dec; 22(6):715- 724. DOI: 10.1007/s13365-016-0437-4. PMID: 27400932; PMC5130607.
Yek C, Gianella S, Plana M, Castro P, Scheffler K, García F, Massanella M, Smith DM. Standard vaccines increase HIV-1 transcription during antiretroviral therapy. AIDS. 2016 Sep 24; 30(15):2289-98. doi: 10.1097/QAD.0000000000001201. PMID: 27427877; PMCID: PMC5559226.
Chaillon A, Hoenigl M, Mehta SR, Weibel N, Little SJ, Smith DM. A practical online tool to estimate antiretroviral coverage for HIV infected and susceptible populations needed to reduce local HIV epidemics. Sci Rep. 2016 Jun 24; 6:28707. doi: 10.1038/srep28707. PMID: 27337983; PMC4919622.
Chaillon A, Gianella S, Little SJ, Caballero G, Barin F, Kosakovsky Pond S, Richman DD, Smith DM, Mehta SR. Characterizing the multiplicity of HIV founder variants during sexual transmission among MSM. Virus Evol. 2016;2(1):vew012. Epub 2016/06/08. doi: 10.1093/ve/vew012. PubMed PMID: 30186625; PubMed Central PMCID: PMC6118227.
Dan JM, Massanella M, Smith DM, Spina CA, Schrier R, Daar ES, Dube MP, Morris SR, Gianella S. Brief Report: Effect of CMV and HIV Transcription on CD57 and PD-1 T-Cell Expression During Suppressive ART. J Acquir Immune Defic Syndr. 2016 Jun 1; 72(2):133-7. doi: 10.1097/QAI.0000000000000936. PMID: 26818740; PMC4868660.
Chin BS, Chaillon A, Mehta SR, Wertheim JO, Kim G, Shin HS, Smith DM. Molecular epidemiology identifies HIV transmission networks associated with younger age and heterosexual exposure among Korean individuals. J Med Virol. 2016 Oct; 88(10):1832-5. doi: 10.1002/jmv.24523. PMID: 26990771; PMC4969179.
Turner SS, Gianella S, Yip MJ, van Seggelen WO, Gillies RD, Foster AL, Barbati ZR, Smith DM, Fierer DS. Shedding of Hepatitis C Virus in Semen of Human Immunodeficiency Virus-Infected Men. Open Forum Infect Dis. 2016 Mar 11; 3(2):ofw057. doi: 10.1093/ofid/ofw057. PMID: 27186582; PMC4866572.
Hoenigl M, Green N, Camacho M, Gianella S, Mehta SR, Smith DM, Little SJ. Signs or Symptoms of Acute HIV Infection in a Cohort Undergoing Community-Based Screening. Emerg Infect Dis. 2016 Mar; 22(3):532-4. doi: 10.3201/eid2203.151607. PMID: 26890854; PMC4766914.
Panichsillapakit T, Patel D, Santangelo J, Richman DD, Little SJ, Smith DM. Colorectal Disorders in Acute Human Immunodeficiency Virus Infection: A Case Series. Open Forum Infect Dis. 2016 Jan 29; 3(1):ofw014. doi: 10.1093/ofid/ofw014. PMID: 26925432; PMC4766383.
Kamat R, Doyle KL, Iudicello JE, Morgan EE, Morris S, Smith DM, Little SJ, Grant I, Woods SP, Translational Methamphetamine ARCG. Neurobehavioral Disturbances During Acute and Early HIV Infection. Cognitive and behavioral neurology : official journal of the Society for Behavioral and Cognitive Neurology. 2016;29(1):1-10. Epub 2016/03/24. doi: 10.1097/WNN.0000000000000084. PubMed PMID: 27008244; PubMed Central PMCID: PMC4806542.
Glinka ER, Smith DM, Johns ST. Timing Matters – Influenza Vaccination to HIV-Infected Patients. HIV Med. 2016 Sep; 17(8):601-4. doi: 10.1111/hiv.12360. Epub 2016 Jan 26. PMID: 26810556; PMC4960000.
Var SR, Day TR, Vitomirov A, Smith DM, Soontornniyomkij V, Moore DJ, Achim CL, Mehta SR, Pérez-Santiago J. Mitochondrial injury and cognitive function in HIV infection and methamphetamine use. AIDS. 2016 Mar 27; 30(6):839-48. doi: 10.1097/QAD.0000000000001027. PMID: 26807965; PMC4785088.
Shi Y, Wang J, Wang Y, Wang A, Guo H, Wei F, Mehta SR, Espitia S, Smith DM, Liu L, Zhang Y, Chen D. A novel mutant 10Ala/Arg together with mutant 144Ser/Arg of hepatitis B virus X protein involved in hepatitis B virus-related hepatocarcinogenesis in HepG2 cell lines. Cancer Lett. 2016 Feb 28; 371(2):285-91. doi: 10.1016/j.canlet.2015.12.008. PMID: 26706415; PMC4934374.
Vanpouille C, Introini A, Morris SR, Margolis L, Daar ES, Dube MP, Little SJ, Smith DM, Lisco A, Gianella S. Distinct cytokine/chemokine network in semen and blood characterize different stages of HIV infection. AIDS. 2016 Jan; 30(2):193-201. doi: 10.1097/QAD.0000000000000964. PMID: 26558730; PMC4862605.
Hoenigl M, Chaillon A, Moore DJ, Morris SR, Smith DM, Little SJ. Clear Links Between Starting Methamphetamine and Increasing Sexual Risk Behavior: A Cohort Study Among Men Who Have Sex With Men. J Acquir Immune Defic Syndr. 2016 Apr 15; 71(5):551-7. doi: 10.1097/QAI.0000000000000888. PMID: 26536321; PMC4788567.
Choi JY, Chaillon A, Oh JO, Ahn JY, Ann HW, Jung IY, Ahn MY, Jeon YD, Ku NS, Smith DM, Kim JM. HIV migration between blood plasma and cellular subsets before and after HIV therapy. J Med Virol. 2016 Apr; 88(4):606-13. doi: 10.1002/jmv.24375. PMID: 26348372; PMC4731240.
Day TR, Smith DM, Heaton RK, Franklin D, Tilghman MW, Letendre S, Jin H, Wu Z, Shi C, Yu X, Pérez-Santiago J. Subtype associations with HIV-associated neurocognitive disorder in China. J Neurovirol. 2016 Apr; 22(2):246-50. doi: 10.1007/s13365-015-0377-4. PMID: 26306690; PMC4769127.
Panichsillapakit T, Smith DM, Wertheim JO, Richman DD, Little SJ, Mehta SR. Prevalence of Transmitted HIV Drug Resistance Among Recently Infected Persons in San Diego, CA 1996- 2013. J Acquir Immune Defic Syndr. 2016 Feb 1; 71(2):228-36. doi: 10.1097/QAI.0000000000000831. PMID: 26413846; PMC4712087.
Dillon SM, Lee EJ, Kotter CV, Austin GL, Gianella S, Siewe B, Smith DM, Landay AL, McManus MC, Robertson CE, Frank DN, McCarter MD, Wilson CC. Gut dendritic cell activation links an altered colonic microbiome to mucosal and systemic T-cell activation in untreated HIV-1 infection. Mucosal Immunol. 2016 Jan; 9(1):24-37. doi: 10.1038/mi.2015.33. PMID: 25921339; PMC4626441.

2015

Heaton RK, Franklin DR Jr, Deutsch R, Letendre S, Ellis RJ, Casaletto K, Marquine MJ, Woods SP, Vaida F, Atkinson JH, Marcotte TD, McCutchan JA, Collier AC, Marra CM, Clifford DB, Gelman BB, Sacktor N, Morgello S, Simpson DM, Abramson I, Gamst AC, Fennema-Notestine C, Smith DM, Grant I; CHARTER Group. Neurocognitive change in the era of HIV combination antiretroviral therapy: the longitudinal CHARTER study. Clin Infect Dis. 2015 Feb 1; 60(3):473-80. doi: 10.1093/cid/ciu862. PMID: 25362201; PMC4303775.
Smith MD, Wertheim JO, Weaver S, Murrell B, Scheffler K, Kosakovsky Pond SL. Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection. Mol Biol Evol. 2015 May; 32(5):1342-53. doi: 10.1093/molbev/msv022. PMID: 25697341; PMC4408413.
Smith DM. What Can We Learn From Measles? No New HIV Infections. Top Antivir Med. 2015 Aug-Sep;23(3):108-10. PMID: 26518393. (PMCID not applicable)
Massanella M, Gianella S, Schrier R, Dan JM, Pérez-Santiago J, Oliveira MF, Richman DD, Little SJ, Benson CA, Daar ES, Dube MP, Haubrich RH, Smith DM, Morris SR. Methamphetamine Use in HIV-infected Individuals Affects T-cell Function and Viral Outcome during Suppressive Antiretroviral Therapy. Sci Rep. 2015 Aug 24; 5:13179. doi: 10.1038/srep13179. PMID: 26299251; PMC4547398.
Rhee SY, Blanco JL, Jordan MR, Taylor J, Lemey P, Varghese V, Hamers RL, Bertagnolio S, Rinke de Wit TF, Aghokeng AF, Albert J, Avi R, Avila-Rios S, Bessong PO, Brooks JI, Boucher CA, Brumme ZL, Busch MP, Bussmann H, Chaix ML, Chin BS, D’Aquin TT, De Gascun CF, Derache A, Descamps D, Deshpande AK, Djoko CF, Eshleman SH, Fleury H, Frange P, Fujisaki S, Harrigan PR, Hattori J, Holguin A, Hunt GM, Ichimura H, Kaleebu P, Katzenstein D, Kiertiburanakul S, Kim JH, Kim SS, Li Y, Lutsar I, Morris L, Ndembi N, Ng KP, Paranjape RS, Peeters M, Poljak M, Price MA, Ragonnet-Cronin ML, Reyes-Terán G, Rolland M, Sirivichayakul S, Smith DM, Soares MA, Soriano VV, Ssemwanga D, Stanojevic M, Stefani MA, Sugiura W, Sungkanuparph S, Tanuri A, Tee KK, Truong HM, van de Vijver DA, Vidal N, Yang C, Yang R, Yebra G, Ioannidis JP, Vandamme AM, Shafer RW. Geographic and temporal trends in the molecular epidemiology and genetic mechanisms of transmitted HIV-1 drug resistance: an individual-patient- and sequence-level meta-analysis. PLoS Med. 2015 Apr 7;12(4):e1001810. doi: 10.1371/journal.pmed.1001810. eCollection 2015 Apr. Erratum in: PLoS Med. 2015 Jun; 12(6):e1001845. PMID: 25849352; PMC4388826.
Wang X, Wu Y, Mao L, Xia W, Zhang W, Dai L, Mehta SR, Wertheim JO, Dong X, Zhang T, Wu H, Smith DM. Targeting HIV Prevention Based on Molecular Epidemiology Among Deeply Sampled Subnetworks of Men Who Have Sex With Men. Clin Infect Dis. 2015 Nov 1; 61(9):1462- 8. doi: 10.1093/cid/civ526. PMID: 26129754; PMC4599390.
Saravanan S, Gomathi S, Kausalya B, Boobalan J, Murugavel KG, Balakrishnan P, Mothi SN, Solomon SS, Kumarasamy N, Selvamuthu P, Solomon S, Smith DM. Differences in Evolution of HIV-1 Subtype C Reverse Transcriptase Between Children and Adults Likely Explained by Maturity of Cytotoxic T-Lymphocyte Responses. AIDS Res Hum Retroviruses. 2015 Jun; 31(6):655-7. doi: 10.1089/AID.2015.0023. PMID: 25839730; PMC4458742.
Mehta SR, Wertheim JO, Brouwer KC, Wagner KD, Chaillon A, Strathdee S, Patterson TL, Rangel MG, Vargas M, Murrell B, Garfein R, Little SJ, Smith DM. HIV Transmission Networks in the San Diego-Tijuana Border Region. EBioMedicine. 2015 Jul 18; 2(10):1456-63. doi: 10.1016/j.ebiom.2015.07.024. PMID: 26629540; PMC4634195.
de Oliveira MF, Murrell B, Pérez-Santiago J, Vargas M, Ellis RJ, Letendre S, Grant I, Smith DM, Woods SP, Gianella S. Circulating HIV DNA Correlates With Neurocognitive Impairment in Older HIV-infected Adults on Suppressive ART. Sci Rep. 2015 Nov 25; 5:17094. doi: 10.1038/srep17094. Erratum in: Sci Rep. 2016;6:19387. Murrel, Ben [corrected to Murrell, Ben]. PMID: 26603568; PMC4658529.
Tilghman M, Tsai D, Buene TP, Tomas M, Amade S, Gehlbach D, Chang S, Ignacio C, Caballero G, Espitia S, May S, Noormahomed EV, Smith DM. Pooled Nucleic Acid Testing to Detect Antiretroviral Treatment Failure in HIV-Infected Patients in Mozambique. J Acquir Immune Defic Syndr. 2015 Nov 1; 70(3):256-61. doi: 10.1097/QAI.0000000000000724. PMID: 26135327; PMC4607635.
Hoenigl M, Anderson CM, Green N, Mehta SR, Smith DM, Little SJ. Repeat HIV-testing is associated with an increase in behavioral risk among men who have sex with men: a cohort study. BMC Med. 2015 Sep 11; 13:218. doi: 10.1186/s12916-015-0458-5. PMID: 26444673; PMC4596465.
de Oliveira MF, Gianella S, Letendre S, Scheffler K, Kosakovsky Pond SL, Smith DM, Strain M, Ellis RJ. Comparative Analysis of Cell-Associated HIV DNA Levels in Cerebrospinal Fluid and Peripheral Blood by Droplet Digital PCR. PLoS One. 2015 Oct 2; 10(10):e0139510. doi: 10.1371/journal.pone.0139510. PMID: 26431315; PMC4592012.
Gianella S, Anderson CM, Richman DD, Smith DM, Little SJ. No evidence of posttreatment control after early initiation of antiretroviral therapy. AIDS. 2015 Oct 23; 29(16):2093-7. doi: 10.1097/QAD.0000000000000816. PMID: 26544575; PMC4638137.
Gianella S, Scheffler K, Mehta SR, Little SJ, Freitas L, Morris SR, Smith DM. Seminal shedding of CMV and HIV transmission among men who have sex with men. International journal of environmental research and public health. 2015; 12(7):7585-92. doi: 10.3390/ijerph120707585. PMID: 26198239; PMC4515676.
Gianella S, Smith DM, Daar ES, Dube MP, Lisco A, Vanpouille C, Margolis L, Haubrich RH, Morris SR. Genital Cytomegalovirus Replication Predicts Syphilis Acquisition among HIV-1 Infected Men Who Have Sex with Men. PLoS One. 2015 Jun 10; 10(6):e0130410. doi: 10.1371/journal.pone.0130410. PMID: 26061824; PMC4465639.
Chin BS, Shin HS, Kim G, Wagner GA, Gianella S, Smith DM. Short Communication: Increase of HIV-1 K103N Transmitted Drug Resistance and Its Association with Efavirenz Use in South Korea. AIDS Res Hum Retroviruses. 2015 Jun; 31(6):603-7. doi: 10.1089/AID.2014.0368. PMID: 25826122; PMC4516954.
Hoenigl M, Weibel N, Mehta SR, Anderson CM, Jenks J, Green N, Gianella S, Smith DM, Little SJ. Development and validation of the San Diego Early Test Score to predict acute and early HIV infection risk in men who have sex with men. Clin Infect Dis. 2015 Aug 1; 61(3):468-75. doi: 10.1093/cid/civ335. PMID: 25904374; PMC4542926.
Li JZ, Smith DM, Mellors JW. The need for treatment interruption studies and biomarker identification in the search for an HIV cure. AIDS. 2015 Jul 31; 29(12):1429-32. doi: 10.1097/QAD.0000000000000658. PMID: 25870989; PMC4529360.
Gianella S, Massanella M, Wertheim JO, Smith DM. The Sordid Affair Between Human Herpesvirus and HIV. J Infect Dis. 2015 Sep 15; 212(6):845-52. doi: 10.1093/infdis/jiv148. PMID: 25748324; PMC4548466.
Murrell B, Weaver S, Smith MD, Wertheim JO, Murrell S, Aylward A, Eren K, Pollner T, Martin DP, Smith DM, Scheffler K, Kosakovsky Pond SL. Gene-wide identification of episodic selection. Mol Biol Evol. 2015 May; 32(5):1365-71. doi: 10.1093/molbev/msv035. PMID: 25701167; PMC4408417.
Ene L, Duiculescu D, Tardei G, Ruta S, Smith DM, Mehta S, Letendre S, Achim CL. Hepatitis B virus compartmentalization in the cerebrospinal fluid of HIV-infected patients. Clin Microbiol Infect. 2015 Apr; 21(4):387.e5-8. doi: 10.1016/j.cmi.2014.11.012. PMID: 25658525; PMC4424164.
Heaton RK, Franklin DR, Jr., Deutsch R, Letendre SL, Ellis RJ, Casaletto K, Marquine MJ, Woods SP, Vaida F, Atkinson JH, Marcotte TD, McCutchan JA, Collier AC, Marra CM, Clifford DB, Gelman BB, Sacktor N, Morgello S, Simpson DM, Abramson I, Gamst A, Fennema-Notestine C, Smith DM, Grant I. Reply to Haddow et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2015;60(9):1442-3. Epub 2015/02/04. doi: 10.1093/cid/civ045. PubMed PMID: 25645217; PubMed Central PMCID: PMC4415055.
Okulicz JF, Le TD, Agan BK, Camargo JF, Landrum ML, Wright E, Dolan MJ, Ganesan A, Ferguson TM, Smith DM, Richman DD, Little SJ, Clark RA, He W, Ahuja SK. Influence of the timing of antiretroviral therapy on the potential for normalization of immune status in human immunodeficiency virus 1-infected individuals. JAMA Intern Med. 2015 Jan; 175(1):88-99. doi: 10.1001/jamainternmed.2014.4010. PMID: 25419650; PMC4286496.
Fisher RG, Smith DM, Murrell B, Slabbert R, Kirby BM, Edson C, Cotton MF, Haubrich RH, Kosakovsky Pond SL, Van Zyl GU. Next generation sequencing improves detection of drug resistance mutations in infants after PMTCT failure. J Clin Virol. 2015 Jan; 62:48-53. doi: 10.1016/j.jcv.2014.11.014. PMID: 25542470; PMC4279108.
Carter CC, Wagner GA, Hightower GK, Caballero G, Phung P, Richman DD, Pond SL, Smith DM. HIV-1 neutralizing antibody response and viral genetic diversity characterized with next generation sequencing. Virology. 2015 Jan 1; 474:34-40. doi: 10.1016/j.virol.2014.10.019. PMID: 25463602; PMC4259848.
Gianella S, Massanella M, Richman DD, Little SJ, Spina CA, Vargas MV, Lada SM, Daar ES, Dube MP, Haubrich RH, Morris SR, Smith DM; California Collaborative Treatment Group 592 Team. Cytomegalovirus replication in semen is associated with higher levels of proviral HIV DNA and CD4+ T cell activation during antiretroviral treatment. J Virol. 2014 Jul; 88(14):7818-27. doi: 10.1128/JVI.00831-14. PMID: 24789781; PMC4097769.
de Oliveira MF, Murrell B, Pérez-Santiago J, Vargas M, Ellis RJ, Letendre S, Grant I, Smith DM, Woods SP, Gianella S. Circulating HIV DNA Correlates With Neurocognitive Impairment in Older HIV-infected Adults on Suppressive ART. Sci Rep. 2015 Nov 25; 5:17094. doi: 10.1038/srep17094. Erratum in: Sci Rep. 2016; 6:19387. Murrel, Ben [corrected to Murrell, Ben]. PMID: 26603568; PMC4658529.

2014

Kim SB, Yoon M, Ku NS, Kim MH, Song JE, Ahn JY, Jeong SJ, Kim C, Kwon HD, Lee J, Smith DM, Choi JY. Mathematical modeling of HIV prevention measures including pre-exposure prophylaxis on HIV incidence in South Korea. PLoS One. 2014 Mar 24; 9(3):e90080. doi: 10.1371/journal.pone.0090080. PMID: 24662776; PMC3963840.
Ku NS, Lee Y, Ahn JY, Song JE, Kim MH, Kim SB, Jeong SJ, Hong KW, Kim E, Han SH, Song JY, Cheong HJ, Song YG, Kim WJ, Kim JM, Smith DM, Choi JY. HIV-associated neurocognitive disorder in HIV-infected Koreans: the Korean NeuroAIDS Project. HIV Med. 2014 Sep; 15(8):470- 7. doi: 10.1111/hiv.12137. PMID: 24580888; PMC4140963.
Desplats P, Dumaop W, Cronin P, Gianella S, Woods S, Letendre S, Smith D, Masliah E, Grant I. Epigenetic alterations in the brain associated with HIV-1 infection and methamphetamine dependence. PLoS One. 2014 Jul 23; 9(7):e102555. doi: 10.1371/journal.pone.0102555. PMID: 25054922; PMC4108358.
Ann HW, Jeon YD, Ahn JY, Ku NS, Kim JM, Shin N-Y, Smith DM, Choi JY, Jun S, Ahn M-Y, Han S, Jung IY. Clinical Usefulness of Brain Functional MRI for Diagnosing HIV-Associated Neurocognitive Disorder in HIV-Infected Patients. Open Forum Infectious Diseases. 2015;2(suppl_1). doi: 10.1093/ofid/ofv133.1215.
Orlov M, Vaida F, Williamson K, Deng Q, Smith DM, Duffy PE, Schooley RT. Antigen-presenting phagocytic cells ingest malaria parasites and increase HIV replication in a tumor necrosis factor α-dependent manner. J Infect Dis. 2014 Nov 15; 210(10):1562-72. doi: 10.1093/infdis/jiu317. PMID: 24903666; PMC4215075.
Chaillon A, Gianella S, Wertheim JO, Richman DD, Mehta SR, Smith DM. HIV migration between blood and cerebrospinal fluid or semen over time. J Infect Dis. 2014 May 15; 209(10):1642-52. doi: 10.1093/infdis/jit678. PMID: 24302756; PMC3997580.
Tilghman MW, Pérez-Santiago J, Osorio G, Little SJ, Richman DD, Mathews WC, Haubrich RH, Smith DM. Community HIV-1 drug resistance is associated with transmitted drug resistance. HIV Med. 2014 Jul; 15(6):339-46. doi: 10.1111/hiv.12122. PMID: 24417811; PMC4055747.
Grant I, Franklin DR Jr, Deutsch R, Woods SP, Vaida F, Ellis RJ, Letendre SL, Marcotte TD, Atkinson JH, Collier AC, Marra CM, Clifford DB, Gelman BB, McArthur JC, Morgello S, Simpson DM, McCutchan JA, Abramson I, Gamst A, Fennema-Notestine C, Smith DM, Heaton RK; CHARTER Group.. Asymptomatic HIV-associated neurocognitive impairment increases risk for symptomatic decline. Neurology. 2014 Jun 10; 82(23):2055-62. doi: 10.1212/WNL.0000000000000492. PMID: 24814848; PMC4118496.
Hepler NL, Scheffler K, Weaver S, Murrell B, Richman DD, Burton DR, Poignard P, Smith DM, Kosakovsky Pond SL. IDEPI: rapid prediction of HIV-1 antibody epitopes and other phenotypic features from sequence data using a flexible machine learning platform. PLoS Comput Biol. 2014 Sep 25; 10(9):e1003842. doi: 10.1371/journal.pcbi.1003842. PMID: 25254639; PMC4177671.
Rotta I, Raboni SM, Ribeiro CE, Riedel M, Winhescki Mda G, Smith DM, Ellis RJ, de Almeida SM. Cerebrospinal fluid can be used for HIV genotyping when it fails in blood. Arq Neuropsiquiatr. 2014 Jul; 72(7):506-9. DOI: 10.1590/0004-282×20140093. PMID: 25054982; PMC4139176.
King HL, Keller SB, Giancola MA, Rodriguez DA, Chau JJ, Young JA, Little SJ, Smith DM. Pre- exposure prophylaxis accessibility research and evaluation (PrEPARE Study). AIDS Behav. 2014 Sep; 18(9):1722-5. doi: 10.1007/s10461-014-0845-5. PMID: 25017425; PMC4127131.
Wertheim JO, Smith MD, Smith DM, Scheffler K, Kosakovsky Pond SL. Evolutionary origins of human herpes simplex viruses 1 and 2. Mol Biol Evol. 2014 Sep; 31(9):2356-64. doi: 10.1093/molbev/msu185. Epub 2014 Jun 10. PMID: 24916030; PMC4137711.
Little SJ, Kosakovsky Pond SL, Anderson CM, Young JA, Wertheim JO, Mehta SR, May S, Smith DM. Using HIV networks to inform real time prevention interventions. PLoS One. 2014 Jun 5; 9(6):e98443. doi: 10.1371/journal.pone.0098443. PMID: 24901437; PMC4047027.
Dillon SM, Lee EJ, Kotter CV, Austin GL, Dong Z, Hecht DK, Gianella S, Siewe B, Smith DM, Landay AL, Robertson CE, Frank DN, Wilson CC. An altered intestinal mucosal microbiome in HIV-1 infection is associated with mucosal and systemic immune activation and endotoxemia. Mucosal Immunol. 2014 Jul; 7(4):983-94. doi: 10.1038/mi.2013.116. PMID: 24399150; PMC4062575.
Kim SB, Kim HW, Kim HS, Ann HW, Kim JK, Choi H, Kim MH, Song JE, Ahn JY, Ku NS, Oh DH, Kim YC, Jeong SJ, Han SH, Kim JM, Smith DM, Choi JY. Pooled nucleic acid testing to identify antiretroviral treatment failure during HIV infection in Seoul, South Korea. Scand J Infect Dis. 2014 Feb; 46(2):136-40. doi: 10.3109/00365548.2013.851415. PMID: 24228824; PMC3894056.
Tilghman MW, Bhattacharya J, Deshpande S, Ghate M, Espitia S, Grant I, Marcotte TD, Smith D, Mehendale S. Genetic attributes of blood-derived subtype-C HIV-1 tat and env in India and neurocognitive function. J Med Virol. 2014 Jan; 86(1):88-96. doi: 10.1002/jmv.23816. PMID: 24150902; PMC3872113.
Saravanan S, Madhavan V, Velu V, Murugavel KG, Waldrop G, Solomon SS, Balakrishnan P, Kumarasamy N, Smith DM, Mayer KH, Solomon S, Thyagarajan SP. High prevalence of hepatitis delta virus among patients with chronic hepatitis B virus infection and HIV-1 in an intermediate hepatitis B virus endemic region. J Int Assoc Provid AIDS Care. 2014 Jan-Feb; 13(1):85-90. doi: 10.1177/2325957413488166. PMID: 23722085; PMC4114572.
Karris MY, Kao YT, Patel D, Dawson M, Woods SP, Vaida F, Spina C, Richman D, Little S, Smith DM. Predictors of virologic response in persons who start antiretroviral therapy during recent HIV infection. AIDS. 2014 Mar 27; 28(6):841-9. doi: 10.1097/QAD.0000000000000149. PMID: 24401640; PMC4049563.
Jeong SJ, Kim MH, Song JE, Ahn JY, Kim SB, Ann HW, Kim JK, Choi H, Ku NS, Han SH, Kim JM, Smith DM, Kim HS, Choi JY. Short communication: prospective comparison of qualitative versus quantitative polymerase chain reaction for monitoring virologic treatment failure in HIV- infected patients. AIDS Res Hum Retroviruses. 2014 Aug; 30(8):827-9. doi: 10.1089/AID.2013.0227. PMID: 24724838; PMC4118713.
Tatro ET, Purnajo I, Richman DD, Smith DM, Gianella S. Antibody response to Achromobacter xylosoxidans during HIV infection is associated with lower CD4 levels and increased lymphocyte activation. Clin Vaccine Immunol. 2014 Jan; 21(1):46-50. doi: 10.1128/CVI.00553-13. PMID: 24173027; PMC3910916.
Chaillon A, Gianella S, Vazquez H, Ignacio C, Zweig AC, Richman DD, Smith DM. Novel codon insert in HIV type 1 clade B reverse transcriptase associated with low-level viremia during antiretroviral therapy. AIDS Res Hum Retroviruses. 2014 Feb; 30(2):165-9. doi: 10.1089/AID.2013.0202. PMID: 24020934; PMC3910474.
Wertheim JO, Leigh Brown AJ, Hepler NL, Mehta SR, Richman DD, Smith DM, Kosakovsky Pond SL. The global transmission network of HIV-1. J Infect Dis. 2014 Jan 15; 209(2):304-13. doi: 10.1093/infdis/jit524. PMID: 24151309; PMC3873788.
Wagner GA, Pacold ME, Kosakovsky Pond SL, Caballero G, Chaillon A, Rudolph AE, Morris SR, Little SJ, Richman DD, Smith DM. Incidence and prevalence of intrasubtype HIV-1 dual infection in at-risk men in the United States. J Infect Dis. 2014 Apr 1; 209(7):1032-8. doi: 10.1093/infdis/jit633. Erratum in: J Infect Dis. 2014 Oct 1;210(7):1166. PMID: 24273040; PMC3952674.
Gianella S, Morris SR, Tatro E, Vargas MV, Haubrich RH, Daar ES, Dube MP, Richman DD, Little SJ, Smith DM. Virologic correlates of anti-CMV IgG levels in HIV-1-infected men. J Infect Dis. 2014 Feb 1; 209(3):452-6. doi: 10.1093/infdis/jit434. PMID: 23964106; PMC3883163.

2013

Weber E, Morgan EE, Iudicello JE, Blackstone K, Grant I, Ellis RJ, Letendre SL, Little S, Morris S, Smith DM, Moore DJ, Woods SP; TMARC Group. Substance use is a risk factor for neurocognitive deficits and neuropsychiatric distress in acute and early HIV infection. J Neurovirol. 2013 Feb; 19(1):65-74. doi: 10.1007/s13365-012-0141-y. PMID: 23250704; PMC3568179.
Morgan EE, Woods SP, Letendre SL, Franklin DR, Bloss C, Goate A, Heaton RK, Collier AC, Marra CM, Gelman BB, McArthur JC, Morgello S, Simpson DM, McCutchan JA, Ellis RJ, Abramson I, Gamst A, Fennema-Notestine C, Smith DM, Grant I, Vaida F, Clifford DB; CNS HIV Antiretroviral Therapy Effects Research (CHARTER) Group. Apolipoprotein E4 genotype does not increase risk of HIV-associated neurocognitive disorders. J Neurovirol. 2013 Apr; 19(2):150-6. doi: 10.1007/s13365-013-0152-3. PMID: 23408335; PMC3668779.
Tang MW, Rhee SY, Bertagnolio S, Ford N, Holmes S, Sigaloff KC, Hamers RL, de Wit TF, Fleury HJ, Kanki PJ, Ruxrungtham K, Hawkins CA, Wallis CL, Stevens W, van Zyl GU, Manosuthi W, Hosseinipour MC, Ngo-Giang-Huong N, Belec L, Peeters M, Aghokeng A, Bunupuradah T, Burda S, Cane P, Cappelli G, Charpentier C, Dagnra AY, Deshpande AK, El-Katib Z, Eshleman SH, Fokam J, Gody JC, Katzenstein D, Koyalta DD, Kumwenda JJ, Lallemant M, Lynen L, Marconi VC, Margot NA, Moussa S, Ndung’u T, Nyambi PN, Orrell C, Schapiro JM, Schuurman R, Sirivichayakul S, Smith D, Zolfo M, Jordan MR, Shafer RW. Nucleoside reverse transcriptase inhibitor resistance mutations associated with first-line stavudine-containing antiretroviral therapy: programmatic implications for countries phasing out stavudine. J Infect Dis. 2013 Jun 15; 207 Suppl 2:S70-7. doi: 10.1093/infdis/jit114. PMID: 23687292; PMC3657117.
Doyle KL, Morgan EE, Morris S, Smith DM, Little S, Iudicello JE, Blackstone K, Moore DJ, Grant I, Letendre SL, Woods SP; Translational Methamphetamine AIDS Research Center (TMARC) Group. Real-world impact of neurocognitive deficits in acute and early HIV infection. J Neurovirol. 2013 Dec; 19(6):565-73. doi: 10.1007/s13365-013-0218-2. PMID: 24277439; PMC3865175.
Perez-Santiago J, Gianella S, Massanella M, Spina CA, Karris MY, Var SR, Patel D, Jordan PS, Young JA, Little SJ, Richman DD, Smith DM. Gut Lactobacillales are associated with higher CD4 and less microbial translocation during HIV infection. AIDS. 2013; 27(12):1921-31. DOI: 10.1097/qad.0b013e3283611816. PMID: 24180001; PMC3816380.
Chaillon A, Wagner GA, Hepler NL, Little SJ, Kosakovsky Pond SL, Caballero G, Pacold ME, Phung P, Wrin T, Richman DD, Wertheim JO, Smith DM. Dynamics of viral evolution and neutralizing antibody response after HIV-1 superinfection. J Virol. 2013 Dec; 87(23):12737-44. doi: 10.1128/JVI.02260-13. PMID: 24049166; PMC3838120.
Desplats P, Dumaop W, Smith D, Adame A, Everall I, Letendre S, Ellis R, Cherner M, Grant I, Masliah E. Molecular and pathologic insights from latent HIV-1 infection in the human brain. Neurology. 2013 Apr 9; 80(15):1415-23. doi: 10.1212/WNL.0b013e31828c2e9e. PMID: 23486877; PMC3662272.
Noormahomed EV, Mocumbi AO, Preziosi M, Damasceno A, Bickler S, Smith DM, Funzamo C, Aronoff-Spencer E, Badaró R, Mabila F, Bila D, Nguenha A, Do Rosário V, Benson CA, Schooley RT, Patel S, Ferrão LJ, Carrilho C. Strengthening research capacity through the medical education partnership initiative: the Mozambique experience. Hum Resour Health. 2013 Dec 5; 11:62. doi: 10.1186/1478-4491-11-62. PMID: 24304706; PMC3895849.
de Almeida SM, Ribeiro CE, de Pereira AP, Badiee J, Cherner M, Smith D, Maich I, Raboni SM, Rotta I, Barbosa FJ, Heaton RK, Umlauf A, Ellis RJ. Neurocognitive impairment in HIV-1 clade C- versus B-infected individuals in Southern Brazil. J Neurovirol. 2013 Dec; 19(6):550-6. doi: 10.1007/s13365-013-0215-5. PMID: 24277437; PMC3923762.
Yuan L, Qiao L, Wei F, Yin J, Liu L, Ji Y, Smith D, Li N, Chen D. Cytokines in CSF correlate with HIV-associated neurocognitive disorders in the post-HAART era in China. J Neurovirol. 2013 Apr; 19(2):144-9. doi: 10.1007/s13365-013-0150-5. PMID: 23389619; PMC4363104.
Kim H, Ku NS, Kim SB, Jeong SJ, Han SH, Kim JM, Smith DM, Choi JY. Simulation of pooled nucleic acid treatment failure during HIV infection in Seoul, South Korea. J Acquir Immune Defic Syndr. 2013 Mar 1; 62(3):e104-5. doi: 10.1097/QAI.0b013e31827e8cc8. PMID: 23924640; PMC3873092.
Morris SR, Smith DM, Little SJ, Gianella S. Reply to Mounzer and DiNubile. J Infect Dis. 2013 Aug 15; 208(4):711-2. doi: 10.1093/infdis/jit218. PMID: 23667136; PMC3719903.
Wagner GA, Pacold ME, Vigil E, Caballero G, Morris SR, Pond SLK, Little SJ, Richman DD, Gianella S, Smith DM. Using ultradeep pyrosequencing to study HIV-1 coreceptor usage in primary and dual infection. Journal of Infectious Diseases. 2013; 208(2):271-4. DOI: 10.1093/infdis/jit168. PMID: 23599311; PMC3685231.
Morris SR, Woods SP, Deutsch R, Little SJ, Wagner G, Morgan EE, Heaton RK, Letendre SL, Grant I, Smith DM. Dual-mixed HIV-1 coreceptor tropism and HIV-associated neurocognitive deficits. J Neurovirol. 2013 Oct; 19(5):488-94. DOI: 10.1007/s13365-013-0203-9. PMID: 24078557; PMC3921071.
Hightower GK, May SJ, Pérez-Santiago J, Pacold ME, Wagner GA, Little SJ, Richman DD, Mehta SR, Smith DM, Pond SLK. HIV-1 clade B pol evolution following primary infection. PloS one. 2013; 8(6):e68188. DOI: 10.1371/journal.pone.0068188. PMID: 23840830; PMC3695957.
Joseph J, Achim CL, Boivin MJ, Brew BJ, Clifford DB, Colosi DA, Ellis RJ, Heaton RK, Gallo-Diop A, Grant I, Kanmogne GD, Kumar M, Letendre S, Marcotte TD, Nath A, Pardo CA, Paul RH, Pulliam L, Robertson K, Royal W, 3rd, Sacktor N, Sithinamsuwan P, Smith DM, Valcour V, Wigdahl B, Wood C. Global NeuroAIDS roundtable. Journal of neurovirology. 2013;19(1):1-9. Epub 01/26. doi: 10.1007/s13365-012-0143-9. PubMed PMID: 23354550.
Saravanan S, Madhavan V, Balakrishnan P, Smith DM, Solomon SS, Sivamalar S, Poongulali S, Kumarasamy N, Schooley RT, Solomon S, Kantor R. Darunavir is a good third-line antiretroviral agent for HIV type 1-infected patients failing second-line protease inhibitor-based regimens in South India. AIDS Res Hum Retroviruses. 2013 Mar; 29(3):630-2. doi: 10.1089/AID.2011.0334. PMID: 23045961; PMC3581023.
Wertheim JO, Scheffler K, Choi JY, Smith DM, Kosakovsky Pond SL. Phylogenetic relatedness of HIV-1 donor and recipient populations. J Infect Dis. 2013 Apr; 207(7):1181-2. doi: 10.1093/infdis/jit021. PMID: 23315327; PMC3583277.
Fierer DS, Dieterich DT, Fiel MI, Branch AD, Marks KM, Fusco DN, Hsu R, Smith DM, Fierer J. Rapid progression to decompensated cirrhosis, liver transplant, and death in HIV-infected men after primary hepatitis C virus infection. Clin Infect Dis. 2013 Apr; 56(7):1038-43. doi: 10.1093/cid/cis1206. PMID: 23264364; PMC3588118.
Gianella S, Morris SR, Vargas MV, Young JA, Callahan B, Richman DD, Little SJ, Smith DM. Role of seminal shedding of herpesviruses in HIV Type 1 Transmission. J Infect Dis. 2013 Jan 15; 207(2):257-61. doi: 10.1093/infdis/jis683. PMID: 23148284; PMC3532824.
Gianella S, Anderson CM, Vargas MV, Richman DD, Little SJ, Morris SR, Smith DM. Cytomegalovirus DNA in semen and blood is associated with higher levels of proviral HIV DNA. J Infect Dis. 2013 Mar 15; 207(6):898-902. doi: 10.1093/infdis/jis777. PMID: 23275608; PMC3571441.
Gianella S, Smith DM, Vargas MV, Little SJ, Richman DD, Daar ES, Dube MP, Zhang F, Ginocchio CC, Haubrich RH, Morris SR; CCTG 592 Team. Shedding of HIV and human herpesviruses in the semen of effectively treated HIV-1-infected men who have sex with men. Clin Infect Dis. 2013 Aug; 57(3):441-7. doi: 10.1093/cid/cit252. PMID: 23595831; PMC3703105.
Gianella S, Morris SR, Anderson C, Spina CA, Vargas MV, Young JA, Richman DD, Little SJ, Smith DM. Herpes viruses and HIV-1 drug resistance mutations influence the virologic and immunologic milieu of the male genital tract. AIDS. 2013 Jan 2; 27(1):39-47. doi: 10.1097/QAD.0b013e3283573305. PMID: 22739399; PMC3769229.
Nguyen A, Rossi S, Croteau D, Best BM, Clifford D, Collier AC, Gelman B, Marra C, McArthur J, McCutchan JA, Morgello S, Simpson D, Ellis RJ, Grant I, Capparelli E, Letendre S, Group C. Etravirine in CSF is highly protein bound. J Antimicrob Chemother. 2013;68(5):1161-8. Epub 2013/01/22. doi: 10.1093/jac/dks517. PubMed PMID: 23335197; PubMed Central PMCID: PMC3625433.
Le T, Wright EJ, Smith DM, He W, Catano G, Okulicz JF, Young JA, Clark RA, Richman DD, Little SJ, Ahuja SK. Enhanced CD4+ T-cell recovery with earlier HIV-1 antiretroviral therapy. N Engl J Med. 2013 Jan 17; 368(3):218-30. doi: 10.1056/NEJMoa1110187. PMID: 23323898; PMC3657555.

2012

Hightower GK, Wong JK, Letendre SL, Umlauf AA, Ellis RJ, Ignacio CC, Heaton RK, Collier AC, Marra CM, Clifford DB, Gelman BB, McArthur JC, Morgello S, Simpson DM, McCutchan JA, Grant I, Little SJ, Richman DD, Kosakovsky Pond SL, Smith DM, Group CS. Higher HIV-1 genetic diversity is associated with AIDS and neuropsychological impairment. Virology. 2012;433(2):498- 505. Epub 2012/09/25. doi: 10.1016/j.virol.2012.08.028. PubMed PMID: 22999095; PubMed Central PMCID: PMC3466337.
Orlov M, Vaida F, Finney OC, Smith DM, Talley AK, Wang R, Kappe SH, Deng Q, Schooley RT, Duffy PE. P. falciparum enhances HIV replication in an experimental malaria challenge system. PloS one. 2012;7(6):e39000. Epub 2012/06/30. doi: 10.1371/journal.pone.0039000. PubMed PMID: 22745697; PubMed Central PMCID: PMCPMC3383717.
Saravanan S, Madhavan V, Solomon SS, Kantor R, Katzenstein D, Sivamalar S, Kumarasamy N, Smith DM, Mayer KH, Solomon S, Balakrishnan P. Reverse transcriptase substitution at codons 208 and 228 among treatment-experienced HIV-1 subtype-C-infected Indian patients is strongly associated with thymidine analogue mutations. Journal of acquired immune deficiency syndromes (1999). 2012;59(2):e26-7. Epub 2012/01/17. doi: 10.1097/QAI.0b013e31823e2d2b. PubMed PMID: 22245718; PubMed Central PMCID: PMCPMC3259528.
Mehta SR, Kosakovsky Pond SL, Young JA, Richman D, Little S, Smith DM. Associations between phylogenetic clustering and HLA profile among HIV-infected individuals in San Diego, California. J Infect Dis. 2012 May 15; 205(10):1529-33. doi: 10.1093/infdis/jis231. PMID: 22448013; PMC3415817.
Choi JY, Hightower GK, Wong JK, Heaton R, Woods S, Grant I, Marcotte TD, Ellis RJ, Letendre SL, Collier AC, Marra CM, Clifford DB, Gelman BB, McArthur JC, Morgello S, Simpson DM, McCutchan JA, Richman DD, Smith DM, Charter G. Genetic features of cerebrospinal fluid-derived subtype B HIV-1 tat. J Neurovirol. 2012;18(2):81-90. Epub 2012/04/25. doi: 10.1007/s13365-011-0059-9. PubMed PMID: 22528397; PubMed Central PMCID: PMCPMC3572198.
Shi Y, Wei F, Hu D, Li Q, Smith D, Li N, Chen D. Mutations in the major hydrophilic region (MHR) of hepatitis B virus genotype C in North China. Journal of medical virology. 2012; 84(12):1901-6. DOI: 10.1002/jmv.23419. PMID: 23080494; PMC3747822.
Gianella S, Mehta SR, Young JA, Vargas MV, Little SJ, Richman DD, Pond SLK, Smith DM. Sexual transmission of predicted CXCR4-tropic HIV-1 likely originating from the source partner’s seminal cells. Virology. 2012; 434(1):2-4. DOI: 10.1016/j.virol.2012.09.010. PMID: 23040890; PMC3485073.
Homann S, Smith D, Little S, Richman D, Guatelli J. Upregulation of BST-2/Tetherin by HIV infection in vivo. J Virol. 2011 Oct; 85(20):10659-68. doi: 10.1128/JVI.05524-11. PMID: 21849457; PMC3187519.
Tilghman MW, May S, Pérez-Santiago J, Ignacio CC, Little SJ, Richman DD, Smith DM. A combined screening platform for HIV treatment failure and resistance. PloS one. 2012; 7(4):e35401. DOI: 10.1371/journal.pone.0035401. PMID: 22563383; PMC3338506.
Saravanan S, Madhavan V, Kantor R, Sivamalar S, Gomathi S, Solomon SS, Kumarasamy N, Smith DM, Schooley RT, Solomon S. Unusual Insertion and deletion at codon 67 and 69 of HIV type 1 subtype C reverse transcriptase among first-line highly active antiretroviral treatment-failing South Indian patients: association with other resistance mutations. AIDS research and human retroviruses. 2012; 28(12):1763-5. DOI: 10.1089/AID.2011.0331. PMID: 22404052; PMC3505055.
Bharti AR, Saravanan S, Madhavan V, Smith DM, Sharma J, Balakrishnan P, Letendre SL, Kumarasamy N. Correlates of HIV and malaria co-infection in Southern India. Malar J. 2012;11:306. Epub 2012/09/05. doi: 10.1186/1475-2875-11-306. PubMed PMID: 22943054; PubMed Central PMCID: PMCPMC3504568.
Aldous JL, Pond SK, Poon A, Jain S, Qin H, Kahn JS, Kitahata M, Rodriguez B, Dennis AM, Boswell SL, Haubrich R, Smith DM. Characterizing HIV transmission networks across the United States. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2012;55(8):1135-43. Epub 2012/07/13. doi: 10.1093/cid/cis612. PubMed PMID: 22784872; PubMed Central PMCID: PMCPMC3529609.
Gianella S, Mehta SR, Strain MC, Young JA, Vargas MV, Little SJ, Richman DD, Pond SLK, Smith DM. Impact of seminal cytomegalovirus replication on HIV‐1 dynamics between blood and semen. Journal of medical virology. 2012; 84(11):1703-9. doi: 10.1002/jmv.23398. PMID: 22997072. PMC3472447.
Zhang Y, Qiao L, Ding W, Wei F, Zhao Q, Wang X, Shi Y, Li N, Smith D, Chen D. An initial screening for HIV-associated neurocognitive disorders of HIV-1 infected patients in China. Journal of neurovirology. 2012; 18(2):120-6. DOI: 10.1007/s13365-012-0089-y. PMID: 22411002; PMC3859527.
Karris MY, Anderson CM, Morris SR, Smith DM, Little SJ. Cost savings associated with testing of antibodies, antigens, and nucleic acids for diagnosis of acute HIV infection. Journal of clinical microbiology. 2012; 50(6):1874-8. DOI: 10.1128/JCM.00106-12. PMID: 22442319; PMC3372146.
Pacold ME, Pond SL, Wagner GA, Delport W, Bourque DL, Richman DD, Little SJ, Smith DM. Clinical, virologic, and immunologic correlates of HIV-1 intraclade B dual infection among men who have sex with men. AIDS. 2012 Jan 14; 26(2):157-65. doi: 10.1097/QAD.0b013e32834dcd26. PMID: 22045341; PMC3807679.
Fisher R, van Zyl GU, Travers SA, Kosakovsky Pond SL, Engelbrech S, Murrell B, Scheffler K, Smith D. Deep sequencing reveals minor protease resistance mutations in patients failing a protease inhibitor regimen. J Virol. 2012 Jun; 86(11):6231-7. doi: 10.1128/JVI.06541-11. PMID: 22457522; PMC3372173.
Gianella S, Strain MC, Rought SE, Vargas MV, Little SJ, Richman DD, Spina CA, Smith DM. Associations between virologic and immunologic dynamics in blood and in the male genital tract. J Virol. 2012 Feb; 86(3):1307-15. doi: 10.1128/JVI.06077-11. PMID: 22114342; PMC3264378.

2011

Jeong J, Kim SR, Lee SH, Lim JH, Choi JI, Park JS, Chang CL, Choi JY, Richman DD, Smith DM. The Use of High Performance Liquid Chromatography to Speciate and Characterize the Epidemiology of Mycobacteria. Lab Med. 2011;42(10):612-7. Epub 2011/10/01. doi: 10.1309/LMDDEHPSYE6ZDM3C. PubMed PMID: 24443588; PubMed Central PMCID: PMCPMC3892985.
Saravanan S, Madhavan V, Balakrishnan P, Solomon SS, Kumarasamy N, Mayer KH, Waldrop G, Solomon S, Smith DM. HIV-1 reverse transcriptase nucleotide substitutions in subtype C- infected, drug-naive, and treatment-experienced patients in South India. Journal of acquired immune deficiency syndromes (1999). 2011;58(3):e94-5. Epub 2011/08/31. doi: 10.1097/QAI.0b013e318232a13c. PubMed PMID: 21876445; PubMed Central PMCID: PMCPMC5091647.
Kim D, Lyoo KS, Smith D, Hur W, Hong SW, Sung PS, Yoon SK, Mehta S. Number of mutations within CTL-defined epitopes of the hepatitis B Virus (HBV) core region is associated with HBV disease progression. J Med Virol. 2011;83(12):2082-7. Epub 2011/10/21. doi: 10.1002/jmv.22226. PubMed PMID: 22012714; PubMed Central PMCID: PMCPMC3872118.
Saravanan S, Madhavan V, Murugavel KG, Balakrishnan P, Solomon SS, Umapathy S, Kantor R, Kumarasamy N, Yepthomi T, Smith DM, Mayer KH, Solomon S. The association between HIV-1 subtype C antiretroviral resistance and HLA prevalence in southern India. Journal of acquired immune deficiency syndromes (1999). 2011;57(1):e17-9. Epub 2011/07/22. doi: 10.1097/QAI.0b013e3182169050. PubMed PMID: 21775932; PubMed Central PMCID: PMCPMC3154011.
Karris MA, Smith DM. Tissue-specific HIV-1 infection: why it matters. Future Virol. 2011;6(7):869- 82. Epub 2011/07/01. doi: 10.2217/fvl.11.48. PubMed PMID: 23946764; PubMed Central PMCID: PMCPMC3741055.
Mehta SR, Nguyen VT, Osorio G, Little S, Smith DM. Evaluation of pooled rapid HIV antibody screening of patients admitted to a San Diego Hospital. J Virol Methods. 2011;174(1-2):94-8. Epub 2011/04/26. doi: 10.1016/j.jviromet.2011.04.002. PubMed PMID: 21513744; PubMed Central PMCID: PMCPMC3095723.
Keller SB, Smith DM. The price of tenofovir-emtricitabine undermines the cost-effectiveness and advancement of pre-exposure prophylaxis. AIDS (London, England). 2011;25(18):2308-10. Epub 2011/11/10. doi: 10.1097/QAD.0b013e32834d3cab. PubMed PMID: 22067201; PubMed Central PMCID: PMCPMC3874210.
Mehta SR, Wertheim JO, Delport W, Ene L, Tardei G, Duiculescu D, Pond SL, Smith DM. Using phylogeography to characterize the origins of the HIV-1 subtype F epidemic in Romania. Infect Genet Evol. 2011;11(5):975-9. Epub 2011/03/29. doi: 10.1016/j.meegid.2011.03.009. PubMed PMID: 21439403; PubMed Central PMCID: PMCPMC3104099.
Tilghman MW, Guerena DD, Licea A, Perez-Santiago J, Richman DD, May S, Smith DM. Pooled nucleic acid testing to detect antiretroviral treatment failure in Mexico. Journal of acquired immune deficiency syndromes (1999). 2011;56(3):e70-4. Epub 2010/12/03. doi: 10.1097/QAI.0b013e3181ff63d7. PubMed PMID: 21124228; PubMed Central PMCID: PMCPMC3039117.
Moore DJ, Letendre SL, Morris S, Umlauf A, Deutsch R, Smith DM, Little S, Rooney A, Franklin DR, Gouaux B, Leblanc S, Rosario D, Fennema-Notestine C, Heaton RK, Ellis RJ, Atkinson JH, Grant I, Group C. Neurocognitive functioning in acute or early HIV infection. J Neurovirol. 2011;17(1):50-7. Epub 2010/12/18. doi: 10.1007/s13365-010-0009-y. PubMed PMID: 21165782; PubMed Central PMCID: PMCPMC3032208.
van Zyl GU, Preiser W, Potschka S, Lundershausen AT, Haubrich R, Smith D. Pooling strategies to reduce the cost of HIV-1 RNA load monitoring in a resource-limited setting. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2011;52(2):264- 70. Epub 2011/02/04. doi: 10.1093/cid/ciq084. PubMed PMID: 21288854; PubMed Central PMCID: PMCPMC3106253.
Homann S, Smith D, Little S, Richman D, Guatelli J. Upregulation of BST-2/Tetherin by HIV infection in vivo. Journal of virology. 2011;85(20):10659-68. Epub 2011/08/19. doi: 10.1128/JVI.05524-11. PubMed PMID: 21849457; PubMed Central PMCID: PMCPMC3187519.
Gianella S, Delport W, Pacold ME, Young JA, Choi JY, Little SJ, Richman DD, Kosakovsky Pond SL, Smith DM. Detection of minority resistance during early HIV-1 infection: natural variation and spurious detection rather than transmission and evolution of multiple viral variants. Journal of virology. 2011;85(16):8359-67. Epub 2011/06/03. doi: 10.1128/JVI.02582-10. PubMed PMID: 21632754; PubMed Central PMCID: PMCPMC3147985.

2010 and before

Rieg G, Butler DM, Smith DM, Daar ES. Seminal plasma HIV levels in men with asymptomatic sexually transmitted infections. Int J STD AIDS. 2010;21(3):207-8. Epub 2010/03/11. doi: 10.1258/ijsa.2009.009331. PubMed PMID: 20215629; PubMed Central PMCID: PMC2917381.
Fierer DS, Dieterich DT, Fiel MI, Branch AD, Marks KM, Fusco DN, Hsu R, Smith DM, Fierer J. Rapid progression to decompensated cirrhosis, liver transplant, and death in HIV-infected men after primary hepatitis C virus infection. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2013;56(7):1038-43. Epub 2012/12/25. doi: 10.1093/cid/cis1206. PubMed PMID: 23264364; PubMed Central PMCID: PMC3588118.
Smith D, Delport W, Butler D, Little S, Richman D, Pond SK. Response to Comment on “The Origins of Sexually Transmitted HIV Among Men Who Have Sex with Men”. Sci Transl Med. 2010;2(50):501r1. Epub 2011/05/03. doi: 10.1126/scitranslmed.3001473. PubMed PMID: 21532938; PubMed Central PMCID: PMC3083242.
Mehta SR, Delport W, Brouwer KC, Espitia S, Patterson T, Pond SK, Strathdee SA, Smith DM. The relatedness of HIV epidemics in the United States-Mexico border region. AIDS research and human retroviruses. 2010;26(12):1273-7. Epub 2010/10/28. doi: 10.1089/aid.2010.0021. PubMed PMID: 20977301; PubMed Central PMCID: PMCPMC3011998.
Woelk CH, Beliakova-Bethell N, Goicoechea M, Zhao Y, Du P, Rought SE, Lozach J, Perez- Santiago J, Richman DD, Smith DM, Little SJ. Gene expression before HAART initiation predicts HIV-infected individuals at risk of poor CD4+ T-cell recovery. AIDS (London, England). 2010;24(2):217-22. Epub 2009/12/03. doi: 10.1097/QAD.0b013e328334f1f0. PubMed PMID: 19952713; PubMed Central PMCID: PMCPMC2915828.
Manosuthi W, Butler DM, Perez-Santiago J, Poon AF, Pillai SK, Mehta SR, Pacold ME, Richman DD, Pond SK, Smith DM. Protease poly morphisms in HIV-1 subtype CRF01_AE represent selection by antiretroviral therapy and host immune pressure. AIDS (London, England). 2010;24(3):411-6. Epub 2009/12/17. doi: 10.1097/QAD.0b013e3283350eef. PubMed PMID: 20009919; PubMed Central PMCID: PMC2913588.
Morris SR, Little SJ, Cunningham T, Garfein RS, Richman DD, Smith DM. Evaluation of an HIV nucleic acid testing program with automated Internet and voicemail systems to deliver results. Ann Intern Med. 2010;152(12):778-85. Epub 2010/06/16. doi: 10.7326/0003-4819-152-12- 201006150-00005. PubMed PMID: 20547906; PubMed Central PMCID: PMCPMC2922925.
Manosuthi W, Butler DM, Chantratita W, Sukasem C, Richman DD, Smith DM. Patients infected with HIV type 1 subtype CRF01_AE and failing first-line nevirapine- and efavirenz-based regimens demonstrate considerable cross-resistance to etravirine. AIDS research and human retroviruses. 2010;26(6):609-11. Epub 2010/05/29. doi: 10.1089/aid.2009.0107. PubMed PMID: 20507208; PubMed Central PMCID: PMC2982719.
May S, Gamst A, Haubrich R, Benson C, Smith DM. Pooled nucleic acid testing to identify antiretroviral treatment failure during HIV infection. Journal of acquired immune deficiency syndromes (1999). 2010;53(2):194-201. Epub 2009/09/23. doi: 10.1097/QAI.0b013e3181ba37a7. PubMed PMID: 19770802; PubMed Central PMCID: PMCPMC2915780.
Pacold M, Smith D, Little S, Cheng PM, Jordan P, Ignacio C, Richman D, Pond SK. Comparison of methods to detect HIV dual infection. AIDS research and human retroviruses. 2010;26(12):1291-8. Epub 2010/10/18. doi: 10.1089/aid.2010.0042. PubMed PMID: 20954840.
DeGruttola V, Smith DM, Little SJ, Miller V. Developing and evaluating comprehensive HIV infection control strategies: issues and challenges. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2010;50 Suppl 3(Suppl 3):S102-7. Epub 2010/04/20. doi: 10.1086/651480. PubMed PMID: 20397937; PubMed Central PMCID: PMCPMC2913596.
Butler DM, Delport W, Kosakovsky Pond SL, Lakdawala MK, Cheng PM, Little SJ, Richman DD, Smith DM. The origins of sexually transmitted HIV among men who have sex with men. Sci Transl Med. 2010;2(18):18re1. Epub 2010/04/08. doi: 10.1126/scitranslmed.3000447. PubMed PMID: 20371483; PubMed Central PMCID: PMC2945226.
Manosuthi W, Butler D, Chantratita W, Sukasem C, Richman D, Smith D, editors. Mutations associated with etravirine resistance among patients infected with HIV-1 subtype CRF01_AE and failing first-line nevirapine-and efavirenz-based regimens. Antiviral Therapy; 2009: Int Medical Press Ltd 2-4 Idol Lane, London EC3R 5DD, England.
Goicoechea M, Smith D, May S, Mathews C, Spina C. Prevalence and T-cell phenotype of slow HIV disease progressors with robust HIV replication. Journal of acquired immune deficiency syndromes (1999). 2009;52(2):299-301. Epub 2010/02/02. doi: 10.1097/QAI.0b013e3181b08d70. PubMed PMID: 20118679; PubMed Central PMCID: PMC2818087.
Jordan PS, Poon A, Eron J, Squires K, Ignacio C, Richman DD, Smith DM. A novel codon insert in protease of clade B HIV type 1. AIDS research and human retroviruses. 2009;25(5):547-50. Epub 2009/04/29. doi: 10.1089/aid.2008.0310. PubMed PMID: 19397401; PubMed Central PMCID: PMC2749665.
Mehta SR, MacGruder C, Looney D, Johns S, Smith DM. Differences in tuberculin reactivity as determined in a veterans administration employee health screening program. Clin Vaccine Immunol. 2009;16(4):541-3. Epub 2009/02/20. doi: 10.1128/CVI.00375-08. PubMed PMID: 19225075; PubMed Central PMCID: PMC2668276.
Butler DM, Pacold ME, Jordan PS, Richman DD, Smith DM. The efficiency of single genome amplification and sequencing is improved by quantitation and use of a bioinformatics tool. J Virol Methods. 2009;162(1-2):280-3. Epub 2009/08/25. doi: 10.1016/j.jviromet.2009.08.002. PubMed PMID: 19698751; PubMed Central PMCID: PMC2761514.
Nugent CT, Dockter J, Bernardin F, Hecht R, Smith D, Delwart E, Pilcher C, Richman D, Busch M, Giachetti C. Detection of HIV-1 in alternative specimen types using the APTIMA HIV-1 RNA Qualitative Assay. J Virol Methods. 2009;159(1):10-4. Epub 2009/05/16. doi: 10.1016/j.jviromet.2009.02.015. PubMed PMID: 19442838; PubMed Central PMCID: PMC2930826.
Bharti AR, Letendre SL, Patra KP, Vinetz JM, Smith DM. Malaria diagnosis by a polymerase chain reaction-based assay using a pooling strategy. Am J Trop Med Hyg. 2009;81(5):754-7. Epub 2009/10/29. doi: 10.4269/ajtmh.2009.09-0274. PubMed PMID: 19861605; PubMed Central PMCID: PMC2770880.
Hightower GK, Letendre SL, Cherner M, Gibson SA, Ellis RJ, Wolfson TJ, Gamst AC, Ignacio CC, Heaton RK, Grant I, Richman DD, Smith DM, Group H. Select resistance-associated mutations in blood are associated with lower CSF viral loads and better neuropsychological performance. Virology. 2009;394(2):243-8. Epub 2009/09/19. doi: 10.1016/j.virol.2009.08.007. PubMed PMID: 19762060; PubMed Central PMCID: PMC3046809.
Smith DM, Zarate S, Shao H, Pillai SK, Letendre SL, Wong JK, Richman DD, Frost SD, Ellis RJ, Group H. Pleocytosis is associated with disruption of HIV compartmentalization between blood and cerebral spinal fluid viral populations. Virology. 2009;385(1):204-8. Epub 2008/12/23. doi: 10.1016/j.virol.2008.11.010. PubMed PMID: 19100592; PubMed Central PMCID: PMC2794037.
Smith DM, May SJ, Perez-Santiago J, Strain MC, Ignacio CC, Haubrich RH, Richman DD, Benson CA, Little SJ. The use of pooled viral load testing to identify antiretroviral treatment failure. AIDS (London, England). 2009;23(16):2151-8. Epub 2009/09/05. doi: 10.1097/QAD.0b013e3283313ca9. PubMed PMID: 19730348; PubMed Central PMCID: PMC2915784.
Kosakovsky Pond SL, Smith DM. Are all subtypes created equal? The effectiveness of antiretroviral therapy against non-subtype B HIV-1. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2009;48(9):1306-9. Epub 2009/04/01. doi: 10.1086/598503. PubMed PMID: 19331584; PubMed Central PMCID: PMC3052852.
Smith DM, May SJ, Tweeten S, Drumright L, Pacold ME, Kosakovsky Pond SL, Pesano RL, Lie YS, Richman DD, Frost SD, Woelk CH, Little SJ. A public health model for the molecular surveillance of HIV transmission in San Diego, California. AIDS (London, England). 2009;23(2):225-32. Epub 2008/12/23. doi: 10.1097/QAD.0b013e32831d2a81. PubMed PMID: 19098493; PubMed Central PMCID: PMC2644048.
Ances BM, Sisti D, Vaida F, Liang CL, Leontiev O, Perthen JE, Buxton RB, Benson D, Smith DM, Little SJ, Richman DD, Moore DJ, Ellis RJ, group H. Resting cerebral blood flow: a potential biomarker of the effects of HIV in the brain. Neurology. 2009;73(9):702-8. Epub 2009/09/02. doi: 10.1212/WNL.0b013e3181b59a97. PubMed PMID: 19720977; PubMed Central PMCID: PMC2734291.
Little SJ, Frost SD, Wong JK, Smith DM, Pond SL, Ignacio CC, Parkin NT, Petropoulos CJ, Richman DD. Persistence of transmitted drug resistance among subjects with primary human immunodeficiency virus infection. Journal of virology. 2008;82(11):5510-8. Epub 2008/03/21. doi: 10.1128/JVI.02579-07. PubMed PMID: 18353964; PubMed Central PMCID: PMC2395184.
Liu L, May S, Richman DD, Hecht FM, Markowitz M, Daar ES, Routy JP, Margolick JB, Collier AC, Woelk CH, Little SJ, Smith DM. Comparison of algorithms that interpret genotypic HIV-1 drug resistance to determine the prevalence of transmitted drug resistance. AIDS (London, England). 2008;22(7):835-9. Epub 2008/04/23. doi: 10.1097/QAD.0b013e3282f5ff71. PubMed PMID: 18427201; PubMed Central PMCID: PMC2716722.
Smith DM. Active duty military personnel presenting for care at a Gay Men’s Health Clinic. J Homosex. 2008;54(3):277-9. Epub 2008/10/02. doi: 10.1080/00918360801982173. PubMed PMID: 18825864.
Cachay ER, Frost SD, Poon AF, Looney D, Rostami SM, Pacold ME, Richman DD, Little SJ, Smith DM. Herpes simplex virus type 2 acquisition during recent HIV infection does not influence plasma HIV levels. Journal of acquired immune deficiency syndromes (1999). 2008;47(5):592-6. Epub 2008/01/17. doi: 10.1097/QAI.0b013e318163bd87. PubMed PMID: 18197122; PubMed Central PMCID: PMC2630881.
Kosakovsky Pond SL, Poon AF, Zarate S, Smith DM, Little SJ, Pillai SK, Ellis RJ, Wong JK, Leigh Brown AJ, Richman DD, Frost SD. Estimating selection pressures on HIV-1 using phylogenetic likelihood models. Statistics in medicine. 2008;27(23):4779-89. Epub 2008/04/03. doi: 10.1002/sim.3192. PubMed PMID: 18381707; PubMed Central PMCID: PMC2634745.
Smith DM, Schooley RT. Running with scissors: using antiretroviral therapy without monitoring viral load. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2008;46(10):1598-600. Epub 2008/04/19. doi: 10.1086/587110. PubMed PMID: 18419496.
Butler DM, Smith DM, Cachay ER, Hightower GK, Nugent CT, Richman DD, Little SJ. Herpes simplex virus 2 serostatus and viral loads of HIV-1 in blood and semen as risk factors for HIV transmission among men who have sex with men. AIDS (London, England). 2008;22(13):1667- 71. Epub 2008/08/02. doi: 10.1097/QAD.0b013e32830bfed8. PubMed PMID: 18670228; PubMed Central PMCID: PMC2653089.
Little SJ, Frost SD, Wong JK, Smith DM, Pond SLK, Ignacio CC, Parkin NT, Petropoulos CJ, Richman DD. Persistence of transmitted drug resistance among subjects with primary human immunodeficiency virus infection. Journal of virology. 2008;82(11):5510-8. DOI: 10.1128/JVI.02579-07.
Little S, Parkin N, Chappey C, Smith D, Richman D, Frost S, editors. Differences in viral load and replication capacity in individuals harbouring virus with or without drug resistance. Antiviral Therapy; 2007: Int Medical Press Ltd 2-4 Idol Lane, London EC3R 5DD, England.
Hightower G, Letendre S, Cachay E, Cherner M, Gibson S, Ellis R, Richman D, Ignacio C, Smith D, editors. Antiretroviral resistance and neuropsychological performance among HIV-infected individuals. Antiviral Therapy; 2007: Int Medical Press Ltd 2-4 Idol Lane, London EC3R 5DD, England.
Goicoechea M, Smith D. Universal HIV testing: is it enough? Clinical Infectious Diseases. 2007;45(10):1375-6. doi:10.1086/522760.
Ances BM, Liang C, Buxton RB, Smith D, Little S, Letendre S, Richman D, Ellis R, editors. Differences in cerebral blood flow (CBF) and cerebral metabolic rate of oxygen consumption (CMRO2) in HIV+ patients compared to seronegative controls using quantitative functional magnetic resonance imaging (qfMRI). Journal of Neurovirology; 2007: Springer 233 Spring St, New York, NY 10013 USA.
Ances B, Liang C, Sisti D, Buxton R, Smith D, Little S, Letendre S, Richman D, Ellis R, editors. Cerebral blood flow (CBF) and cerebral metabolic rate of oxygen consumption (CMRO2) are elevated in both early and chronically infected HIV plus patients compared to seronegative controls using quantitative functional magnetic resonance imaging (qfMRI). Journal of Neurovirology; 2007: Taylor & Francis Inc 325 Chestnut St, Suite 800, Philadelphia, PA 19106 USA.
Ances B, Perthen J, Liang C, Leontiev O, Smith D, Little S, Richman D, Letendre S, Buxton R, Ellis R, editors. Acute and chronic HIV reduce the BOLD signal magnitude. Annals of Neurology; 2007: Wiley-Liss Div John Wiley & Sons Inc, 111 River St, Hoboken, NJ 07030 USA.
Cachay ER, Moini N, Kosakovsky Pond SL, Pesano R, Lie YS, Aiem H, Butler DM, Letendre S, Mathews WC, Smith DM. Active methamphetamine use is associated with transmitted drug resistance to non-nucleoside reverse transcriptase inhibitors in individuals with HIV infection of unknown duration. Open AIDS J. 2007;1:5-10. Epub 2008/10/17. doi: 10.2174/1874613600701010005. PubMed PMID: 18923691; PubMed Central PMCID: PMC2556194.
Noviello CM, Pond SLK, Lewis MJ, Richman DD, Pillai SK, Yang OO, Little SJ, Smith DM, Guatelli JC. Maintenance of Nef-mediated modulation of major histocompatibility complex class I and CD4 after sexual transmission of human immunodeficiency virus type 1. Journal of virology. 2007;81(9):4776-86. Epub 2007/02/28. doi: 10.1128/JVI.01793-06. PubMed PMID: 17329339; PubMed Central PMCID: PMC1900175.
Cachay ER, Frost SDW, Richman DD, Smith DM, Little SJ. Herpes simplex virus type 2 infection does not influence viral dynamics during early HIV-1 infection. The Journal of infectious diseases. 2007;195(9):1270-7. Epub 2007/03/15. doi: 10.1086/513568. PubMed PMID: 17396995.
Smith DM, Mathews WC. Physicians’ attitudes toward homosexuality and HIV: survey of a California Medical Society- revisited (PATHH-II). J Homosex. 2007;52(3-4):1-9. Epub 2007/06/28. doi: 10.1300/J082v52n03_01. PubMed PMID: 17594969.
Smith D, Moini N, Pesano R, Cachay E, Aiem H, Lie Y, Richman D, Little S. Clinical utility of HIV standard genotyping among antiretroviral-naive individuals with unknown duration of infection. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2007;44(3):456-8. Epub 2006/12/28. doi: 10.1086/510748. PubMed PMID: 17205459.
Smith DM, Wong JK, Shao H, Hightower GK, Mai SHT, Moreno JM, Ignacio CC, Frost SDW, Richman DD, Little SJ. Long-term persistence of transmitted HIV drug resistance in male genital tract secretions: implications for secondary transmission. The Journal of infectious diseases. 2007;196(3):356-60. Epub 2007/06/19. doi: 10.1086/519164. PubMed PMID: 17597449.
Butler DM, Smith DM. Serosorting can potentially increase HIV transmissions. AIDS (London, England). 2007;21(9):1218-20. doi: 10.1097/QAD.0b013e32814db7bf. PubMed PMID: 17502737.
Smith DM, Strain MC, Frost SDW, Pillai SK, Wong JK, Wrin T, Liu Y, Petropolous CJ, Daar ES, Little SJ, Richman DD. Lack of neutralizing antibody response to HIV-1 predisposes to superinfection. Virology. 2006;355(1):1-5. Epub 2006/09/07. doi: 10.1016/j.virol.2006.08.009. PubMed PMID: 16962152.
Mehta S, Herndier N, Smith D. Mycobacterium szulgai causing knee abscess and osteomyelitis in a patient with acquired immunodeficiency syndrome and subsequent immune reconstitution Syndrome. Infectious Diseases in Clinical Practice. 2006;14. doi: 10.1097/01.idc.0000214370.54423.2f.
Smith DM. The controversies of nevirapine for preventing mother-to-child HIV transmission. AIDS (London, England). 2006;20(2):281-3. doi: 10.1097/01.aids.0000198095.00820.82. PubMed PMID: 16511423.
Smith DM, Drumright LN, Frost SDW, Cheng WS, Espitia S, Daar ES, Little SJ, Gorbach PM. Characteristics of recently HIV-infected men who use the Internet to find male sex partners and sexual practices with those partners. Journal of acquired immune deficiency syndromes (1999). 2006;43(5):582-7. doi: 10.1097/01.qai.0000243100.49899.2a. PubMed PMID: 17019370.
Pillai SK, Pond SLK, Liu Y, Good BM, Strain MC, Ellis RJ, Letendre S, Smith DM, Günthard HF, Grant I, Marcotte TD, McCutchan JA, Richman DD, Wong JK. Genetic attributes of cerebrospinal fluid-derived HIV-1 env. Brain : a journal of neurology. 2006;129(Pt 7):1872-83. Epub 2006/05/30. doi: 10.1093/brain/awl136. PubMed PMID: 16735456.
Smith DM, Strain MC, Frost SDW, Pillai SK, Wong JK, Wrin T, Liu Y, Petropolous CJ, Daar ES, Little SJ, Richman DD. Lack of neutralizing antibody response to HIV-1 predisposes to superinfection. Virology. 2006;355(1):1-5. Epub 2006/09/07. doi: 10.1016/j.virol.2006.08.009. PubMed PMID: 16962152.
Goicoechea M, Smith DM, Liu L, May S, Tenorio AR, Ignacio CC, Landay A, Haubrich R. Determinants of CD4+ T cell recovery during suppressive antiretroviral therapy: association of immune activation, T cell maturation markers, and cellular HIV-1 DNA. The Journal of infectious diseases. 2006;194(1):29-37. Epub 2006/05/18. doi: 10.1086/504718. PubMed PMID: 16741879.
Little SJ, Smith DM. HIV treatment decisions and transmitted drug resistance. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2005;41(2):233-5. doi: 10.1086/431215. PubMed PMID: 15983921.
Smith D, Wong J, Mai H, Moreno J, Russell T, Ignacio C, Frost S, Richman D, Little S, editors. Slow reversion of HIV transmitted drug resistance to non-nucleoside reverse transcriptase inhibitors in semen. Antiviral Therapy; 2005: Int Medical Press LTD, London, England.
Pillai SK, Kosakovsky Pond SL, Woelk CH, Richman DD, Smith DM. Codon volatility does not reflect selective pressure on the HIV-1 genome. Virology. 2005;336(2):137-43. doi: 10.1016/j.virol.2005.03.014. PubMed PMID: 15892955.
Pillai SK, Good B, Pond SK, Wong JK, Strain MC, Richman DD, Smith DM. Semen-specific genetic characteristics of human immunodeficiency virus type 1 env. Journal of virology. 2005;79(3):1734-42. doi: 10.1128/JVI.79.3.1734-1742.2005. PubMed PMID: 15650198.
Yang OO, Daar ES, Jamieson BD, Balamurugan A, Smith DM, Pitt JA, Petropoulos CJ, Richman DD, Little SJ, Brown AJL. Human immunodeficiency virus type 1 clade B superinfection: evidence for differential immune containment of distinct clade B strains. Journal of virology. 2005;79(2):860- 8. doi: 10.1128/JVI.79.2.860-868.2005. PubMed PMID: 15613314.
Smith DM, Wong JK, Hightower GK, Ignacio CC, Koelsch KK, Petropoulos CJ, Richman DD, Little SJ. HIV drug resistance acquired through superinfection. AIDS (London, England). 2005;19(12):1251-6. doi: 10.1097/01.aids.0000180095.12276.ac. PubMed PMID: 16052079.
Strain MC, Letendre S, Pillai SK, Russell T, Ignacio CC, Günthard HF, Good B, Smith DM, Wolinsky SM, Furtado M, Marquie-Beck J, Durelle J, Grant I, Richman DD, Marcotte T, McCutchan JA, Ellis RJ, Wong JK. Genetic composition of human immunodeficiency virus type 1 in cerebrospinal fluid and blood without treatment and during failing antiretroviral therapy. Journal of virology. 2005;79(3):1772-88. doi: 10.1128/JVI.79.3.1772-1788.2005. PubMed PMID: 15650202.
Smith DM, Richman DD, Little SJ. HIV superinfection. The Journal of infectious diseases. 2005;192(3):438-44. Epub 2005/06/30. doi: 10.1086/431682. PubMed PMID: 15995957.
Frost SDW, Wrin T, Smith DM, Kosakovsky Pond SL, Liu Y, Paxinos E, Chappey C, Galovich J, Beauchaine J, Petropoulos CJ, Little SJ, Richman DD. Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection. Proceedings of the National Academy of Sciences of the United States of America. 2005;102(51):18514-9. Epub 2005/12/09. doi: 10.1073/pnas.0504658102. PubMed PMID: 16339909.
Wong JK, Smith D, Richman D. Chapter 34 – HIV Drug Susceptibility Testing. In: Wormser GP, editor. AIDS and Other Manifestations of HIV Infection (Fourth Edition). San Diego: Academic Press; 2004. p. 883-904.
Richman DD, Little SJ, Smith DM, Wrin T, Petropoulos C, Wong JK. HIV evolution and escape. Trans Am Clin Climatol Assoc. 2004;115:289-303. PMID: 17060974. PubMed PMID: 17060974.
Smith DM, Kingery JD, Wong JK, Ignacio CC, Richman DD, Little SJ. The prostate as a reservoir for HIV-1. AIDS (London, England). 2004;18(11):1600-2. doi: 10.1097/01.aids.0000131364.60081.01. PubMed PMID: 15238781.
Smith DM, Wong JK, Hightower GK, Ignacio CC, Koelsch KK, Daar ES, Richman DD, Little SJ. Incidence of HIV superinfection following primary infection. JAMA. 2004;292(10):1177-8. doi: 10.1001/jama.292.10.1177. PubMed PMID: 15353529.
Koelsch KK, Smith DM, Little SJ, Ignacio CC, Macaranas TR, Brown AJ, Petropoulos CJ, Richman DD, Wong JK. Clade B HIV-1 superinfection with wild-type virus after primary infection with drug-resistant clade B virus. AIDS (London, England). 2003;17(7):F11-F6. doi: 10.1097/00002030-200305020-00001. PubMed PMID: 12700477.
Smith D, Koelsch K, Wong J, Hightower G, Ignacio C, Richman D, Little S, editors. Male genital tract compartmentalization and transmission of 215L revertant. Antiviral Therapy; 2003: Int Medical Press Ltd 2-4 Idol Lane, London EC3R 5DD, England.
Mackowiak PA, Chardos JF, Smith D. Demyelinating Encephalitis. Clinical infectious diseases. 2003;36(10):1332-4. doi: 10.1086/374893.
Strain MC, Günthard HF, Havlir DV, Ignacio CC, Smith DM, Leigh-Brown AJ, Macaranas TR, Lam RY, Daly OA, Fischer M, Opravil M, Levine H, Bacheler L, Spina CA, Richman DD, Wong JK. Heterogeneous clearance rates of long-lived lymphocytes infected with HIV: intrinsic stability predicts lifelong persistence. Proceedings of the National Academy of Sciences of the United States of America. 2003;100(8):4819-24. Epub 2003/04/08. doi: 10.1073/pnas.0736332100. PubMed PMID: 12684537.
Smith D, Bannykh S, Ziegler E. A woman kicked in the head by a horse. Infectious Diseases in Clinical Practice. 2002;11(1):28-9.
Smith D, Wong J. Continue antiretroviral therapy during virologic failure? Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2002;34(4):553-6. doi: 10.1086/338017. PubMed PMID: 11797186.
Rought S, Sasik R, Smith D, Corbeil J. Chipping Away at HIV Pathogenesis. In: Shaw Kj, editor. Pathogen Genomics. Totowa, New Jersey: Humana Press Inc; 2002. p. 13-24.
Smith D, Metzgar D, Wills C, Fierer J. Fatal Saccharomyces cerevisiae aortic graft infection. J Clin Microbiol. 2002;40(7):2691-2. doi: 10.1128/jcm.40.7.2691-2692.2002. PubMed PMID: 12089311.
Smith D, Letendre S. Viral pneumonia as a serious complication of etanercept therapy. Ann Intern Med. 2002;136(2):174-. doi: 10.7326/0003-4819-136-2-200201150-00020. PubMed PMID: 11790076.
Smith DM, Rickman LS. Echinococcosis: A Drop of Water—Review on Human Disease, Diagnosis, and Management. Infectious Diseases in Clinical Practice. 2001;10(7):355-9. DOI: 10.1097/00019048-200109000-00003.
Smith DM, Ziegler EJ, Rickman LS. Primary Meningococcal Polyarthritis, Cellulitis, and Pneumonia in an Elderly, Immunocompetent Woman. Infectious Diseases in Clinical Practice. 1999;8(4):215-8.