Quantitative Methods for HIV/AIDS Research

R25 AI140495

Dr. Cliburn Chan is the PI of a five year NIAID research education grant to provide training in quantitative methods for HIV/AIDS research.  With recent technological advances, HIV/AIDS research is generating increasingly large and complex data sets. Given the data complexity, major HIV/AIDS research projects must adopt a multi-disciplinary team science approach.  While HIV/AIDS researchers must to understand the data science and statistical analysis challenges associated with large data sets; statistical, computational and mathematical researchers also need to understand the challenges specific to HIV/AIDS research. 

The training program directly addresses those needs and is comprised of a series of workshops for HIV/AIDS researchers in Data Science, Statistical Thinking, and Multi-parameter Assay Analysis, together with a summer internship program. The internship program will fund 12 graduate students in quantitative disciplines such as Biostatistics, Data Science, Statistics, Computer Science, Mathematics and Engineering to work with leading researchers at Duke and UNC Chapel Hill on challenging problems in HIV/AIDS. Combined, the workshops and internships will build a cadre of HIV/AIDS and quantitative scientists able to effectively bridge disciplinary communication barriers, and form effective and productive collaborative partnerships.

Faculty and staff leading this research education program are Cliburn Chan, Josh Granek, Tina Davenport, Janice McCarthy, Lynn Lin and Kouros Owzar and the Duke Center for AIDS Research (CFAR).  Please contact cliburn.chan@duke.edu for more information about opportunities to participate.



Publications from the Quantitative Methods for HIV/AIDS Research Program

Year Title Authors Citation PMID PMCID
2023 Longitudinal changes in neurocognitive performance related to drug use intensity in a sample of persons with and without HIV who use illicit stimulants Towe, Sheri L; Tang, Runshi; Gibson, Matthew J; Zhang, Anru R; Meade, Christina S Drug Alcohol Depend. 2023 Oct 1;251:110923. doi: 10.1016/j.drugalcdep.2023.110923. Epub 2023 Aug 9. 37598454 PMC10538396
2023 Assessing the impact of autologous neutralizing antibodies on viral rebound in postnatally SHIV-infected ART-treated infant rhesus macaques Mainou, Ellie; Berendam, Stella J; Obregon-Perko, Veronica; Uffman, Emilie A; Phan, Caroline T; Shaw, George M; Bar, Katherine J; Kumar, Mithra R; Fray, Emily J; Siliciano, Janet M; Siliciano, Robert F; Silvestri, Guido; Permar, Sallie R; Fouda, Genevieve G; McCarthy, Janice; Chahroudi, Ann; Conway, Jessica M; Chan, Cliburn bioRxiv. 2023 Sep 14:2023.07.22.550159. doi: 10.1101/2023.07.22.550159. Preprint. 37502921 PMC10370170
2023 A simple model for viral decay dynamics and the distribution of infected cell life spans in SHIV-infected infant rhesus macaques Sass J, Awasthi A, Obregon-Perko V, McCarthy J, Lloyd AL, Chahroudi A, Permar S, Chan C. Math Biosci. 2023 Feb;356:108958. doi: 10.1016/j.mbs.2022.108958. Epub 2022 Dec 22. 36567003 PMC9918703
2022 Comparing the effectiveness of secondary distribution of HIV/syphilis dual self-testing to testing card referral in promoting HIV testing among gay, bisexual, and other men who have sex with men in Guangzhou, China: a quasi-experimental study Sha, Yongjie; Xiong, Yuan; Ong, Jason J; Wang, Yehua; Cheng, Mengyuan; Ni, Yuxin; Lu, Ying; Tucker, Joseph D; Tang, Weiming Sex Health. 2022 Aug;19(4):357-366. doi: 10.1071/SH21176. 35614024  
2022 Understanding Retention in Pre-Exposure Prophylaxis Care in the South: Insights from an Academic HIV Prevention Clinic Burns CM, Borges M, Frye J, Keicher K, Elliott S, Schwartz S, Shipp K, Okeke NL, McKellar MS. AIDS Res Hum Retroviruses. 2022 Apr;38(4):306-312. doi: 10.1089/AID.2021.0177. 35172632 PMC9048170
2022 Monetary incentives and peer referral in promoting secondary distribution of HIV self-testing among men who have sex with men in China: A randomized controlled trial Zhou Y, Lu Y, Ni Y, Wu D, He X, Ong JJ, Tucker JD, Sylvia SY, Jing F, Li X, Huang S, Shen G, Xu C, Xiong Y, Sha Y, Cheng M, Xu J, Jiang H, Dai W, Huang L, Zou F, Wang C, Yang B, Mei W, Tang W. PLoS Med. 2022 Feb 14;19(2):e1003928. doi: 10.1371/journal.pmed.1003928. eCollection 2022 Feb. 35157727 PMC8887971
2022 Kinetics of pneumococcal antibodies among HIV-exposed, uninfected infants in Botswana Uffman EA, Li SH, Chen JL, Allen N, Boiditswe S, Fouda GG, Hurst JH, Patel MZ, Steenhoff AP, Cunningham CK, Qin E, Davenport CA, Kelly MS. Vaccine. 2022 Jun 27:S0264-410X(22)00828-3. doi: 10.1016/j.vaccine.2022.06.059. Online ahead of print. 35773120  
2021 Gender minority stress and access to health care services among transgender women and transfeminine people: results from a cross-sectional study in China Sha, Yongjie; Dong, Willa; Tang, Weiming; Zheng, Lingling; Huang, Xi; Muessig, Kathryn E; Tucker, Joseph D BMC Infect Dis. 2021 Oct 14;21(1):1065. doi: 10.1186/s12879-021-06782-5. 34649507 PMC8514805
2021 Transportability From Randomized Trials to Clinical Care: On Initial HIV Treatment With Efavirenz and Suicidal Thoughts or Behaviors Mollan KR, Pence BW, Xu S, Edwards JK, Mathews WC, O'Cleirigh C, Crane HM, Eaton EF, Collier AC, Weideman AMK, Westreich D, Cole SR, Tierney C, Bengtson AM; CFAR Network of Integrated Clinical Systems and the AIDS Clinical Trials Group. Am J Epidemiol. 2021 Oct 1;190(10):2075-2084. doi: 10.1093/aje/kwab136. 33972995 PMC8576379
2021 Prognosis and treatment effects of HIV-associated talaromycosis in a real-world patient cohort Klus J, Ly VT, Chan C, Le T. Med Mycol. 2021 Apr 6;59(4):392-399. doi: 10.1093/mmy/myab005. 33644813 PMC8023982
2021 Machine learning prediction of neurocognitive impairment among people with HIV using clinical and multimodal magnetic resonance imaging data Xu Y, Lin Y, Bell RP, Towe SL, Pearson JM, Nadeem T, Chan C, Meade CS. J Neurovirol. 2021 Feb;27(1):1-11. doi: 10.1007/s13365-020-00930-4. Epub 2021 Jan 19. 33464541 PMC8001877
2021 HIV self-testing partially filled the HIV testing gap among men who have sex with men in China during the COVID-19 pandemic: results from an online survey Jiang H, Xie Y, Xiong Y, Zhou Y, Lin K, Yan Y, Tucker J, Ong JJ, Wu D, Yang F, Tang W. J Int AIDS Soc. 2021 May;24(5):e25737. doi: 10.1002/jia2.25737. 34036750 PMC8150052
2020 Simian-Human Immunodeficiency Virus SHIV.C.CH505 Persistence in ART-Suppressed Infant Macaques Is Characterized by Elevated SHIV RNA in the Gut and a High Abundance of Intact SHIV DNA in Naive CD4(+) T Cells Obregon-Perko V, Bricker KM, Mensah G, Uddin F, Kumar MR, Fray EJ, Siliciano RF, Schoof N, Horner A, Mavigner M, Liang S, Vanderford T, Sass J, Chan C, Berendam SJ, Bar KJ, Shaw GM, Silvestri G, Fouda GG, Permar SR, Chahroudi A. J Virol. 2020 Dec 22;95(2):e01669-20. doi: 10.1128/JVI.01669-20. Print 2020 Dec 22. 33087463 PMC7944446