Previous Summer Internship Projects
Summer 2023
| Project |
Intern |
School |
PI |
Quantitative mentors |
| Single cell transcriptomic analysis of broadly neutralizing B cells in humans |
Mohammad Samsul Alam |
NCSU |
Kevin Wiehe |
Lynn Lin |
| Predicting FcR function from antibody glycosylation profiles |
Ellie Anderson |
DUKE |
Daniel Schuster |
Lynn Lin |
| HIV disclosure across social network ties of adolescents with HIV in Cape Town, South Africa |
Mark Austin |
NCSU |
Marta Mulawa |
Ricahrd Barfield |
| Determinants associated with retention and re-engagement in HIV pre-exposure prophylaxis (PrEP) care at Duke and Lincoln Health Center |
Evan Chenault |
DUKE |
Naseem Alavian |
Tina Davenport |
| Development of a predictive model (and scoring system) for Tm antigenemia to make screening program more efficient/cost effective using a prospective Tm antigen screening cohort N=500 |
Jose Singer-Freeman |
NCSU |
Thuy Le |
Lynn Lin |
| Deep learning to explore the effect of cannabis use in people with HIV based on connectomic features of multimodal MRI brain images |
Xin Gai |
DUKE |
Christina Meade |
Anru Zhang |
| Mathematical modeling of binding kinetics for a mixture of monoclonal HIV-1 antibodies to a heterogeneous bivalent epitope |
Hui Huang |
DUKE |
Moses Sekaran |
Janice McCarthy |
| Optimal selection of antibody combinations |
Jinting (Justin) Liu |
DUKE |
Guido Ferrari |
Janice McCarthy |
| Associations between human antibody/FcR genetic variation and vaccine-elicited immune responses |
Song Young Oh |
DUKE |
Justin Pollara |
Cliburn Chan |
| Parameter selection and model analysis of a non-autonomous ordinary differential equation model of antibody neutralization in acute HIV infection |
Xin Tan |
DUKE |
|
Janice McCarthy |
| Exploring relationship between gene expression and TCR sequence similarities using single-cell RNA- and TCR-seq data from HIV and other diseases |
Hao Wang |
DUKE |
|
Jason Ji |
| Metabolic perturbations during acute and chronic SIV infection in rhesus macaques |
Peng Wu |
DUKE |
Keith Reeves |
Pixu Shi |
| Comparative single cell analysis of brain tissue in wild type and osteopontin KO mice as a model for cryptococcal fungal infection during immune reconstitution inflammatory syndrome (IRIS) |
Jae Yong |
NCSU |
Mari Shinohara |
Josh Granek |
Summer 2022
| Project |
Intern |
School |
PI |
Quantitative mentors |
| Dimension reduction of longitudinal microbiome data associated with HIV infection |
Mohammad Samsul Alam |
NCSU |
Pixu Shi |
Pixu Shi, Josh Granek |
| Patient-level determinants associated with re-engagement in HIV care at Duke |
Andrea Carmack |
UNC |
Lance Okeke |
Tina Davenport, Pixu Shi |
| High-dimensional flow cytometry bioinformatics |
Jingya Cheng |
Duke |
Cliburn Chan |
Cliburn Chan |
| Mathematical modeling of acute HIV-1 infection and the effect of gp41-antibody on viral infectivity in RV217 cohort |
Yuqing Dai |
Duke |
Georgia Tomaras |
Janice McCarthy, Cliburn Chan |
| Mapping flow cytometry data across EQAPOL laboratories using the Minimized Aggregated Wasserstein (MAW) distance |
Dana Droz |
NCSU |
Guido Ferrari |
Lynn Lin, Cliburn Chan |
| Development of a prediction model and a scoring algorithm for Talaromyces antigen positivity in patients with advanced HIV disease |
Orlando Ferrer |
Duke |
Thuy Le |
Lynn Lin, Tina Davenport |
| Healthcare utilization among participants of the EXTRA-CVD trial: Does having a nurse coordinating managing CVD risk decrease overall care utilization in persons living with HIV |
Mahmoud Harding |
NCSU |
Lance Okeke |
Tina Davenport, Pixu Shi |
| To design and test in vitro the best combinations of monoclonal antibodies that can be used to prevent and/or treat HIV-1 infection. |
Shabaz Khan |
Duke |
Guido Ferrari |
Janice McCarthy, Cliburn Chan |
| Analysis of serial quantitative Talaromyces antigen in the IVAP trial to determine whether antigen clearance dynamics is correlated with mortality and disease relapse |
Grace Kovic |
Duke |
Thuy Le |
Tina Davenport, Pixu Shi |
| Modeling multivalent and polyclonal antibody kinetics in multiplexed assays of antibody binding kinetics |
Kyle Nguyen |
NCSU |
Moses Sekaran |
Janice McCarthy, Lynn Lin |
| Interpretable dimension reduction for pseudo-time trajectories |
Yiren Shao |
Duke |
Cliburn Chan |
Cliburn Chan, Janice McCarthy |
| Longitudinal changes in neurocognitive performance related to HIV disease and drug use intensity |
Runshi Tang |
University of Wisconsin |
Christina Meade |
Anru Zhang, Cliburn Chan |
| Optimizing the design of HIV testing policies using stated preferences: Can machine learning yield better predictions from Discrete Choice Experiments than traditional inferential statistics? |
Tengjie Tang |
Duke |
Nathan Thielman |
Ethan, Cliburn Chan |
| Mathematical modeling of antigen binding parameters and strength of B cell activation |
Eric Zhang |
UNC |
Munir Alam |
Cliburn Chan, Janice McCarthy |
| To determine and compare underlying reasons for hypertension and hyperlipidemia medication nonadherence for PLWH; identify corelates of blood pressure control for PLWH |
Tiya Zhang |
Duke |
Charles Muiruri |
Lynn Lin, Tina Davenport |
Summer 2021
| Project |
Intern |
School |
PI |
Quantitative mentors |
| Vaccine Responses in HIV-Exposed, Uninfected and HIV-Unexposed, Uninfected Infants in Botswana |
Noel Allen |
Duke |
Matt Kelly |
Matt Kelly |
| Analysis of serial quantitative Talaromyces antigen in the IVAP trial to determine whether antigen clearance dynamics is correlated with treatment outcomes |
Danielle Baldwin |
NCSU |
Thuy Le |
Tina Davenport |
| Modeling the cellular and humoral determinants of time to rebound after treatment interruption in infant Rhesus macaques |
Ellie Mainou |
Penn State |
Genevieve Fouda Amouou |
Janice McCarthy |
| Modeling viral and immune determinants of vertical CMV transmission in HIV-infected CMV-seropositive mothers |
Yishu Gong |
Duke |
Sallie Permar |
Cliburn Chan |
| Immunologic and virologic factors that predict vertical CMV transmission in seronegative rhesus monkeys |
Julian Sass |
NCSU |
Sallie Permar |
Janice McCarthy |
| Analysis of IgG pharmacokinetics and pharmacodynamics (PK/PD) in a passive immunization challenge study of infant Rhesus macaques |
Yvonne Niyonzima |
NCSU |
Genevieve Fouda Amouou |
Pixu Shi |
| Modeling and analysis of Fc-FcR interactions and its role in vaccine immunogenicity and efficacy |
Shakthi Unnithan |
NCSU |
Justin Pollara |
Josh Granek |
| Bioinformatics and statistical analysis of the polyfunctional anti-viral vaccine-induced responses |
Pu Zeng |
Duke |
Guido Ferrari |
Cliburn Chan |
| Bayesian reanalysis of latent tuberculosis treatment trials with decision analysis to optimize treatment decisions |
Saahithi Rao |
Duke |
Jason Stout |
Pixu Shi |
| Machine learning for structural and functional MRI connectome data in patients with HIV |
Chen An |
Duke |
Christina Meade |
Anru Zhang |
| Modeling multivalent and polyclonal antibody kinetics in multiplexed assays of antibody binding kinetics |
Kyle Nguyen |
NCSU |
Moses Sekaran |
Janice McCarthy |
| Bioinformatics analysis of high-dimensional flow cytometry data from blood and CSF of people with HIV who use marijuana or cocaine |
Zhicheng Guo |
Duke |
David Murdoch |
Cliburn Chan |
| A highly conserved gut microbial environment is associated with increased risk of postnatal HIV infection in infants |
Danting Jiang |
Duke |
Neil Surana |
Neil Surana |
| Discovery of hidden low-rank structure from high-dimensional tensor data from cryo-EM images |
Chenyin Gao |
NCSU |
Priyamvada Acharya |
Anru Zhang |
Summer 2020
| Project |
Intern |
School |
PI |
Quantitative mentors |
| Examining Structural Barriers to Optimal HIV Care Engagement: Is Neighborhood of Residence a Risk Factor for HIV Patient Atrition? |
Felipe Montano-Campos |
Duke |
Lance Okeke, Jason Stout |
Jason Stout |
| Developing a Predictive Model for HIV Clinical Care Disengagement at Duke |
Monica Borges |
UNC |
Lance Okeke |
Cliburn Chan |
| Persistent Elevation of Liver Transaminases Following HCV Virologic Cure Among HCV Mono-infected and HIV/HCV Co-infected Adults |
Hayley Nemeth |
Duke |
Susanna Naggie |
Tina Davenport |
| Defining the role of immune heterogeneity and preexisting CMV immunity in protective HIV-1 vaccination through systems vaccinology |
Hira Anees Awan |
Duke |
Georgia Tomaras (Cesar Lopez Angel) |
Janice McCarthy |
| Deep learning to predict HIV-associated neurocognitive impairment based on graph features of multimodal MRI brain images |
Yvonne Niyonzima |
NCSU |
Christina Meade (Yunan Xu) |
Cliburn Chan, John Pearson |
| Impact of Maternal HIV Infection on the Respiratory Microbiome of Infants |
Yahe Yu |
NCSU |
Matt Kelly |
Josh Granek |
| Mathematical modeling to predict time to HIV rebound from viral reservoir size after treatment interruption in postnatally infected infant rhesus macaques |
Safa Janajra |
Duke |
Sallie Permar (Ria Goswami) |
Cliburn Chan |
| Mathematical and statistical modeling of HIV rebound dynamics following treatment interruption in infant macaques |
Fan Bu |
Duke |
Sallie Permar |
Cliburn Chan |
| Disparities in viral load and CD4 count trends among HIV infected children in South Carolina |
Courtney Jacks |
NCCU |
Rishi Chakraborty |
Rishi Chakraborty |
| Modeling Pharmacokinetics and Pharmacodynamics of Topical Anti-HIV Products and Translation of this Framework into Rational Product Design |
Machao Deng |
Duke |
David Katz |
Cliburn Chan |
| Validation of biomarkers for estimating HIV-1 incidence |
Dena Ho |
Duke |
Georgia Tomaras (Rachel Spreng) |
Janice McCarthy |
| Mathematical and statistical modeling of HIV rebound dynamics following treatment interruption in infant macaques |
Julian Sass |
NCSU |
Sallie Permar |
Cliburn Chan |
| Mathematical modeling to predict time to HIV rebound from viral reservoir size after treatment interruption in postnatally infected infant rhesus macaques |
Ellie Mainou |
Penn St |
Sallie Permar (Ria Goswami) |
Cliburn Chan |
| Modeling vertical transmission of CMV |
Yishu Gong |
Duke |
Salie Permar |
Cliburn Chan |
Summer 2019
| Project |
Intern |
School |
PI |
Quantitative mentors |
| Longitudinal data analysis of a group-based mental health intervention for adolescents living with HIV in Tanzania |
Ashley Zhao |
Duke |
Dorothy Dow (John Gallis) |
Tuner/Davenport |
| Mathematical modeling of HIV rebound dynamics following treatment interruption in infant macaques |
Julian Sass |
NCSU |
Sallie Permar (Ria Goswami) |
McCarthy/Chan |
| Structural basis for broad and potent HIV-1 neutralization |
Shana M. McDowell |
NCCU |
Priyamvada Acharya |
McCarthy/Granek |
| Development of a prognostic scoring system for HIV-associated Talaromycosis |
Jonathan K. Klus |
Duke |
Thuy Le |
Davenport/Chan |
| Estimating diversity in the naïve B cell repertoire |
Yiwei Gong |
Duke |
Kevin Wiehe |
Granek/Chan |
| Multidimensional immune profiling in HIV-associated neuroinflammation |
Yishu Gong |
Duke |
David Murdoch |
Chan/Granek |
| Modeling the cost-effectiveness of a crowdsourced intervention to prevent HIV transmission among Chinese gay men |
Xuan Liu |
NCSU |
Tucker, Joseph D |
Kate Mitchell |
| Individualized prediction of HIV-associated neurocognitive impairment using machine learning techniques |
Yizi Lin |
Duke |
Christina Meade |
Pearson/Chan |
| Applying cutting-edge methods to generalize findings from randomized clinical trials to a target population in routine HIV care |
Steven Xu |
NCSU |
Brian Pence, Katie Mollan, Angie Bengtson |
Stephen R Cole, Issa Dahabreh |
| A highly conserved gut microbial environment is associated with increased risk of postnatal HIV infection in infants |
LaTricha Parks |
St. Augustine |
Sallie Permar |
Chan/Granek |
