For a complete list of publications, see Julie Overbaugh’s NCBI bibliography.
Select Publications (past ten years):
Depierreux DM, Ruiz F, Lilly M, Guenthoer J, Chohan V, Overbaugh J. Determinants of Natural Killer Cell-Mediated Antibody Dependent Cellular Cytotoxicity in SARS-CoV-2 Antibodies. PLoS Pathogens, 22(3),e1014026, 2026.
Lilly M, Ruiz F, Foreman W, Chohan V, Guenthoer J, Depierreux DM, Baharani, V, Ralph D, Harteloo A, Chu H, Bieniasz P, Starr T, Overbaugh J. Re-infection with SARS-CoV-2 is associated with increased antibody breadth and potency against diverse sarbecovirus strains. mBio, 17(4),e03612-25, 2026.
Chen C, Lovendahl KN, Overbaugh J. Lee KK. Interprotomer crosstalk in mosaic viral glycoprotein trimers provides insight into polyvalent immunogen co-assembly. PLoS Pathogens, 21(9):e1013143, 2025.
Willcox AC, Gobillot TA, Kikawa C, Baumgarten NE, Stoddard CI, Sung K, Bhattacharya T, Freeman TS, Marceau J, Humes D, Overbaugh J. Identification of AMOTL2 as an antiviral factor that enhances the type I interferon response against Zika virus. PNAS, 122(36):e2507955122, 2025.
Pearson RA, Krish KN, Whatney WE, Jaoko W, Overbaugh J, Graham SM, McClelland RS, Hicks SL, Maurer J, Scharer CD, Day CL. Single-cell transcriptomics reveals depletion and dysregulation of Mycobacterium tuberculosis-specific Th1 and Th17 cells early after acquision of HIV. J. Infect. Dis 232(4):835-846, 2025.
Reeves DB, Litchford M, Fish CS, Farrell-Sherman A, Poindexter M, Ahmed N, Cassidy NAJ, Neary J, Wamalwa D, Langat A, Chebet D, Moraa H, Antar AAR, Slyker J, Benki-Nugent S, Cohn LB, Schiffer JT, Overbaugh J, John-Stewart G, Lehman DA. Intact HIV DNA decays in children with and without complete viral suppression. PLoS Pathogens 21 (4), e1013003, 2025.
Kwendakwema CN, Sabo MC, Roberts ST, Masese L, McClelland RC, Shafi J, Lehman DA, Overbaugh J, Graham SM. Sexual violence, genital cytokines, and colposcopy findings: A cross-sectional study of women engaged in sex work in Mombasa, Kenya. Sexually Trasnmitted Diseases, 52:39-36, 2025.
Ruiz F, Foreman W, Lilly M, Baharani VA, Depierreux DM, Chohan V, Taylor A, Guentoer J, Ralph D, Matsen EA IV, Chu HY, Bieniasz P, Cote M, Starr TN, Overbaugh J. Delineating the functional activity of antibodies with cross- reactivity to SARS-CoV-2, SARS-CoV-1 and related sarbecoviruses. PLoS Pathogens 20(10), e1012650, 2024.
Guenthoer J, Garrett ME, Lilly M, Deprierreux DM, Ruiz F, Chi M, Stoddard CS, Chohan V, Sung K, Ralph D, Chu HY, Matsen FA IV, Overbaugh J. The S2 subunit of spike encodes diverse targets for functional antibody responses to SARS-CoV-2, PLoS Pathogens, 20(8): e1012383, 2024.
Itell HL, Guenthoer J, Humes D, Baumgarten NE, Overbaugh J. Host cell glycosylation selects for infection with CCR5-versus CXCR4-tropic HIV-1. Nature Microbiology, 9: 2985-2996, 2024.
Wilks AJ, Marceau JO, Kazer SW, Fleming I, Miao VN, Galvez-Reyes J, Shalek AK, Holmes S, Kimata J, Overbaugh J, Blish CA. Pro-inflammatory feedback loops define immune responses to pathogenic lentivirus infection. Genome Medicine16 (1): 24, 2024. (bioRxiv. 533358).
Neary J, Nijuguna I, Wagner AD, Richardson BA, Chebet D, Langat A, Ngugi E, Benki-Nugent S, Moraa H, Hawes S, Overbaugh J, Lehman DA, Wamalwa D, John-Stewart G. Group-based trajectory modeling to determine long-term viral load trends among children with HIV in Kenya. JAIDS, 96:311-317, 2024.
Russel ML, Fish CS, Drescher S, Cassidy NAJ, Chanana P, Benki-Nugent S, Slyker J, Ngacha DM, Bosire R, Richardson B, Walmalwa D, Obimbo EM, Overbaugh J, John-Stewart G, Matsen FA, Lehman DA. Using viral sequence diversity to estimate time of HIV infection in infants. PLoS Pathogens 19 (12): e1011861, 2023.
Itell HL, Humes D, Overbaugh J. Several cell-intrinsic effectors drive type I interferon-mediated restriction of HIV-1 in primary CD4+ T cells. Cell Reports 42(6):112556, 2023.
Stoddard CI, Sung K, Yaffe ZA, Weight H, Beaudon-Bussieres G, Galloway JG, Gantt S, Achiambo J, Bengel ER, Ojee E, Slyker J, Wamalwa D, Kinuthia J, Finzi A, Matsen FA IV, Lehman DA, Overbaugh J. Elevated binding and functional antibody responses to SARS-CoV-2 in infants versus mothers. Nature Communications 14 (1), 4864, 2023.
Yaffe ZA, Sung K, Bosire R, Farquhar C, Ngacha DM, Lohman-Payne B, Nduati R, John-Stewart G, Matsen FA, Overbaugh J. Passively-acquired C5-specific antibodies are associated with improved survival in infants who acquire HIV. Open Forum Infectious Diseases ofad316, 2023.
Radford CE, Schommers P, Gieselmann L, Crawford KHD, Dadonaite B, Yu TC, Dingens AS, Overbaugh J, Klein F, Bloom JD. Mapping the neutralizing specificty of human anti-HIV serum by deep mutational scanning. Cell Host and Microbe, 31, 1-16, 2023.
Guenthoer J, Lilly M, Starr TN, Dadonaite B, Lovendahl KN, Croft JT, Stoddard CS, Chohan V, Ding S, Ruiz F, Kopp MS, Finzi A, Bloom JD, Chu HY, Lee KK, Overbaugh J. Identification of broad and potent antibodies to functionally contrained regions of SARS-CoV-2 spike following a breakthrough infection. PNAS 120 (23) e2220938120, 2023.
Yaffe ZA, Ding S, Sung K, Chohan V, Marchitto L, Doepker L, Ralph D, Nduati R, Matsen FA, Finzi A, Overbaugh J. Reconstruction of a polyclonal ADCC antibody repertoire from an HIV-1 non-transmitted mother. iScience 26 (5) 2023.
Stoddard CI, Sung K, Ojee E, Achiambo J, Bengel ER, Slyker J,Gantt S, Matsen FA IV, Kinuthia J, Wamalwa D, Overbaugh J, Lehman DA. Distinct antibody responses to endemic coronaviruses pre- and post-SARS-CoV-2 infection in Kenyan infants and mothers. Viruses 14 (7) 1514, 2022.
Willcox, AC, Sung K, Garrett ME, Galloway, Erasmus JE, Logue JK, Hawman DW, Chu HY, Hasenkrug KJ, Fuller DH, Matsen FA, Overbaugh J. Macaque-human differences in SARS-CoV-2 Spike antibody response elicited by vaccination or infection. PLoS Pathog., 18 (4), e1010155, 2022.
Garrett ME, Galloway J, Wolf CR, Logue JK, Franko N, Chu HY, Matsen FA, Overbaugh J. Comprehensive characterization of the antibody responses to SARS-CoV-2 Spike protein after infection and/or vaccination. eLife. 11:e73490, 2022.
Itell HL, Weight H, Fish CS, Logue JK, Franko N, Wolf CR, McCulloch DJ, Galloway J, Matsen FA, Chu HY, Overbaugh J. SARS-CoV-2 Antibody Binding and Neutralization in Dried Blood Spot Eluates and Paired Plasma. Microbiol Spectr. 9(2):e0129821, 2021.
Simonich C, Shipley MM, Doepker L, Gobillot T, Garrett ME, Cale EM, Hennessy B, Itell H, Chohan V, Doria-Rose N, Nduati R, Overbaugh J. A diverse collection of B cells responded to HIV infection in infant BG505. Cell Rep Med. 10: e64281, 2021.
Yaffe Z, Naimen NE, Slyker J, Wines BD, Richardson BA, Bosire R, Farquhar C, Ngacha M, Nduati R, John-Stewart G, Overbaugh J. Improved HIV-infected infant survival is correlated with high levels of HIV-specific ADCC activity in multiple cohorts. Cell Rep Med. 20;2(4), 2021.
Stoddard CI, Galloway J, Chu H, Itell HL, Shipley MM, Wolf C, Logue J, Magedson A, Sung K, Garrett M, Matsen FA, Overbaugh J. Viral proteome-wide epitope profiling reveals binding signatures of SARS-CoV-2 immune response and cross-reactivity with endemic human coronaviruses. Cell Rep.35(8):109164 , 2021.
Shipley MM, Prasad VM, Doepker LE, Dingens A, Ralph D, Harkins E, Dhar A, Arenz D, Chohan V, Weight H, Mandaliya K, Bloom JD, Matsen FA, Lee KK, Overbaugh J. Functional development of a V3/glycan-specific broadly neutralizing antibody isolated from a case of HIV superinfection. eLife. 10:e68110, 2021.
Garrett ME, Galloway J, Chu HY, …, Weight, H, Matsen FA, Overbaugh J. High-resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies. Cell. 184:2927-2938, 2021.
Dingens A, Pratap P, Malone K, Hilton SK, Ketas T, Cottrell CA, Overbaugh J, Moore JP, Klasse PJ, Ward AB, Bloom JD. High-resolution mapping of the neutralizing and binding specificities of polyclonal sera post-HIV Env trimer vaccination. Elife. 10: e64281, 2021.
Doepker LE, Danon S, Harkins E, Ralph D, Yaffe Z, Dhar Amrit, Wagner C, Stumpf M, Arenz A, Williams JA, Lee KK, Matsen FA, Overbaugh J. Development of antibody-dependent cell cytotoxicity function in HIV-1 antibodies. Elife. 2021 Jan 11;10:e63444.
Humes D, Rainwater, S, Overbaugh J. TOP vector: a new high-titer lentiviral construct for delivery of sgRNAs and transgenes to primary T-cells. Molecular Therapy: Methods and Clinical Development Mol Ther Methods Clin Dev. 2020 Oct 27;20:30-38.
Garrett ME, Itell HL, Crawford K, Basom R, Bloom JD, Overbaugh J. Phage-DMS: a comprehensive method for fine mapping of antibody epitopes. iScience. 2020 Sep 29;23(10):101622.
Gobillot T, Humes D, Sharma A, Kikawa C, Overbaugh J. The robust restriction of Zika virus by type-I Interferon in A549 cells varies by viral lineage and is not determined by IFITM3. Viruses. 2020 May; 12(5):503.
Naiman NE, Slyker J, Nduati R, Overbaugh J. Maternal Envelope gp41 Ectodomain-Specific Antibodies Are Associated With Increased Mother-to-Child Transmission of Human Immunodeficiency Virus-1. J Infect Dis. 2020 Jan 2;221(2):232-237.
Pankau MD, Reeves DB, Harkins E, Ronen K, Jaoko W, Mandaliya K, Graham SM, McClelland RS, Matsen FA, Schiffer JT, Overbuagh J, Lehman DA. Dynamics of HIV DNA reservoir seeding in a cohort of superinfected Kenyan women. PLoS Pathog. 2020 Feb; 16(2): e1008286.
Naiman NE, Slyker J, Richardson BA, John-Stewart G, Nduati R, Overbaugh J. Antibody-dependent cellular cytotoxicity targeting CD4-inducible epitopes predicts mortality in mother-to-child transmission of HIV-1. EBioMedicine. 2019 Sep;47:257-268.
Doepker L, Simonich C, Duncan R, Gobillot T, Garrett M, Vigdorovich V, Sather DN, Nduati R, Matsen FA, Overbaugh J. Diversity and function of maternal HIV-1-specific antibodies at time of vertical transmission. J Virol. Feb 19 2020. Pii: JVI.01594-19. Epub ahead of print. PMID 32075936.
Sharma A, McLaughlin RN, Basom RS, OhAinle M, Kikawa C, Yount JS, Emerman M, Overbugh J. Macaque IFITMs limit replication of SHIVs derived from circulating HIV-1 in an Envelope-dependent manner. PLoS Pathogens. 2019 Jul; 15(7): e1007925. doi: 10.1371/journal.ppat.1007925.
Gobillot T, Kikawa C, Lehman D, Kinuthia J, Drake A, Jaoko W, Mandaliya K, John-Stewart G, McClelland RS, Overbaugh J. Zika virus circulates at low levels in Western and Coastal Kenya. J Infect Dis. 2020 Apr 3. pii: jiaa158. doi: 10.1093/infdis/jiaa158. Epub ahead of print.
Simonich CA,, Doepker LN, Ralph D, Williams JA, Dhar A, Yaffe Z, Gentles L, Small CT, Oliver B, Vigdorovich V, Prasad VM, Nduati R, Sather DN, Lee KK, Matsen FA, Overbaugh J. Rapid development of an infant-derived HIV-1 broadly neutralizing antibody lineage. Nature Communication, 10: article 2190, 2019.
Williams KL, Stumpf M, Naiman N, Ding S, Garrett M, Gobillot T, Vezina D, Dusenbury K, Ramadoss NS, Basom R, Kim PS, Finzi A, Overbaugh J. Identification of HIV gp41-specific antibodies that mediate killing of infected cells. PLoS Pathog. 2019 Feb 19;15(2):e1007572.
Dingens AS, Arenz D, Weight H, Overbaugh J, Bloom JD. An antigenic atlas of HIV-1 escape from broadly neutralizing antibodies. Immunity. 2019 Feb 19;50(2):520-532.e3.
Ohainle M, Pendergast L, Vermeire J, Roesch F, Humes D, Basom R, Delrow J, Overbaugh J, Emerman M. A Virus-Packageable CRISPR Screen Identities Host Factors Mediating Interferon Inhibition of HIV. eLife, 7:e39823, 2018.
McClelland RS, Lingappa JR, Srinivasan S, Kinuthia J, John-Stewart GC, Jaoko W, Richardson BA, Yuhas K, Fiedler TL, Mandaliya KN, Munch MM, Mugo NR, Cohen CR, Baeten JM, Celum C, Overbaugh J, Fredricks DN. Evaluation of the association between the concentrations of key vaginal bacteria and the increased risk of HIV acquisition in African women from five cohorts: a nested case-control study. Lancet Infect Dis, 18(5):554-564, 2018.
Williams KL, Wang B, Arenz D, Williams JA, Dingens AS, Cortez V, Simonich CA, Lehman DA, Rainwater S, Lee KK, Overbaugh J. Superinfection drives HIV neutralizing antibody responses from several B cell lineages that contribute to a polyclonal response. Cell Reports, 23(3):682-691, 2018.
Dingens AS, Haddox HK, Overbaugh J, Bloom JD. Comprehensive Mapping of HIV-1 Escape from Broadly Neutralizing Antibody. Cell Host & Microbe, 21(6): 777-787, 2017.
Ronen K, Dingens AS, Graham SM, Jaoko W, Mandaliya K, McClelland RS, Overbaugh J. Comprehensive Characterization of Humoral Correlates of Human Immunodeficiency Virus 1 Superinfection Acquisition in High-Risk Kenyan Women. EBioMedicine, 18, 216-244, 2017.
Boyd DF, Sharma A, Humes D, Cheng-Mayer C and Overbaugh J. Adapting SHIVs in vivo selects for Envelope-mediated Interferon- resistance. PLos Pathogens 12(7): e1005727, 2016.
Simonich CA, Williams KL, Verkerke HP, Williams JA, Nduati R, Lee KK and Overbaugh J. HIV-1 neutralizing antibodies with limited hypermuation from an infant. Cell, 166:77-87, 2016.
Milligan C, Omenda MM, Chohan V, Odem-Davis K, Richardson BA, Nduati R and Overbaugh J. Maternal neutralization-resistant virus variants do not predict infant HIV infection risk. mBio 7, 2016.
Select Recent Reviews and Commentaries
Yaffe Z, Overbaugh J. HIV-1 protection: Antibodies move in for the kill. Cell Rep Med, in press, 2021.
Overbaugh J. Understanding protection from SARS-CoV-2 reinfection. Nature Med, 26, 1680-1681. Nat Med. 2020 Nov;26(11):1680-1681
Clynes M, Corbett A, Overbaugh J. Why we need good mentoring. Nature Reviews Cancer, in press, 2019.
Overbaugh J. Defining the barriers to women publishing in high-impact journals. J Virol, 92(7), 2018.
Overbaugh J. Gender Bias: track revisions and appeals. Nature: 543: 40, 2017.
Ronen K, Sharma A, Overbaugh J. HIV transmission biology: translation for HIV prevention. AIDS 29: 2219-2227, 2015
Overbaugh, J. Mother-Infant HIV Transmission: Do maternal HIV-specific antibodies protect the infant? PLoS Pathogens 10:e1004283, 2014.
Overbaugh J. 24/7 isn’t the only way: A healthy work-life balance can enhance research. Nature 477(7362): 27-28, 2011.