Interferon-mediated viral immunity

Identification of AMOTL2 as an antiviral factor that enhances the human type I interferon response against Zika virus

Willcox AC, Gobillot TA, Kikawa C, Baumgarten NE, Stoddard CI, Sung K, Bhattacharya T, Freeman TS, Marceau J, Humes D, Overbaugh J. PNAS. 2025.

Coronavirus Adaptive Immunity

The S2 subunit of spike encodes diverse targets for functional antibody responses to SARS-CoV-2

Guenthoer J, Garrett ME, Lilly M, Depierreux DM, Ruiz F, Chi M, Stoddard CI, Chohan V, Sung K, Ralph D, Chu HY, Matsen FA, Overbaugh J. PNAS. 2024.

phippery: a software suite for PhIP-seq data analysis

Galloway JG, Sung K, Minot SS, Garrett ME, Stoddard CI, Willcox AC, Yaffe ZA, Yucha R, Overbaugh J, Matsen FA. Bioinformatics. 2023.

Elevated binding and functional antibody responses to SARS-CoV-2 in infants versus mothers

Stoddard CI, Sung K, Yaffe ZA, Weight H, Beaudoin-Bussieres G, Galloway J, Gantt S, Adhiambo J, Begnel ER, Ojee E, Slyker J, Wamalwa D, Kinuthia J, Finzi A, Matsen FA 4th, Lehman DA, Overbaugh J. Nat Comm. 2023.

Identification of broad, potent antibodies to functionally constrained regions of SARS-CoV-2 spike following a breakthrough infection

Guenthoer J, Lilly M, Starr TN, Dadonaite B, Lovendahl KN, Croft JT, Stoddard CI, Chohan V, Ding S, Ruiz F, Kopp MS, Finzi A, Bloom JD, Chu HY, Lee KK, Overbaugh J. PNAS. 2022.

Distinct antibody responses to endemic coronaviruses pre- and post-SARS-CoV-2 infection in Kenyan infants and mothers

Stoddard CI, Sung K, Ojee E, Adhiambo J, Begnel ER, Slyker J, Gantt S, Matsen FA 4th, Kinuthia J, Wamalwa D, Overbaugh J, Lehman DA. Viruses. 2022.

Epitope profiling reveals binding signatures of SARS-CoV-2 immune response and cross-reactivity with endemic HCoVs

Stoddard CI, Galloway J, Chu HY, Shipley MM, Itell HI, Wolf CR, Logue JK, Magedson A, Sung K, Garrett M, Crawford KHD, Laserson U, Matsen IV FA, Overbaugh J. Cell Rep. 2021.

High resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies

Garrett ME, Galloway J, Chu HY, Itell HL, Stoddard CI, Wolf CR, Logue JK, McDonald D, Matsen IV FA, Overbaugh J. Cell. 2021.

Pre-viruses: Biochemistry and Structural Biology

ATP Hydrolysis by the SNF2 domain of the ultraspecific maintenance methylase Dnmt5 drives recognition and modification of hemimethylated DNA

Dumesic PA, Stoddard CI, Catania S, Narlikar GJ, Madhani HD. Mol Cell. 2020.

Evolutionary persistence of DNA methylation for millions of years after ancient loss of a de novo methyltransferase

Catania S, Dumesic PA, Pimentel H, Nasif A, Stoddard CI, Burke JE, Diedrich JK, Cook S, Shea T, Geinger E, Lintner R, Yates JR, Hajkova P, Narlikar GJ, Cuomo CA, Pritchard JK, Madhani HD. Cell. 2020.

A nucleosome bridging mechanism for activation of a maintenance DNA methyltransferase

Stoddard CI, Feng S, Campbell MG, Liu W, Wang H, Bernatavichute Y, Cheng Y, Jacobsen SE, Narlikar GJ. Mol Cell. 2019.

Regulation of Rvb1/Rvb2 by a domain within the INO80 chromatin remodeling complex implicates the yeast Rvbs as protein assembly chaperones

Zhou CY, Stoddard CI, Johnston JB, Trnka MJ, Escheverria I, Palovcak E, Sali A, Burlingame AL, Cheng Y, Narlikar GJ. Cell Rep. 2017.