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Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.
16 papers
Recent·Most cited
J. Guenthoer, M. E. Garrett, M. Lilly, D. M. Depierreux, F. Ruiz, M. Chi, C. I. Stoddard, V. Chohan, K. Sung, D. Ralph, H. Y. Chu, F. A. Matsen, J. Overbaugh
This paper identifies diverse functional antibodies targeting the S2 subunit of SARS-CoV-2 spike, including one with broad neutralization activity across multiple coronaviruses.
bioRxiv · Feb 26, 2024 · PreprintImmunology
F. C. Welsh, R. T. Eguia, J. M. Lee, H. K. Haddox, J. Galloway, N. V. Vinh, A. N. Loes, J. Huddleston, T. C. Yu, M. Q. Le, N. T. Nhat, N. T. L. Thanh, A. L. Greninger, H. Y. Chu, J. A. Englund, , J. D. Bloom
The paper maps how HA mutations affect neutralization by serum from different age groups, showing age-dependent antigenic effects and implications for viral evolution.
bioRxiv · Dec 12, 2023Microbiology
J. Lubow, L. M. Levoir, D. K. Ralph, L. Belmont, M. Contreras, C. H. Cartwright-Acar, C. Kikawa, S. Kannan, E. Davidson, B. J. Doranz, V. Duran, D. E. Sanchez, A. M. Sanz, F. Rosso, S. Einav, , L. Goo
The paper uses single-cell transcriptomics to identify new broadly neutralizing antibodies against flaviviruses, including an IgA1 isotype with unique neutralizing properties.
PLOS Pathogens · Oct 9, 2023Peer-reviewedMicrobiology
C. I. Stoddard, K. Sung, Z. A. Yaffe, H. Weight, G. Beaudoin-Bussieres, J. G. Galloway, S. Gantt, J. Adhiambo, E. R. Begnel, E. Ojee, J. Slyker, D. Wamalwa, J. Kinuthia, A. Finzi, F. A. Matsen, , J. Overbaugh
The paper compares SARS-CoV-2 antibody responses between infants and mothers, finding higher binding and functional antibody levels in infants, particularly in the fusion peptide region.
bioRxiv · Feb 6, 2023Immunology
M. L. Russell, N. Simon, P. Bradley, F. A. Matsen
The paper uses a probabilistic model to analyze TCRβ repertoire data and identifies sequence features that predict nucleotide trimming during V(D)J recombination.
bioRxiv · Dec 8, 2022Immunology
T. C. Yu, Z. T. Thornton, W. H. Hannon, W. S. DeWitt, C. E. Radford, F. A. Matsen, J. D. Bloom
This paper introduces a biophysical model to predict viral escape from polyclonal antibodies by analyzing how mutations affect antibody activity against specific epitopes.
bioRxiv · Sep 17, 2022Evolutionary Biology
C. I. Stoddard, K. Sung, E. Ojee, J. Adhiambo, E. R. Begnel, J. Slyker, S. Gantt, F. A. Matsen, J. Kinuthia, D. Wamalwa, J. Overbaugh, D. A. Lehman
This study examines antibody responses to endemic coronaviruses before and after SARS-CoV-2 infection in Kenyan mothers and infants, finding increased eHCoV antibodies in mothers but not infants post-infection.
bioRxiv · Jun 2, 2022Microbiology
A. Willcox, K. Sung, M. E. Garrett, J. G. Galloway, M. A. OConnor, J. H. Erasmus, J. K. Logue, D. W. Hawman, H. Y. Chu, K. J. Hasenkrug, D. H. Fuller, F. A. Matsen, J. Overbaugh
This study compares SARS-CoV-2 Spike antibody responses between macaques and humans after vaccination or infection, identifying shared and distinct epitope recognition patterns and escape pathways.
bioRxiv · Dec 1, 2021 · PreprintImmunology
M. L. Russell, A. Souquette, D. M. Levine, E. K. Allen, G. Kuan, N. Simon, A. Balmaseda, A. Gordon, P. Thomas, F. A. Matsen, P. G. Bradley
The paper infers genetic loci influencing V(D)J recombination probabilities by combining TCR repertoires and genome-wide genotypes from a human cohort.
bioRxiv · Sep 17, 2021Immunology
M. E. Garrett, J. Galloway, H. Y. Chu, H. L. Itell, C. I. Stoddard, C. R. Wolf, J. K. Logue, D. McDonald, F. A. Matsen, J. Overbaugh
This study identifies antibody escape pathways for SARS-CoV-2 spike protein using Phage-DMS, revealing variable escape mutations in immunodominant regions and individual epitope targeting differences.
bioRxiv · Nov 16, 2020Immunology
C. I. Stoddard, J. Galloway, H. Y. Chu, M. M. Shipley, H. L. Itell, C. R. Wolf, J. K. Logue, A. Magedson, K. Sung, M. Garrett, K. H. Crawford, U. Laserson, F. A. Matsen, Julie Overbaugh
This study maps SARS-CoV-2 antibody epitopes and identifies cross-reactive sequences with endemic HCoVs in COVID-19 patients.
bioRxiv · Oct 29, 2020 · PreprintImmunology
L. E. Doepker, S. Danon, E. Harkins, D. Ralph, Z. Yaffe, A. Dhar, C. Wagner, M. Stumpf, D. Arenz, J. A. Williams, W. Jaoko, K. Mandaliya, K. K. Lee, F. A. Matsen, J. Overbaugh
This study reconstructs the developmental pathways of HIV-specific ADCC antibodies and identifies mutations required for antigen binding and ADCC function.
bioRxiv · Sep 24, 2020 · PreprintImmunology
B. J. Olson, P. Moghimi, C. Schramm, A. Obraztsova, D. Ralph, J. A. Vander Heiden, M. Shugay, A. Shepherd, W. Lees, F. A. Matsen
sumrep is an R package for analyzing and comparing immune receptor repertoires, showing that recombination features are more discriminative than amino acid composition summaries and that generative models capture some but not all repertoire properties.
bioRxiv · Aug 6, 2019Immunology
C. A. Simonich, L. Doepker, D. Ralph, J. A. Williams, A. Dhar, Z. Yaffe, L. Gentles, C. T. Small, B. Oliver, V. Vigdorovich, V. Mangala Prasad, R. Nduati, D. N. Sather, K. K. Lee, F. A. Matsen, J. Overbaugh
This study reconstructs the developmental lineage of an infant-derived HIV-1 broadly neutralizing antibody, showing a rapid evolution with fewer mutations compared to adult antibodies.
bioRxiv · Sep 13, 2018Immunology
W. S. DeWitt, A. Smith, G. Schoch, J. A. Hansen, F. A. Matsen, P. H. Bradley
The paper analyzes TCR repertoire data to uncover associations between MHC alleles, immune exposures, and TCR sequences in a human cohort, revealing patterns linked to pathogen exposure and genetic background.
bioRxiv · May 2, 2018Immunology