PUBLICATIONS

See our current publications on Google Scholar or PubMed

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    Applying high-throughput technologies to engineer a potent antibody drug for malaria protection.

    Highly protective anti-malarial antibodies via precision yeast display library generation and screening.

    Banach BB, Tripathi P, Pereira L, Gorman J, Nguyen TD, Dillon M, Fahad AS, Kiyuka P, Madan B, Wolfe JR, Bonilla B, Flynn B, Francica JR, Hurlburt NK, Liu T, Ou L, Rawi R, Schön A, Shen C-H, Teng I-T, Zhang B, Pancera M, Idris AH, Seder RA, Kwong PD, DeKosky B

    Journal of Experimental Medicine, 219:8, 2022 DOI: 10.1084/jem.20220323 PMID: 35736810

    Antibodies Computational immunology Drug discovery Infectious diseases Malaria
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    Mapping molecular pathways for improved antibodies against the HIV-1 fusion peptide, which is a key vaccine and drug target.

    Understanding potent immunity against HIV-1

    Mutational Fitness Landscapes of a Broadly Neutralizing Fusion Peptide-Directed Antibody Reveal Multiple Pathways to Improve HIV-1 Neutralization

    Bharat Madan*, Baoshan Zhang*, Kai Xu, Jacy Wolfe, Ahmed Fahad, Cara W. Chao, Gwo-Yu Chuang, Hui Geng, Rui Kong, Mark K. Louder, Sijy O’Dell, Reda Rawi, Rajanu Fnu, Tongqing Zhou, Thuy-Duong Nguyen, Arne Schon, Zizhang Sheng, Bob Lin, Nicole A. Doria-Rose, Lawrence Shapiro, Peter D. Kwong, Brandon J. DeKosky

    Proceedings of the National Academy of Sciences of the USA, 118 (10) e2011653118,, 2021 DOI: 10.1073/pnas.2011653118 PMID: 33649208,

    Antibodies Computational immunology Drug discovery HIV-1 Immune development Infectious diseases
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    Understanding the ways that antibody responses can contribute to COVID-19.

    Studying the mechanisms driving severe COVID-19

    Antibody-dependent enhancement and SARS-CoV-2 vaccines and therapies

    Lee, W. S., Wheatley, A. K., Kent, S. J. & DeKosky, B. J.

    Nature Microbiology, 5: 1185–1191, 2020 DOI: 10.1038/s41564-020-00789-5 PMID: 32908214

    Antibodies COVID-19 Immune development Infectious diseases
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    A new approach to immortalize human antibody immune responses for functional screening and drug discovery.

    Advancing techniques to study antibody immunity

    Functional Interrogation and Mining of Natively-Paired VH:VL Human Antibody Repertoires

    Wang B*, DeKosky BJ*, Timm MR, Lee J, Normandin E, Misasi J, Kong R, McDaniel JR, Delidakis G, Leigh KE, Niezold T, Choi CW, Viox EG, Fahad A, Cagigi A, Ploquin A, Leung K, Yang ES, Kong W-P, Voss WN, Schmidt AG, Moody MA, Ambrozak DR, Henry AR, Laboune F, Ledgerwood JE, Graham BS, Connors MR, Douek DC, Sullivan NJ, Ellington AD, Mascola JR**, Georgiou G**

    Nature Biotechnology, 36: 152–155, 2018 DOI: 10.1038/nbt.4052 PMID: 29309060

    Antibodies Computational immunology Drug discovery HIV-1 Immune development Infectious diseases Single-cell technologies

Anti-Malaria Antibody Engineering Broadens Recognition Motifs and Reveals New Homotypic Interactions that Enhance Protective Breadth

Jihwan Chun, Prabhanshu Tripathi, Yevel Flores-Garcia, Bharat Madan, Gene A. Lee, Ahmed S. Fahad, Haotian Lei, I-Ting Teng, View ORCID ProfileNicholas K. Hurlburt, Barbara J. Flynn, View ORCID ProfileMarie Pancera, Kazutoyo Miura, Tongqing Zhou, Azza H. Idris, Fidel Zavala, Robert A. Seder, Peter D. Kwong, View ORCID ProfileBrandon J. DeKosky

Pre-print, bioRxiv, 2025. DOI: 10.1101/2025.09.30.679367

Antibodies Drug discovery Malaria

Yeast display reveals plentiful mutations that improve fusion-peptide vaccine-elicited antibodies beyond 59% HIV-1-neutralization breadth

Camila T. França*, Sergei Pletnev*, Bharat Madan*, Phinikoula S. Katsamba, Krisha McKee, Nicholas C. Morano, Baoshan Zhang, Fabiana Bahna,  Tatsiana Bylund, Bob C. Lin, Mark K. Louder, Seetha Mannepalli, Rajani Nimrania, Sijy O’Dell, Nicole A. Doria-Rose, Peter D. Kwong, Lawrence Shapiro, Zizhang Sheng, Tongqing Zhou, Brandon J. DeKosky

In press, Vaccines (Basel), 2025. DOI: 10.20944/preprints202509.2071.v1

Antibodies Drug discovery HIV-1

The Evolution of Display Technologies for Antibody Discovery

Julian Rojo Gallegos*, Jason Tang*, Mark Yarmarkovich§, Brandon J. DeKosky§

Pre-print, 2025. DOI: 10.5281/zenodo.17095811

Antibodies Drug discovery Single-cell technologies

Potent Monoclonal Antibodies Against Circulating Yellow Fever Virus Strains from Donors Immunized with the 17D Vaccine

Matheus O. de Souza, Danielle Saunders, Andrew Miller, Ahmed S. Fahad, Morgan R. Timm, Kimberly D. Dowd, Bharat Madan, Jacy Wolfe, Erica Normandin, Amy R. Henry, Farida Laboune, Yulia Petrova, John Misasi, Túlio M. Lima, Renata G. F. Alvim, Sanchez, E.M., Katherine E. Burgomaster, Xiaoli Pan, Daniel C. Douek, Barney S. Graham, John R. Mascola, Theodore C. Pierson, Leda R. Castilho, Richard Kuhn, Yan-Jang S. Huang, Brandon J. DeKosky

American Journal of Tropical Medicine & Hygiene, In press, 2025.

Antibodies Drug discovery Infectious diseases

The Adaptive Immune Receptors in a Big Data World

DeKosky BJ

Pre-print, 2025. DOI: 10.5281/zenodo.17095771

Antibodies Computational immunology Immune development Single-cell technologies T cell receptors

High-Throughput Antibody Neutralization Screening in Massively Parallel Droplet Arrays

Matias Gutierrez-Gonzalez*, Ahmed S. Fahad*, Cyrille L. Delley, Cheng-Yu Chung, Shuyan Jin, Nicoleen Boyle, Matheus Oliveira de Souza, Azady Pirhanov, Nicolas M.S. Galvez, Camila T. França, Samantha Marglous, Evan Bhagat, Donovan Vincent, Daniel Neumeier, Yi Cao, Nicole Doria-Rose, Sai T. Reddy, Aaron G. Schmidt, Alejandro B. Balazs, Adam R. Abate, Brandon J. DeKosky

Pre-print, bioRxiv, 2025. DOI: 10.1101/2025.01.31.635965

Antibodies Computational immunology Drug discovery Single-cell technologies

Gene syntax defines supercoiling-mediated transcriptional feedback

Christopher P. Johnstone, Kasey S. Love, Sneha Kabaria, Emma L. Peterman, Ross Jones, Albert Blanch-Asensio, Deon S. Ploessl, Rachel Lee, Jiyoung Yun, Conrad G. Oakes, Christine L. Mummery, Richard P. Davis, Brandon J. DeKosky, Peter W. Zandstra, Kate E. Galloway

Pre-print, bioRxiv, 2025. DOI: 10.1101/2025.01.19.633652

Synthetic Gene Circuits

Expanding the Landscape of Antibody Discovery

Shelbe Johnson and Brandon J. DeKosky

Cell Reports Methods, 16;4(12): 100936., 2024. PMID: 39689694. DOI: 10.1016/j.crmeth.2024.100936

Antibodies Computational immunology Single-cell technologies

Optimized Single-Cell Gates for Yeast Display Screening

Xiaoli Pan*, Matheus O. de Souza*, Francisco M. Figueiras, Aric Huang, Bailey B. Banach, Jacy R. Wolfe, Azady Pirhanov, Bharat Madan, Brandon J. DeKosky

Protein Engineering, Design, and Selection, 2024. PMID: 39667035. DOI: 10.1093/protein/gzae018

Antibodies Computational immunology Single-cell technologies

Clonal Variant Analysis of Antibody Engineering Libraries

Ahmed S. Fahad*, Matias F. Gutierrez-Gonzalez*, Bharat Madan, Brandon J. DeKosky

Cold Spring Harbor Protocols, 2024. PMID: 39586683. DOI: 10.1101/pdb.prot108626

Antibodies Computational immunology Drug discovery