PUBLICATIONS

See our current publications on Google Scholar or PubMed

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

New antibodies against malaria

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
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
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
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

New antibodies against malaria

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. PMID: 35736810. DOI: 10.1084/jem.20220323

Antibodies Computational immunology Drug discovery Infectious diseases Malaria

Bioinformatic Analysis of Natively Paired VH:VL Antibody Repertoires for Antibody Discovery

Fahad AS*, Madan B*, DeKosky BJ

Computer-Aided Antibody Design, Methods in Molecular Biology (Springer US), ISBN-13: 9781071626, 2022.

Antibodies Computational immunology Drug discovery Single-cell technologies

Mapping monoclonal anti-SARS-CoV-2 antibody repertoires against diverse coronavirus antigens

Matheus Oliveira de Souza*, Bharat Madan*, I-Ting Teng, Aric Huang, Lihong Liu, Ahmed S. Fahad, Sheila N. Lopez-Acevedo, Xiaoli Pan, Mallika Sastry, Matias Gutierrez-Gonzalez, Michael T. Yin, Tongqing Zhou, David D. Ho, Peter D. Kwong, Brandon J. DeKosky.

Frontiers in Immunology, 2022.

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

Strategies to screen anti-AQP4 antibodies from yeast surface display libraries

Aric Huang, Wei Jin, Ahmed S. Fahad, Brooklyn K. Mussman, Grazia Paola Nicchia, Bharat Madan, Matheus Oliveira De Souza, J. Daniel Griffin, Jeffrey L. Bennett, Antonio Frigeri, Cory J. Berkland, Brandon J. DeKosky.

Antibodies, 11:39, 2022. PMID: 35735358. DOI: 10.3390/antib11020039

Antibodies Autoimmunity Drug discovery

Molecular Probes of Spike and Subdomains for SARS-CoV-2 Variants

I-Ting Teng, Alexandra F. Nazzari, Misook Choe, Tracy Liu, Matheus Oliveira de Souza, Yuliya Petrova, Yaroslav Tsybovsky, Baoshan Zhang, Mykhaylo Artamonov, Bharat Madan, Aric Huang, Sheila N. Lopez Acevedo, Xiaoli Pan, Tracy J. Ruckwardt, Shuishu Wang, Brandon J. DeKosky, John R. Mascola, John Misasi, Nancy J. Sullivan, Tongqing Zhou, Peter D. Kwong.

PLoS One, 2022. PMID: 3560908. DOI: 10.1371/journal.pone.0268767

Antibodies Computational immunology COVID-19 Drug discovery Infectious diseases Single-cell technologies

The AIRR Community Guide to Quality Control: Chain Pairing Precision and Monitoring of Cross-Sample Contamination

Chung C-Y, Gutiérrez-González M, López Acevedo SN, Fahad AS, DeKosky BJ

Immunogenetics: Methods and Protocols, Methods in Molecular Biology, y, (Springer Nature) ISBN: 9781071621141 , 2022.

Antibodies Computational immunology Drug discovery Single-cell technologies T cell receptors

Immortalization and Functional Screening of Natively Paired Human T Cell Receptor Repertoires

Ahmed S. Fahad, Cheng Yu Chung, Sheila N. Lopez Acevedo, Nicoleen Boyle, Bharat Madan, Matias F. Gutiérrez-González, Rodrigo Matus-Nicodemos, Amy D. Laflin, Rukmini R. Ladi, John Zhou, Shauna Moore, Jacy Wolfe, Daniel C. Douek, Sian Llewellyn-Lacey, Henry H. Balfour Jr., David A. Price, Brandon J. DeKosky.

Protein Engineering, Design, and Selection, 35:gzab03, 2022. PMID: 3517485. DOI: 10.1093/protein/gzab034

Computational immunology Drug discovery Infectious diseases Single-cell technologies T cell receptors

Pharmaceutical Biotechnology, Martin’s Physical Pharmacy and Pharmaceutical Sciences

Middaugh CR, Siahaan T, DeKosky BJ

Lippincott Williams & Wilkins, Ch. 20, 2022.

Antibodies Drug discovery

Optimized production of Fc fusion proteins by sortase enzymatic ligation

Kyle D. Apley, Amy D. Laflin, Stephanie N. Johnson, Noora Batrash, J. Daniel Griffin, Cory J. Berkland, Brandon J. DeKosky.

Industrial & Engineering Chemistry Research, 60 (47), 16839–1685, 2021. DOI: 10.1021/acs.iecr.1c02842

Antibodies Drug discovery

Human antibody immune responses are personalized by selective removal of MHC-II peptide epitopes

Matias Gutiérrez-González, Ahmed S. Fahad, Matt Ardito, Padma Nanaware, Erica Normandin, Bharat Madan, Joseph Tivin, Emily Coates, Amy R. Henry, Farida Laboune, Barney S. Graham, Daniel C. Douek, Julie E. Ledgerwood, John R. Mascola, William D. Martin, Lawrence J. Stern, Annie S. de Groot, Brandon J. DeKosky

bioRxiv, 2021. DOI: 1101/2021.01.15.426750

Antibodies Autoimmunity Computational immunology Drug discovery Immune development Single-cell technologies

PUBLICATIONS

New antibodies against malaria

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

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

Studying the mechanisms driving severe COVID-19

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

Advancing techniques to study antibody immunity

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

New antibodies against malaria

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

Bioinformatic Analysis of Natively Paired VH:VL Antibody Repertoires for Antibody Discovery

Mapping monoclonal anti-SARS-CoV-2 antibody repertoires against diverse coronavirus antigens

Strategies to screen anti-AQP4 antibodies from yeast surface display libraries

Molecular Probes of Spike and Subdomains for SARS-CoV-2 Variants

The AIRR Community Guide to Quality Control: Chain Pairing Precision and Monitoring of Cross-Sample Contamination

Immortalization and Functional Screening of Natively Paired Human T Cell Receptor Repertoires

Pharmaceutical Biotechnology, Martin’s Physical Pharmacy and Pharmaceutical Sciences

Optimized production of Fc fusion proteins by sortase enzymatic ligation

Human antibody immune responses are personalized by selective removal of MHC-II peptide epitopes