DEKOSKY LAB PUBLICATIONS 20210916 - MIT CHEMICAL ...
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DeKosky lab publications 20210916
Accepted
35. Brian M. Petersen, Sophia A. Ulmer, Emily R. Rhodes, Matias F Gutierrez Gonzalez,
Brandon J Dekosky, Kayla G Sprenger, Timothy A. Whitehead, “Regulatory approved
monoclonal antibodies contain framework mutations predicted from human antibody
repertoires,” Frontiers in Immunology, Accepted, September 2021
34. Bharat Madan, Eswar Reddem, Pengfei Wang, Ryan Casner, Manoj Nair, Yaoxing Huang,
Ahmed Fahad, Matheus de Souza, Bailey Banach, Sheila Lopez Acevedo, Xiaoli Pan,
Rajani Nimrania, I-Ting Teng, Fabiana Bahna, Tongqing Zhou, Baoshan Zhang, Michael
Yin, David Ho, Peter Kwong, Lawrence Shapiro, Brandon DeKosky, “Antibody Screening at
Reduced pH Enables Preferential Selection of Potently Neutralizing Antibodies Targeting
SARS-CoV-2,” Accepted, AIChE Journal, Futures Issue, August 2021
33. Bailey B. Banach*, Gabriele Cerutti*, Ahmed S. Fahad, Chen-Hsiang Shen, Matheus Olivera
de Souza, Phinikoula S. Katsamba, Yaroslav Tsybovsky, Pengfei Wang, Manoj S. Nair,
Yaoxing Huang, Irene Francino, Paul J. Steiner, Matias Gutiérrez-González, Lihong Liu,
Sheila N. Lopez Acevedo, Alexandra Nazzari, Jacy R. Wolfe, Yang Luo, Adam S. Olia, I-
Ting Teng, Jian Yu, Tongqing Zhou, Xiaoli Pan, Bharat Madan, Amy D. Laflin, Rajani
Madan, Kwon-Tung Yuen, Timothy A. Whitehead, David D. Ho, Peter D. Kwong, Lawrence
Shapiro, Brandon J. DeKosky, “Paired heavy and light chain signatures contribute to potent
SARS-CoV-2 neutralization in IGHV3-53/3-66 public antibody responses,” Cell Reports,
Accepted, August 2021, bioRxiv 2020, DOI: 10.1101/2020.12.31.424987
32. Gwo-Yu Chuang, Chen-Hsiang Shen, Crystal Sao-Fong Cheung, Jason Gorman, Adrian
Creanga, M. Gordon Joyce, Kwanyee Leung, Reda Rawi, Lingshu Wang, Eun Sung Yang,
Yongping Yang, Baoshan Zhang, Yi Zhang, Masaru Kanekiyo, Tongqing Zhou, Brandon J.
DeKosky, Barney S. Graham, John R. Mascola, Peter D. Kwong, “Sequence-Signature
Optimization Enables Improved Identification of Human HV6-1-Derived Class Antibodies
that Neutralize Diverse Influenza A Viruses,” Frontiers in Immunology, 2021.
PMID: 34135892, PMCID: PMC8201785, DOI: 10.3389/fimmu.2021.662909
31. Maryam Mukhamedova, Daniel Wrapp, Chen-Hsiang Shen, Morgan S.A. Gilman, Tracy J
Ruckwardt, Chaim S. Schramm, Larissa Ault, Lauren Chang, Alexandrine Derrien-Colemyn,
Sarah A.M. Lucas, Amy Ransier, Samuel Darko, Emily Phung, Lingshu Wang, Yi Zhang,
Scott A. Rush, Bharat Madan, Guillaume B. E. Stewart-Jones, Pamela J. Costner, LaSonji
A. Holman, Somia P. Hickman, Nina M. Berkowitz, Nicole A. Doria-Rose, Kaitlyn M.
Morabito, Brandon J. DeKosky, Martin R. Gaudinski, Grace L. Chen, Michelle C. Crank,
John Misasi, Nancy J. Sullivan, Daniel C. Douek, Peter D. Kwong, Barney S. Graham,
Jason S. McLellan, John R. Mascola, “Vaccination with Prefusion-Stabilized Respiratory
Syncytial Virus Fusion Protein Induces a Genetically and Antigenically Diverse Antibody
Response,” Immunity, S1074-7613(21)00116-3, 2021. PMID: 33823129, DOI:
10.1016/j.immuni.2021.03.004
30. 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, “Mutational FitnessLandscapes of a Broadly Neutralizing Fusion Peptide-Directed Antibody Reveal Multiple
Pathways to Improve HIV-1 Neutralization,” Proceedings of the National Academy of
Sciences of the USA, 118 (10) e2011653118, 2021. PMID: 33649208, PMCID:
PMC7958426 (available on 2021-09-01), DOI: 10.1073/pnas.2011653118
29. Ahmed S. Fahad, Morgan R. Timm, Bharat Madan, Katherine E. Burgomaster, Kimberly A.
Dowd, Erica Normandin, Matías F. Gutiérrez-González, Joseph M. Pennington, Amy R.
Henry, Farida Laboune, Lingshu Wang, David R. Ambrozak, Ingelise J. Gordon, Daniel C.
Douek, Julie E. Ledgerwood, Barney S. Graham, Leda R. Castilho, Theodore C. Pierson,
John R. Mascola, & Brandon J. DeKosky, “Comprehensive Functional Profiling of Anti-Zika
Virus Antibodies in Convalescent Patients,” Frontiers in Immunology, 12:615102, 2021.
PMID: 33732238, PMCID: PMC7959826, DOI: 10.3389/fimmu.2021.615102
28. Peter D. Kwong, Brandon J. DeKosky, Jeffrey B. Ulmer, “Antibody-guided structure-based
vaccines,” Seminars in Immunology, 50:101428, 2020. PMID: 33246736, PMCID:
pending, DOI: 10.1016/j.smim.2020.101428
27. J. Daniel Griffin*, Kyle D. Apley*, Stephanie N. Johnson, Cory J. Berkland, Brandon J.
DeKosky, “Tetrameric Fluorescent Antigen Arrays for Single-Step Identification of Antigen-
Specific B Cells,” Journal of Visual Experimentation, Advanced Online Publication, 2020.
PMID: 33165322, PMCID: pending, DOI: 10.3791/61827
26. Tongqing Zhou, I-Ting Teng, Adam S. Olia, Gabriele Cerutti, Jason Gorman, Alexandra
Nazzari, Wei Shi, Yaroslav Tsybovsky, Lingshu Wang, Shuishu Wang, Baoshan Zhang, Yi
Zhang, Phini Katsamba, Yuliya Petrova, Bailey B. Banach, Ahmed S. Fahad, Lihong Liu,
Sheila N. Lopez Acevedo, Bharat Madan, Matheus Olivera de Souza, Xiaoli Pan, Pengfei
Wang, Jacy R. Wolfe, Michael Yin, David D. Ho, Emily Phung, Anthony DiPiazza, Lauren
Chang, Olubukula Abiona, Brandon J. DeKosky, Barney S. Graham, John R. Mascola, John
Misasi, Tracy Ruckwardt, Nancy J. Sullivan, Lawrence Shapiro, Peter D. Kwong, “Structure-
Based Design with Tag-Based Purification and In-Process Biotinylation Enable Streamlined
Development of SARS-CoV-2 Spike Molecular Probes,” Cell Reports, 33(4):108322, 2020.
PMID: 33091382, PMCID: PMC7550166, DOI: 10.1016/j.celrep.2020.108322
25. Wen Shi Lee, Adam K. Wheatley, Stephen J. Kent*, Brandon J. DeKosky*, “Antibody-
dependent Enhancement and SARS-CoV-2 Vaccines and Therapies,” Nature
Microbiology, 5:1185–1191, 2020. PMID: 32908214, PMCID: pending, DOI:
10.1038/s41564-020-00789-5.
24. Stephanie N. Johnson*, J. Daniel Griffin*, Chrys Hulbert, Brandon J. DeKosky, James W.
Thomas, and Cory J. Berkland, “Multimeric insulin desensitizes insulin-specific B cells,” ACS
Applied Bio Materials, Advanced online publication, 2020. DOI:
https://doi.org/10.1021/acsabm.0c00782
23. Anna V. Mentesh, Matias Gutierrez-Gonzalez, Brandon J. DeKosky, Yariv Wine, “The
molecular mechanisms that underline the immune biology of anti-drug antibody formation
following treatment with monoclonal antibodies,” Frontiers in Immunology, 11:1951, 2020.
PMID: 33013848, PMCID: PMC7461797, DOI: 10.3389/fimmu.2020.01951
22. Aric Huang*, Melissa M. Pressnall*, Ruolin Lu, Sebastian G. Huayamares, J. Daniel Griffin,
Brandon J. DeKosky, M. Laird Forrest, Cory J. Berkland, “Human intratumoral therapy:
Linking drug properties and tumor transport of drugs in clinical trials,” Journal of Controlled
Release, 326:203-221, 2020. PMID: 32673633, PMCID: pending, DOI:
10.1016/j.jconrel.2020.06.02921. Wei Jin, Bharat Madan, Brooklyn K. Mussman, Amen T. Hailemariam, Ahmed S. Fahad,
Jacy R. Wolfe, Young Do Kwon, Baoshan Zhang, Lawrence Shapiro, Peter D. Kwong,
Brandon J. DeKosky, “The Covalent SNAP Tag for Protein Display Quantification and Low-
pH Protein Engineering,” Journal of Biotechnology, 320:50-56, 2020. PMID: 32561362,
PMCID: 32561362, DOI: 10.1016/j.jbiotec.2020.06.011
20. J. Daniel Griffin*, Jimmy Y. Song*, Joshua O. Sestak, Brandon J. DeKosky, Cory J.
Berkland, “Linking autoantigen properties to mechanisms of immunity,” Advanced Drug
Delivery Reviews, 2020, PMID: 32325104, PMCID: PMC7572523, DOI:
10.1016/j.addr.2020.04.005
19. Shen C-H, DeKosky BJ*, Chuang G-Y*, Xu K*, Kilam D, Ko SH, Kong R, Ransier A, Huang
J, Normandin E, Our L, Zhang B, Zhou T, Chao CW, Corcoran MM, Feng E, Gu Y, Liu K,
Louder MK, O’Dell S, Rawi R, Sastry M, Schmidt SD, Wang S, Wang Y, Chuang G-Y, Doria-
Rose NA, Lin B, Boritz EA, Connors M, Douek DC, Hedestam GBK, Sheng Z, Shapiro L,
Mascola JR, Kwong PD, “VRC34-Antibody Lineage Development Reveals How a Required
Rare Mutation Shapes the Maturation of a Broad HIV-Neutralizing Lineage,” Cell Host
Microbe, 27(4):531-543.e6. 2020. PMID: 32130953, PMCID: PMC7467872, DOI:
10.1016/j.chom.2020.01.027
18. Lagerman CE*, López Acevedo SN*, Fahad AS, Hailemariam A, Madan B, DeKosky BJ,
“Ultrasonically-Guided Flow Focusing Generates Precise Emulsion Droplets for High-
Throughput Single Cell Analyses,” J Biosci Boeng, pii: S1389-1723(18)31136-8. 2019.
PMID: 30904454, PMCID: PMC6688500, DOI: 10.1016/j.jbiosc.2019.01.020
17. 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**, “Functional Interrogation and Mining of Natively-Paired
VH:VL Human Antibody Repertoires,” Nature Biotechnology, 36: 152–155, 2018. PMID:
29309060, PMCID: PMC5801115, DOI: 10.1038/nbt.4052
1. KU News: https://news.ku.edu/2018/01/16/breakthrough-enables-screening-millions-
human-antibodies-new-drug-discovery
2. Science & Enterprise: https://sciencebusiness.technewslit.com/?p=32432
3. R&D Mag: https://www.rdmag.com/article/2018/01/new-tech-allows-millions-antibodies-be-
screened-leading-drug-discovery
Perspectives (non peer-reviewed)
16. DeKosky BJ, A molecular trap against COVID-19. Science, 369(6508):1167-1168, 2020.
PMID: 32883851, PMCID: pending, DOI: 10.1126/science.abe0010
Mentored peer-reviewed journal publications
15. Duan H*, Chen X*, Boyington JC*, Cheng C*, Zhang Y, Jafari AJ, Stephens T, Tsybovsky Y,
Kalyuzhniy O, Zhao P, Menis S, Nason MC, Normandin E, Mukhamedova M, DeKosky BJ,
Wells L, Schief WR, Tian M, Alt F, Kwong PD, Mascola JR, “Glycan-masking Focuses
Immune Responses to the HIV-1 CD4-Binding Site and Enhances Elicitation of VRC01-
Class Precursor Antibodies,” Immunity, 49(2):301-311.e5, 2018. PMID: 3007610, PMCID:
PMC6896779, DOI: 10.1016/j.immuni.2018.07.00514. Lau D, Lan LY, Andrews SF, Huang M, Huang Y, DeKosky BJ, Rojas KT, Henry C, Neu KE,
Palm EI, Ippolito GC, Georgiou G, Wilson PC, “Low CD21 expression defines a population
of recent germinal center graduates primed for plasma cell differentiation” Science
Immunology, 2(7):eaai8153, 2017. PMID: 28783670, PMCID: PMC5896567, DOI:
10.1126/sciimmunol.aai8153
13. Peter D. Kwong, Gwo-Yu Chuang, Brandon J. DeKosky, Tatyana Gindin, Ivelin S. Georgiev,
Thomas Lemmin, Chaim A. Schramm, Zizhang Sheng, Cinque Soto, An-Suei Yang,
Lawrence Shapiro, “Antibodyomics: Bioinformatics Technologies for Understanding B Cell
Immunity to HIV-1” Immunological Reviews, 275(1):108-128, 2017. PMID: 28133812,
PMCID: PMC5516196, DOI: 10.1111/imr.12480
12. Lee J, Boutz DR, Chromikova V, Joyce MG, Vollmers C, Leung K, Horton AP, DeKosky BJ,
Lee C-H, Lavinder JJ, Murrin EM, Chrysostomou C, Hoi KH, Tsybovsky Y, Thomas PV,
Druz A, Zhang B, Zhang Y, Wang L, Kong W-P, Park D, Popova LI, Dekker CL, Davis MM,
Carter CE, Ross TM, Ellington AD, Wilson PC, Marcotte EM, Mascola JR, Ippolito GC,
Krammer F, Quake SR, Kwong PD, Georgiou G, “Quantitative, molecular-level analysis of
the serum antibody repertoire in young adults before and after seasonal influenza
vaccination”, Nature Medicine, 22(12):1456-1464, 2016. PMID: 27820605, PMCID:
PMC5301914, DOI: 10.1038/nm.4224
11. Ming Tian, Cheng Cheng, Xuejun Chen, Hongying Duan, Hwei-Ling Cheng, Mai Dao,
Zizhang Sheng, Michael Kimble, Lingshu Wang , Sherry Lin, Stephen D. Schmidt, Zhou Du,
M. Gordon Joyce, Yiwei Chen, Brandon J. DeKosky, Yimin Chen, Erica Normandin,
Elizabeth Cantor, Rita Chen, Nicole A Doria-Rose, Yi Zhang, Wei Shi, Wing-Pui Kong,
Misook Choe, Amy R. Henry, Farida Laboune, Ivelin S. Georgiev, Pei-Yi Huang, Suvi Jain,
Andrew T. McGuire, Eric Georgeson, Sergey Menis, Daniel C. Douek, William R. Schief,
Leonidas Stamatatos, Peter D. Kwong, Lawrence Shapiro, Barton F. Haynes, John R.
Mascola, and Frederick W. Alt, “Induction of HIV Neutralizing Antibody Lineages in Mice with
Diverse Precursor Repertoires,” Cell, 166(6):1471-1484.e18, 2016. PMID: 27610571,
PMCID: PMC5103708, DOI: 10.1016/j.cell.2016.07.029
10. DeKosky BJ*, Lungu OI*, Park D, Johnson EL, Charab W, Chrysostomou C, Kuroda D,
Ippolito GC, Ellington AD, Gray J, Georgiou G, “Large-Scale Sequence and Structural
Comparisons of Human Naïve and Antigen-Experienced Antibody Repertoires,”
Proceedings of the National Academy of Sciences, USA, 113(19):E2636-45, 2016.
PMID: 27114511, PMCID: PMC4868480, DOI: 10.1073/pnas.1525510113
9. Gorman J, Soto C, Yang MM, Davenport TM, Guttman M, Bailer RT, Chuang G, DeKosky
BJ, Doria-Rose NA, Druz A, Ernandes MG, Georgiev IS, Jarosinski MC, Joyce MG, Lemmin
TM, Leung S, Louder MK, McDaniels J, Narpala S, Pancera M, Stuckey J, Wu X, Yang Y,
Zhang B, Zhou T, NISC Comparative Sequencing Program, Mullikin JC, Baxa U, Georgiou
G, McDermott AB, Bonsignori M, Haynes BF, Moore PL, Morris L, Lee KK, Shapiro L,
Mascola JR, Kwong PD, “HIV-1-Env structures with V1V2-directed broadly neutralizing
antibodies reveal commonalities that enable ontogeny-specific vaccine design,” Nature
Structural & Molecular Biology, 23:81–90, 2016. PMID: 26689967, PMCID: PMC4833398,
DOI: 10.1038/nsmb.3144
8. McDaniel JR*, DeKosky BJ*, Tanno H, Ellington AD, Georgiou G, "Ultra-high throughput
sequencing of the immune receptor repertoire from millions of lymphocytes," Nature
Protocols, 11:429–442, 2016. PMID: 26844430, DOI: 10.1038/nprot.2016.024
7. Murzabaev M, Kojima T, Mizoguchi T, Kobayashi I, DeKosky BJ, Georgiou G, Nakano H,
“Handmade microfluidic device for biochemical applications in emulsion,” Journal ofBioscience and Bioengineering, 121(4):471-6, 2016. PMID: 26386750, DOI:
10.1016/j.jbiosc.2015.08.001
6. Wang B*, Kluwe CA*, Lungu OI*, DeKosky BJ, Kerr SA, Johnson EJ, Jung J, Reizigh AB,
Carroll SM, Reyes A, Bentz JR, Villanueva I, Altman AL, Davey R, Ellington AD, Georgiou
G, "Facile discovery of a diverse panel of anti-ebola virus antibodies by immune repertoire
mining," Scientific Reports, 5:13926, 2015. PMID: 26355042, PMCID: PMC4564727, DOI:
10.1038/srep13926
5. DeKosky BJ, Kojima T, Rodin A, Charab W, Ippolito GC, Ellington AD, Georgiou G, “In-
depth determination and analysis of the human paired heavy and light chain antibody
repertoire,” Nature Medicine, 21(1): 86-91, 2015. PMID: 25501908, DOI: 10.1038/nm.3743
1. Nature Technology Review:
http://www.nature.com/nature/journal/v525/n7569/full/525409a.html
4. Lavinder JJ, Wine Y, Giesecke C, Ippolito GC, Horton AP, Lungu OI, Hoi KH, DeKosky BJ,
Murrin EM, Wirth MM, Ellington AD, Dörner T, Marcotte EM, Boutz DR, Georgiou G
“Identification and characterization of the constituent human serum antibodies elicited by
vaccination,” Proceedings of the National Academy of Sciences, 111(6): 2259–2264,
2014. PMID: 24469811, PMCID: PMC3926051, DOI: 10.1073/pnas.1317793111
3. Doria-Rose NA*, Schramm CA*, Gorman J*, Moore PL*, Bhiman JN, DeKosky BJ, Ernandes
MJ, Georgiev IS, Kim HJ, Pancera M, Staupe RP, Altae-Tran HR, Bailer RT, Crooks ET,
Cupo A, Druz A, Garrett NJ, Hoi KH, Kong R, Louder MK, Longo NS, McKee K, Nonyane M,
O’Dell S, Roark RS, Rudicell RS, Schmidt SD, Sheward DJ, Soto C, Wibmer CK, Yang Y,
Zhang Z, NISC Comparative Sequencing, Mullikin JC, Binley JM, Sanders RW, Wilson IA,
Moore JP, Ward AB, Georgiou G, Williamson C, Abdool Karim SS, Morris L**, Kwong PD**,
Shapiro L**, Mascola JR** “Developmental pathway for potent V1V2-directed HIV-
neutralizing antibodies,” Nature, 509(7498): 55–62, 2014. PMID: 24590074, PMCID:
PMC4395007, DOI: 10.1038/nature13036
1. MedicalXpress: http://medicalxpress.com/news/2014-03-antibody-evolution-hiv-vaccine.html
2. Science Newsline: http://www.sciencenewsline.com/articles/2014030414220027.html
3. Medical News Today: http://www.medicalnewstoday.com/releases/273504.php
4. F1000 selected as a “Recommended” paper: http://f1000.com/prime/718297894
2. DeKosky BJ, Ippolito GC, Deschner RP, Lavinder JJ, Wine Y, Rawlings BM, Varadarajan N,
Giesecke C, Dörner T, Andrews SF, Wilson PC, Hunicke-Smith SP, Willson CG, Ellington
AD, Georgiou G, “High-throughput sequencing of the paired human immunoglobulin heavy
and light chain repertoire,” Nature Biotechnology, 31(2): 166-169, 2013. PMID: 23334449,
PMCID: PMC3910347, DOI: 10.1038/nbt.2492
1. The Scientist: http://www.the-scientist.com/?articles.view/articleNo/39777/title/Accelerating-Antibody-
Discovery/
1. DeKosky BJ, Dormer NH, Ingavle GC, Roatch CH, Lomakin J, Detamore MS, Gehrke SH,
“Hierarchically designed agarose and poly(ethylene glycol) interpenetrating network
hydrogels for cartilage tissue engineering,” Tissue Engineering Part C: Methods, 16(6):
1533-1542, 2010. PMID: 20626274, PMCID: PMC2988644, DOI: 10.1089/ten.tec.2009.0761
1. 12th most recently-cited article in TEC, Dec 2014
Book Chapters1. Middaugh CR, Siahaan T, DeKosky BJ, Ch. 20: Pharmaceutical Biotechnology, Martin’s Physical Pharmacy and Pharmaceutical Sciences (Lippincott Williams & Wilkins), In revision, 2021 Books 1. DeKosky BJ, Decoding the Antibody Repertoire: High Throughput Sequencing of Multiple Transcripts from Single B Cells (Springer), 2017, ISBN: 978-3-319-58517-8, DOI: 10.1007/978-3-319-58518-5
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