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PUBLICATIONS & PRESENTATIONS

Biomarkers

Protein-Based Immunome Wide Association Studies (PIWAS) for the Discovery of Significant Disease-Associated Antigens

Winston A. Haynes, Kathy Kamath, Rebecca Waitz, Patrick S. Daugherty and John C. Shon
April 2021

Cancer

Phase Ib study of patients with metastatic castrate-resistant prostate cancer treated with different sequencing regimens of atezolizumab and sipuleucel-T

Tanya Dorff, Yosuke Hirasawa, Jared Acoba, Ian Pagano, David Tamura, Sumanta Pal, Minlu Zhang, Rebecca Waitz, Abhilash Dhal, Winston Haynes, John Shon, Mark Scholz, Hideki Furuya, Owen T M Chan, Jeffrey Huang, Charles Rosser
August 2021

Autoantibody landscape of advanced prostate cancer

William S. Chen, Winston A. Haynes, Rebecca Waitz, Kathy Kamath, Agustin Vega-Crespo, Raunak Shrestha, Adam Foye, Ignacio Baselga Carretero, Meng Zhang, Shuang G. Zhao, Martin Sjöström, David A. Quigley, Jonathan Chou, Tomasz M. Beer, Matthew Rettig, Martin Gleave, Christopher P. Evans, Primo Lara, Kim N. Chi, Robert E. Reiter, Joshi J. Alumkal, Rahul Aggarwal, Eric J. Small, Patrick S. Daugherty, Antoni Ribas, David Y. Oh, John C. Shon, Felix Y. Feng
October 2020

COVID RUO

High-affinity, neutralizing antibodies to SARS-CoV-2 can be made in the absence of T follicular helper cells

Jennifer S. Chen, Ryan D. Chow, Eric Song, Tianyang Mao, Benjamin Israelow, Kathy Kamath, Joel Bozekowski, Winston A. Haynes, Renata B. Filler, Bridget L. Menasche, Jin Wei, Mia Madel Alfajaro, Wenzhi Song, Lei Peng, Lauren Carter, Jason S. Weinstein, Uthaman Gowthaman, Sidi Chen, Joe Craft, John C. Shon, Akiko Iwasaki, Craig B. Wilen, Stephanie C. Eisenbarth
June 2021

Plasmodium infection induces cross-reactive antibodies to carbohydrate epitopes on the SARS-CoV-2 Spike protein

Sarah Lapidus, Feimei Liu, Arnau Casanovas-Massana, Yile Dai, John D Huck, Carolina Lucas, Jon Klein, Renata B Filler, Madison S Strine, Mouhamad Sy, Awa B Deme, Aida S Badiane, Baba Dieye, Ibrahima Mbaye Ndiaye, Younous Diedhiou, Amadou Moctar Mbaye, Cheikh Tidiane Diagne, Inés Vigan-Womas, Alassane Mbengue, Bacary D Sadio, Moussa M Diagne, Adam J Moore, Khadidiatou Mangou, Fatoumata Diallo, Seynabou D Sene, Mariama N Pouye, Rokhaya Faye, Babacar Diouf, Nivison Nery, Federico Costa, Mitermayer Reis, M Catherine Muenker, Daniel Z Hodson, Yannick Mbarga, Ben Z Katz, Jason R Andrews, Melissa Campbell, Ariktha Srivathsan, Kathy Kamath, Elisabeth Baum-Jones, Ousmane Faye, Amadou Alpha Sall, Juan Carlos Quintero Vélez, Michael Cappello, Michael Wilson, Choukri Ben-Mamoun, Fabrice A Somé, Roch K Dabiré, Carole Else Eboumbou Moukoko, Jean Bosco Ouédraogo, Yap Boum, John Shon, Daouda Ndiaye, Adam Wisnewski, Sunil Parikh, Akiko Iwasaki, Craig B Wilen, Albert I Ko, Aaron M Ring, Amy K Bei
May 2021

Cytokine release syndrome in a patient with colorectal cancer after vaccination with BNT162b2

Lewis Au, Annika Fendler, Scott T. C. Shepherd, Karolina Rzeniewicz, Maddalena Cerrone, Fiona Byrne, Eleanor Carlyle, Kim Edmonds, Lyra Del Rosario, John Shon, Winston A. Haynes, Barry Ward, Ben Shum, William Gordon, Camille L. Gerard, Wenyi Xie, Nalinie Joharatnam-Hogan, Kate Young, Lisa Pickering, Andrew J. S. Furness, James Larkin, Ruth Harvey, George Kassiotis, Sonia Gandhi, Crick COVID-19 Consortium, Charles Swanton, Charlotte Fribbens, Katalin A. Wilkinson, Robert J. Wilkinson, David K. Lau, Susana Banerjee, Naureen Starling, Ian Chau, CAPTURE Consortium & Samra Turajlic
May 2021

Immunogenic Amino Acid Motifs and Linear Epitopes of COVID-19 mRNA Vaccines

Adam V Wisnewski, Carrie A Redlich, Kathy Kamath, Queenie-Ann Abad, Richard F Smith, Louis Fazen, Romero Santiago, Jian Liu, Julian Campillo Luna, Brian Martinez, Elizabeth Baum-Jones, Rebecca Waitz, Winston A Haynes, John C Shon
May 2021

Longitudinal immune profiling of a SARS-CoV-2 reinfection in a solid organ transplant recipient

Jonathan Klein, Anderson F. Brito, Paul Trubin, Peiwen Lu, Patrick Wong, Tara Alpert, Mario A. Peña-Hernández, Winston Haynes, Kathy Kamath, Feimei Liu, Chantal B. F. Vogels, Joseph R. Fauver, Carolina Lucas, Jieun Oh, Tianyang Mao, Julio Silva, Anne L. Wyllie, M. Catherine Muenker, Arnau Casanovas-Massana, Adam J. Moore, Mary E. Petrone, Chaney C. Kalinich, Yale IMPACT Research Team, Charles Dela Cruz, Shelli Farhadian, Aaron Ring, John Shon, Albert I. Ko, Nathan D. Grubaugh, Benjamin Israelow, Akiko Iwasaki, Marwan M. Azar
March 2021

Impact of B.1.1.7 variant mutations on antibody recognition of linear SARS-CoV-2 epitopes

Winston A. Haynes, Kathy Kamath, Carolina Lucas, John Shon, Akiko Iwasaki
January 2021

Rapid Reviews COVID-19: Reviews of "Impact of B.1.1.7 variant mutations on antibody recognition of linear SARS-CoV-2 epitopes"

Reviewers: Debmalya Barh (IIOAB) | Gregory Towers (University College London)
June 2021

High-resolution mapping and characterization of epitopes in COVID-19 patients

Winston A. Haynes, Kathy Kamath, Joel Bozekowski, Elisabeth Baum-Jones, Melissa Campbell, Arnau Casanovas-Massana, Patrick S. Daugherty, Charles S. Dela Cruz, Abhilash Dhal, Shelli F. Farhadian, Lynn Fitzgibbons, John Fournier, Michael Jhatro, Gregory Jordan, Debra Kessler, Jon Klein, Carolina Lucas, Larry L. Luchsinger, Brian Martinez, Mary C. Muenker, Lauren Pischel, Jack Reifert, Jaymie R. Sawyer, Rebecca Waitz, Elsio A. Wunder Jr., Minlu Zhang, Yale IMPACT Team, Akiko Iwasaki, Albert I. Ko, John C. Shon
November 2020

Prevalence of antibodies to SARS-CoV-2 in healthy blood donors in New York

Kathy Kamath, Elisabeth Baum-Jones, Gregory Jordan, Winston Haynes, Rebecca Waitz, John Shon, Steve Kujawa, Lyn Fitzgibbons, Debra Kessler, Larry Luchsinger, Yale IMPACT Team, Patrick Daugherty
October 2020

Diagnostic Panels

Tick-borne Disease and Lyme

Serum epitope repertoire analysis enables early detection of Lyme disease with improved sensitivity in an expandable multiplex format

Jack Reifert, Kathy Kamath, Joel Bozekowski, Ewa Lis, Elizabeth J. Horn, Dane Granger, Elitza S. Theel, John Shon, Jaymie R. Sawyer and Patrick S. Daugherty
October 2020

Performance of Serum Epitope Repertoire Analysis (SERA) for Multiplex Testing for Tick-borne Disease

K. Kamath, J. Reifert, S. Friedline, B. Waitz, E. Baum-Jones, G. Jordan, B. Martinez, J. Bozekowski, T. Johnston, C. Gable, W. Haynes, B. Himmetoglu, J. Sawyer, D. Granger, J. Shon, E. S. Theel, P. Daugherty
Poster
June 2019

Celiac

Identification of disease-specific motifs in the antibody specificity repertoire via next-generation sequencing

Robert J. Pantazes, Jack Reifert, Joel Bozekowski, Kelly N. Ibsen, Joseph A. Murray, Patrick S. Daugherty
Nature Scientific Reports
August 2016

Epitope Mapping

Serum and Cervicovaginal Fluid Antibody Profiling in Herpes Simplex Virus (HSV) Seronegative Recipients of the HSV529 Vaccine

Kening Wang, Lesia Dropulic, Joel Bozekowski, Harlan L Pietz, Sinthujan Jegaskanda, Kennichi Dowdell, Joshua S Vogel, Doreen Garabedian, Makinna Oestreich, Hanh Nguyen, Mir A Ali, Keith Lumbard, Sally Hunsberger, Jack Reifert, Winston A Haynes, Jaymie R Sawyer, John C Shon, Patrick S Daugherty, Jeffrey I Cohen
March 2021

Autoantibody landscape of advanced prostate cancer

William S. Chen, Winston A. Haynes, Rebecca Waitz, Kathy Kamath, Agustin Vega-Crespo, Raunak Shrestha, Adam Foye, Ignacio Baselga Carretero, Meng Zhang, Shuang G. Zhao, Martin Sjöström, David A. Quigley, Jonathan Chou, Tomasz M. Beer, Matthew Rettig, Martin Gleave, Christopher P. Evans, Primo Lara, Kim N. Chi, Robert E. Reiter, Joshi J. Alumkal, Rahul Aggarwal, Eric J. Small, Patrick S. Daugherty, Antoni Ribas, David Y. Oh, John C. Shon, Felix Y. Feng
October 2020

Antibody epitope repertoire analysis enables rapid antigen discovery and multiplex serology

Kathy Kamath, Jack Reifert, Timothy Johnston, Cameron Gable, Robert J. Pantazes, Hilda N. Rivera, Isabel McAuliffe, Sukwan Handali & Patrick S. Daugherty
March 2020

A General Approach for Predicting Protein Epitopes Targeted by Antibody Repertoires Using Whole Proteomes.

Paull ML, Johnston T, Ibsen KN, Bozekowski JD, Daugherty PS.
PLoS One
September 2019

Serum Epitope Repertoire Analysis (SERA) Enables Serologic Immune Monitoring

K. Kamath, J. Reifert, J. Bozekowski, B. Martinez, C. Gable, T. Johnston, P. Daugherty
Poster
June 2019

Polyplex infectious disease serology enabled by antibody epitope repertoire sequencing

Kathryn Kamath, Jack Reifert, Skyler Friedline, Robert Pantazes, Cameron Gable, Tim Johnston, Jaymie Sawyer, John Shon and Patrick S. Daugherty
Poster
August 2018

Mapping serum antibody repertoires using peptide libraries

Michael L Paull, Patrick S. Daugherty
Current Opinion in Chemical Engineering
March 2018

High-titer antibody depletion enhances discovery of diverse serum antibody specificities.

Bozekowski JD, Graham AJ, Daugherty PS.
J Immunol Methods. 2018 Apr;455:1-9. doi: 10.1016/j.jim.2018.01.003. Epub 2018 Jan 24.

Antibody Biomarker Discovery Via In Vitro Evolution of Peptides.

Ballew JT, Reifert JR, Daugherty PS.
Methods Mol Biol. 2018;1785:249-268. doi: 10.1007/978-1-4939-7841-0_17.

Prediction of antibody structural epitopes via random peptide library screening and next generation sequencing.

Ibsen KN, Daugherty PS.
J Immunol Methods. 2017 Dec;451:28-36. doi: 10.1016/j.jim.2017.08.004. Epub 2017 Aug 18.

Identification of disease-specific motifs in the antibody specificity repertoire via next-generation sequencing

Robert J. Pantazes, Jack Reifert, Joel Bozekowski, Kelly N. Ibsen, Joseph A. Murray, Patrick S. Daugherty
Nature Scientific Reports
August 2016

Persistence of elevated deamidated gliadin peptide antibodies on a gluten-free diet indicates nonresponsive coeliac disease.

Spatola BN, Kaukinen K, Collin P, Mäki M, Kagnoff MF, Daugherty PS.
Aliment Pharmacol Ther. 2014 Feb;39(4):407-17. doi: 10.1111/apt.12603. Epub 2014 Jan 6.

Antibody biomarker discovery through in vitro directed evolution of consensus recognition epitopes.

Ballew JT, Murray JA, Collin P, Mäki M, Kagnoff MF, Kaukinen K, Daugherty PS.
Proc Natl Acad Sci U S A. 2013 Nov 26;110(48):19330-5. doi: 10.1073/pnas.1314792110. Epub 2013 Nov 12.

Quantitative specificity-based display library screening identifies determinants of antibody-epitope binding specificity.

Hall SS, Daugherty PS.
Protein Sci. 2009 Sep;18(9):1926-34. doi: 10.1002/pro.203.

Directed evolution of a biterminal bacterial display scaffold enhances the display of diverse peptides.

Rice JJ, Daugherty PS.
Protein Eng Des Sel. 2008 Jul;21(7):435-42. doi: 10.1093/protein/gzn020. Epub 2008 May 13.

Vaccines

Immunogenic Amino Acid Motifs and Linear Epitopes of COVID-19 mRNA Vaccines

Adam V Wisnewski, Carrie A Redlich, Kathy Kamath, Queenie-Ann Abad, Richard F Smith, Louis Fazen, Romero Santiago, Jian Liu, Julian Campillo Luna, Brian Martinez, Elizabeth Baum-Jones, Rebecca Waitz, Winston A Haynes, John C Shon
May 2021