About the Authors

Devin Sok

Contributed equally to this work with: Devin Sok, Uri Laserson, Jonathan Laserson, Yi Liu

Affiliations Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America, Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California, United States of America

Uri Laserson

Contributed equally to this work with: Devin Sok, Uri Laserson, Jonathan Laserson, Yi Liu

Affiliations Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America, Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America

Jonathan Laserson

Contributed equally to this work with: Devin Sok, Uri Laserson, Jonathan Laserson, Yi Liu

Affiliation Department of Computer Science, Stanford University, Stanford, California, United States of America

Yi Liu

Contributed equally to this work with: Devin Sok, Uri Laserson, Jonathan Laserson, Yi Liu

Affiliations Department of Computer Science, Stanford University, Stanford, California, United States of America, Biomedical Informatics Training Program, Stanford University School of Medicine, Stanford, California, United States of America

Francois Vigneault

Affiliations Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America, AbVitro Inc., Boston, Massachusetts, United States of America

Jean-Philippe Julien

Affiliations IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America, Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California, United States of America, Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America

Bryan Briney

Affiliations Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America, Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California, United States of America

Alejandra Ramos

Affiliations Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America, Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California, United States of America, International AIDS Vaccine Initiative, New York, New York, United States of America

Karen F. Saye

Affiliations Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America, Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California, United States of America

Khoa Le

Affiliations Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America, Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California, United States of America

Alison Mahan

Affiliation Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, Massachusetts, United States of America

Shenshen Wang

Affiliations Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America

Mehran Kardar

Affiliation Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America

Gur Yaari

Affiliation Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America

Laura M. Walker

Affiliation Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America

Birgitte B. Simen

Affiliation 454 Life Sciences – A Roche Company, Branford, Connecticut, United States of America

Elizabeth P. St. John

Affiliation 454 Life Sciences – A Roche Company, Branford, Connecticut, United States of America

Po-Ying Chan-Hui

Affiliation Theraclone Sciences, Inc., Seattle, Washington, United States of America

Kristine Swiderek

Affiliation Theraclone Sciences, Inc., Seattle, Washington, United States of America

Stephen H. Kleinstein

Affiliation Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America

Galit Alter

Affiliation Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, Massachusetts, United States of America

Michael S. Seaman

Affiliation Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America

Arup K. Chakraborty

Affiliations Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, Massachusetts, United States of America, Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America, Department of Chemistry, Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America

Daphne Koller

Affiliation Department of Computer Science, Stanford University, Stanford, California, United States of America

Ian A. Wilson

Affiliations IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America, Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California, United States of America, Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America

George M. Church

Affiliations Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America, Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America

Dennis R. Burton

burton@scripps.edu

Affiliations Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America, Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California, United States of America, Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, Massachusetts, United States of America

Pascal Poignard

Affiliations Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America, IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America, International AIDS Vaccine Initiative, New York, New York, United States of America

Competing Interests

Authors BBS and EPSJ are employed by 454 Life Sciences - Roche Sequencing Solutions. Authors PYCH and KS are employed by Theraclone-Sciences. FV is employed by, UL and GMC are advisors to, and FV, UL, and GMC own stock in AbVitro, which owns intellectual property in various immune sequencing technologies. The IAVI and Theraclone hold U.S. patent 61/515,528 on the PGT antibodies. All other authors declare no competing interests. This does not alter our adherence to all PLOS Pathogens policies on sharing data and materials.

Author Contributions

Conceived and designed the experiments: DS UL JL YL FV JPJ BB LMW DRB PP. Performed the experiments: DS UL JL YL FV JPJ BB AR KFS KL AM BBS EPSJ PYCH KS MSS. Analyzed the data: DS UL JL YL FV JPJ BB SW MK AKC IAW DRB PP. Contributed reagents/materials/analysis tools: GY SHK. Wrote the paper: DS UL JL YL FV JPJ BB IAW DRB PP. Supervised research: GA DK GMC.