Sökresultat - "Gygi JP"

Putting computational models of immunity to the test-An invited challenge to predict B.pertussis vaccination responses.

Shinde P; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, California, United States of America., Willemsen L; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, California, United States of America., Anderson M; Division of Biostatistics and Health Data Science, University of Minnesota, Minneapolis, Minnesota, United States of America., Aoki M; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, California, United States of America., Basu S; Division of Biostatistics and Health Data Science, University of Minnesota, Minneapolis, Minnesota, United States of America., Burel JG; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, California, United States of America., Cheng P; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America., Ghosh Dastidar S; Division of Biostatistics and Health Data Science, University of Minnesota, Minneapolis, Minnesota, United States of America., Dunleavy A; School of Statistics, University of Minnesota, Minneapolis, Minnesota, United States of America., Einav T; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, California, United States of America.; Department of Medicine, University of California San Diego, San Diego, California, United States of America., Forschmiedt J; Division of Biostatistics and Health Data Science, University of Minnesota, Minneapolis, Minnesota, United States of America., Fourati S; Department of Medicine, Division of Allergy and Immunology, Feinberg School of Medicine and Center for Human Immunobiology, Northwestern University, Chicago, Illinois, United States of America., Garcia J; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America., Gibson W; Vaccine Research Center, National Institute of Allergy and Infectious Disease, National Institute of Health, Bethesda, Maryland, United States of America., Greenbaum JA; LJI Bioinformatics Core, La Jolla Institute for Immunology, La Jolla, California, United States of America., Guan L; Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America., Guan W; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America., Gygi JP; Program in Computational Biology & Bioinformatics, Yale University, New Haven, Connecticut, United States of America., Ha B; LJI Bioinformatics Core, La Jolla Institute for Immunology, La Jolla, California, United States of America., Hou J; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America., Hsiao J; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America., Huang Y; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America.; Department of Global Health, University of Washington, Seattle, Washington, United States of America., Jansen R; Biostatistics Core, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America., Kakoty B; Division of Biostatistics and Health Data Science, University of Minnesota, Minneapolis, Minnesota, United States of America., Kang Z; Division of Biostatistics and Health Data Science, University of Minnesota, Minneapolis, Minnesota, United States of America., Kobie JJ; Department of Medicine, Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, United States of America., Kojima M; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, California, United States of America., Konstorum A; Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America.; Laboratory for Systems Biology, University of Florida, Gainesville, Florida, United States of America., Lee J; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, California, United States of America., Lewis SA; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, California, United States of America., Li A; Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, Minnesota, United States of America., Lock EF; Division of Biostatistics and Health Data Science, University of Minnesota, Minneapolis, Minnesota, United States of America., Mahita J; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, California, United States of America., Mendes M; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, California, United States of America., Meng H; Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America., Neher A; Division of Biostatistics and Health Data Science, University of Minnesota, Minneapolis, Minnesota, United States of America., Nili S; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, California, United States of America., Olsen LR; Department of Immunology and Microbiology, LEO Foundation Skin Immunology Research Center, University of Copenhagen, Copenhagen, Denmark., Orfield S; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, California, United States of America., Overton JA; Knocean, Inc., Toronto, Canada., Pai N; Division of Biostatistics and Health Data Science, University of Minnesota, Minneapolis, Minnesota, United States of America., Parker C; National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, Maryland, United States of America., Qian B; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America., Rasmussen M; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, California, United States of America., Reyna J; Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, California, United States of America.; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, California, United States of America., Richardson E; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, California, United States of America., Safo S; Division of Biostatistics and Health Data Science, University of Minnesota, Minneapolis, Minnesota, United States of America., Sorenson J; Division of Biostatistics and Health Data Science, University of Minnesota, Minneapolis, Minnesota, United States of America., Srinivasan A; Division of Biostatistics and Health Data Science, University of Minnesota, Minneapolis, Minnesota, United States of America., Thrupp N; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, California, United States of America., Tippalagama R; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, California, United States of America., Trevizani R; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, California, United States of America.; Fundação Oswaldo Cruz, Fiocruz - Ceará, Brazil., Ventz S; Division of Biostatistics and Health Data Science, University of Minnesota, Minneapolis, Minnesota, United States of America., Wang J; Division of Biostatistics and Health Data Science, University of Minnesota, Minneapolis, Minnesota, United States of America., Wu CC; Division of Biostatistics and Health Data Science, University of Minnesota, Minneapolis, Minnesota, United States of America., Ay F; Department of Medicine, University of California San Diego, San Diego, California, United States of America.; Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, California, United States of America.; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, California, United States of America., Grant B; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America., Kleinstein SH; Program in Computational Biology & Bioinformatics, Yale University, New Haven, Connecticut, United States of America.; Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America., Peters B; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, California, United States of America.; Department of Medicine, University of California San Diego, San Diego, California, United States of America.

Journal Article , 2025

Identification of a multi-omics factor predictive of long COVID in the IMPACC study.

Gabernet G; Yale School of Medicine, New Haven, CT 06511, USA.; These authors contributed equally., Maciuch J; Northwestern Feinberg School of Medicine, Chicago, IL 60611, USA.; These authors contributed equally., Gygi JP; Yale School of Medicine, New Haven, CT 06511, USA.; These authors contributed equally., Moore JF; The University of Texas at Austin, Austin, TX 78712, USA.; These authors contributed equally., Hoch A; Clinical and Data Coordinating Center (CDCC), Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA., Syphurs C; Clinical and Data Coordinating Center (CDCC), Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA., Chu T; Yale School of Medicine, New Haven, CT 06511, USA., Jayavelu ND; Benaroya Research Institute, University of Washington, Seattle, WA 98101, USA., Corry DB; Baylor College of Medicine and the Center for Translational Research on Inflammatory Diseases, Houston, TX 77030, USA., Kheradmand F; Baylor College of Medicine and the Center for Translational Research on Inflammatory Diseases, Houston, TX 77030, USA., Baden LR; Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115., Sekaly RP; Case Western Reserve University and University Hospitals of Cleveland, Cleveland, OH 44106, USA., McComsey GA; Case Western Reserve University and University Hospitals of Cleveland, Cleveland, OH 44106, USA., Haddad EK; Drexel University, Tower Health Hospital, Philadelphia, PA 19104, USA., Cairns CB; Drexel University, Tower Health Hospital, Philadelphia, PA 19104, USA., Rouphael N; Emory School of Medicine, Atlanta, GA 30322, USA., Fernandez-Sesma A; Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Simon V; Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Metcalf JP; Oklahoma University Health Sciences Center, Oklahoma City, OK 73104., Agudelo Higuita NI; Oklahoma University Health Sciences Center, Oklahoma City, OK 73104., Hough CL; Oregon Health & Science University, Portland, OR 97239, USA., Messer WB; Oregon Health & Science University, Portland, OR 97239, USA., Davis MM; Stanford University School of Medicine, Palo Alto, CA 94305, USA., Nadeau KC; Stanford University School of Medicine, Palo Alto, CA 94305, USA., Pulendran B; Stanford University School of Medicine, Palo Alto, CA 94305, USA., Kraft M; University of Arizona, Tucson AZ 85721, USA., Bime C; University of Arizona, Tucson AZ 85721, USA., Reed EF; David Geffen School of Medicine at the University of California Los Angeles, Los Angeles CA 90095, USA., Schaenman J; David Geffen School of Medicine at the University of California Los Angeles, Los Angeles CA 90095, USA., Erle DJ; University of California San Francisco, San Francisco, CA 94115, USA., Calfee CS; University of California San Francisco, San Francisco, CA 94115, USA., Atkinson MA; University of Florida, Gainesville, FL 32611, USA., Brackenridge SC; University of Florida, Gainesville, FL 32611, USA., Melamed E; The University of Texas at Austin, Austin, TX 78712, USA., Shaw AC; Yale School of Medicine, New Haven, CT 06511, USA., Hafler DA; Yale School of Medicine, New Haven, CT 06511, USA., Ozonoff A; Clinical and Data Coordinating Center (CDCC), Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA., Bosinger SE; Emory School of Medicine, Atlanta, GA 30322, USA., Eckalbar W; University of California San Francisco, San Francisco, CA 94115, USA., Maecker HT; Stanford University School of Medicine, Palo Alto, CA 94305, USA., Kim-Schulze S; Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Steen H; Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA., Krammer F; Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Westendorf K; La Jolla Institute for Immunology, La Jolla, CA 92037, USA., Peters B; La Jolla Institute for Immunology, La Jolla, CA 92037, USA., Fourati S; Northwestern Feinberg School of Medicine, Chicago, IL 60611, USA., Altman MC; Benaroya Research Institute, University of Washington, Seattle, WA 98101, USA., Levy O; Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA., Smolen KK; Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA., Montgomery RR; Yale School of Medicine, New Haven, CT 06511, USA., Diray-Arce J; Clinical and Data Coordinating Center (CDCC), Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA., Kleinstein SH; Yale School of Medicine, New Haven, CT 06511, USA.; These authors contributed equally., Guan L; Yale School of Medicine, New Haven, CT 06511, USA.; These authors contributed equally., Ehrlich LIR; The University of Texas at Austin, Austin, TX 78712, USA.; These authors contributed equally.; Lead Contact.

IMPACC Network

Journal Article; Preprint , 2025

Unraveling SARS-CoV-2 Host-Response Heterogeneity through Longitudinal Molecular Subtyping.

Wang K, Nie Y, Maguire C, Syphurs C, Sheen H, Karoly M, Lapp L, Gygi JP, Jayavelu ND, Patel RK, Hoch A, Corry D, Kheradmand F, McComsey GA, Fernandez-Sesma A, Simon V, Metcalf JP, Higuita NIA, Messer WB, Davis MM, Nadeau KC, Kraft M, Bime C, Schaenman J, Erle D, Calfee CS, Atkinson MA, Brackenridge SC, Hafler DA, Shaw A, Rahman A, Hough CL, Geng LN, Ozonoff A, Haddad EK, Reed EF, van Bakel H, Kim-Schultz S, Krammer F, Wilson M, Eckalbar W, Bosinger S, Langelier CR, Sekaly RP, Montgomery RR, Maecker HT, Krumholz H, Melamed E, Steen H, Pulendran B, Augustine AD, Cairns CB, Rouphael N, Becker PM, Fourati S, Shannon CP, Smolen KK, Peters B, Kleinstein SH, Levy O, Altman MC, Iwasaki A, Diray-Arce J, Ehrlich LIR, Guan L

IMPACC Network

Journal Article; Preprint , 2024

Putting computational models of immunity to the test - an invited challenge to predict B. pertussis vaccination outcomes.

Shinde P; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA., Willemsen L; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA., Anderson M; Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA., Aoki M; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA., Basu S; Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA., Burel JG; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA., Cheng P; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA., Dastidar SG; Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA., Dunleavy A; School of Statistics, University of Minnesota, Minneapolis, MN, USA., Einav T; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA.; Department of Medicine, University of California San Diego, San Diego, CA, USA., Forschmiedt J; Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA., Fourati S; Department of Medicine, Division of Allergy and Immunology, Feinberg School of Medicine and Center for Human Immunobiology, Northwestern University, Chicago, IL, USA., Garcia J; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA., Gibson W; Vaccine Research Center, National Institute of Allergy and Infectious Disease, National Institute of Health, Bethesda, MD, USA., Greenbaum JA; LJI Bioinformatics Core, La Jolla Institute for Immunology, La Jolla, CA, USA., Guan L; Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA., Guan W; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA., Gygi JP; Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, USA., Ha B; LJI Bioinformatics Core, La Jolla Institute for Immunology, La Jolla, CA, USA., Hou J; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA., Hsiao J; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA., Huang Y; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.; Department of Global Health, University of Washington, Seattle, WA, USA., Jansen R; Biostatistics Core, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA., Kakoty B; Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA., Kang Z; Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA., Kobie JJ; Department of Medicine, Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, USA., Kojima M; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA., Konstorum A; Department of Pathology, Yale School of Medicine, New Haven, CT, USA.; Laboratory for Systems Biology, University of Florida., Lee J; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA., Lewis SA; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA., Li A; Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA., Lock EF; Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA., Mahita J; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA., Mendes M; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA., Meng H; Department of Pathology, Yale School of Medicine, New Haven, CT, USA., Neher A; Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA., Nili S; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA., Olsen LR; University of Denmark, Denmark., Orfield S; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA., Overton JA; Knocean, Inc., Toronto, Canada., Pai N; Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA., Parker C; National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA., Qian B; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA., Rasmussen M; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA., Reyna J; Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, USA.; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, San Diego, CA, USA., Richardson E; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA., Safo S; Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA., Sorenson J; Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA., Srinivasan A; Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA., Thrupp N; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA., Tippalagama R; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA., Trevizani R; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA.; Fundação Oswaldo Cruz, Fiocruz - Ceará, Brazil., Ventz S; Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA., Wang J; Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA., Wu CC; Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA., Ay F; Department of Medicine, University of California San Diego, San Diego, CA, USA.; Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, USA., Grant B; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA., Kleinstein SH; Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, USA.; Department of Pathology, Yale School of Medicine, New Haven, CT, USA., Peters B; Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA.; Department of Medicine, University of California San Diego, San Diego, CA, USA.

Journal Article; Preprint , 2024

A supervised Bayesian factor model for the identification of multi-omics signatures.

Gygi JP; Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT 06520, United States., Konstorum A; Department of Pathology, Yale School of Medicine, New Haven, CT 06520, United States., Pawar S; Department of Genetics, Yale Center for Genomic Analysis (YCGA), Yale School of Medicine, New Haven, CT 06520, United States., Aron E; Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT 06520, United States., Kleinstein SH; Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT 06520, United States.; Department of Pathology, Yale School of Medicine, New Haven, CT 06520, United States.; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, United States., Guan L; Department of Biostatistics, Yale School of Public Health, New Haven, CT 06520, United States.

Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't , 2024

Integrated longitudinal multiomics study identifies immune programs associated with acute COVID-19 severity and mortality.

Gygi JP; Yale School of Medicine, New Haven, Connecticut, USA., Maguire C; The University of Texas at Austin, Austin, Texas, USA., Patel RK; UCSF, San Francisco, California, USA., Shinde P; La Jolla Institute for Immunology, La Jolla, California, USA., Konstorum A; Yale School of Medicine, New Haven, Connecticut, USA., Shannon CP; Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada.; Prevention of Organ Failure (PROOF) Centre of Excellence, Providence Research, Vancouver, British Columbia, Canada., Xu L; Yale School of Public Health, New Haven, Connecticut, USA., Hoch A; Clinical and Data Coordinating Center (CDCC) and.; Precision Vaccines Program, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA., Jayavelu ND; Benaroya Research Institute, Seattle, Washington, USA., Haddad EK; Drexel University, Tower Health Hospital, Philadelphia, Pennsylvania, USA., Reed EF; David Geffen School of Medicine at the UCLA, Los Angeles, California, USA., Kraft M; Icahn School of Medicine at Mount Sinai, New York, New York, USA., McComsey GA; Case Western Reserve University and University Hospitals of Cleveland, Cleveland, Ohio, USA., Metcalf JP; Oklahoma University Health Sciences Center, Oklahoma City, Oklahoma, USA., Ozonoff A; Clinical and Data Coordinating Center (CDCC) and.; Precision Vaccines Program, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA.; Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.; Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA., Esserman D; Yale School of Public Health, New Haven, Connecticut, USA., Cairns CB; Drexel University, Tower Health Hospital, Philadelphia, Pennsylvania, USA., Rouphael N; Emory School of Medicine, Atlanta, Georgia, USA., Bosinger SE; Emory School of Medicine, Atlanta, Georgia, USA., Kim-Schulze S; Icahn School of Medicine at Mount Sinai, New York, New York, USA., Krammer F; Icahn School of Medicine at Mount Sinai, New York, New York, USA.; Ignaz Semmelweis Institute, Interuniversity Institute for Infection Research, Medical University of Vienna, Vienna, Austria., Rosen LB; National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA., van Bakel H; Icahn School of Medicine at Mount Sinai, New York, New York, USA., Wilson M; UCSF, San Francisco, California, USA., Eckalbar WL; UCSF, San Francisco, California, USA., Maecker HT; Stanford University School of Medicine, Palo Alto, California, USA., Langelier CR; UCSF, San Francisco, California, USA., Steen H; Precision Vaccines Program, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA.; Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA., Altman MC; Benaroya Research Institute, Seattle, Washington, USA., Montgomery RR; Yale School of Medicine, New Haven, Connecticut, USA., Levy O; Precision Vaccines Program, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA.; Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.; Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA., Melamed E; The University of Texas at Austin, Austin, Texas, USA., Pulendran B; Stanford University School of Medicine, Palo Alto, California, USA., Diray-Arce J; Clinical and Data Coordinating Center (CDCC) and.; Precision Vaccines Program, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA.; Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA., Smolen KK; Precision Vaccines Program, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA.; Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA., Fragiadakis GK; UCSF, San Francisco, California, USA., Becker PM; National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA., Sekaly RP; Case Western Reserve University and University Hospitals of Cleveland, Cleveland, Ohio, USA., Ehrlich LI; The University of Texas at Austin, Austin, Texas, USA., Fourati S; Case Western Reserve University and University Hospitals of Cleveland, Cleveland, Ohio, USA., Peters B; La Jolla Institute for Immunology, La Jolla, California, USA.; Department of Medicine, UCSD, La Jolla, California, USA., Kleinstein SH; Yale School of Medicine, New Haven, Connecticut, USA., Guan L; Yale School of Public Health, New Haven, Connecticut, USA.

IMPACC Network

Journal Article; Observational Study; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't , 2024

A multi-omics systems vaccinology resource to develop and test computational models of immunity.

Shinde P; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA., Soldevila F; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA., Reyna J; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, San Diego, CA, USA., Aoki M; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA., Rasmussen M; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA; Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark., Willemsen L; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA., Kojima M; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA., Ha B; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA., Greenbaum JA; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA., Overton JA; Knocean Inc., 107 Quebec Avenue, Toronto, Ontario M6P 2T3, Canada., Guzman-Orozco H; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA., Nili S; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA., Orfield S; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA., Gygi JP; Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, USA., da Silva Antunes R; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA., Sette A; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, San Diego, CA, USA., Grant B; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA., Olsen LR; Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark., Konstorum A; Department of Pathology, Yale University School of Medicine, New Haven, CT, USA., Guan L; Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA., Ay F; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, San Diego, CA, USA., Kleinstein SH; Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT, USA., Peters B; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, San Diego, CA, USA. Electronic address: bpeters@lji.org.

Journal Article , 2024

Integrated longitudinal multi-omics study identifies immune programs associated with COVID-19 severity and mortality in 1152 hospitalized participants.

Gygi JP, Maguire C, Patel RK, Shinde P, Konstorum A, Shannon CP, Xu L, Hoch A, Jayavelu ND, Network I, Haddad EK, Reed EF, Kraft M, McComsey GA, Metcalf J, Ozonoff A, Esserman D, Cairns CB, Rouphael N, Bosinger SE, Kim-Schulze S, Krammer F, Rosen LB, van Bakel H, Wilson M, Eckalbar W, Maecker H, Langelier CR, Steen H, Altman MC, Montgomery RR, Levy O, Melamed E, Pulendran B, Diray-Arce J, Smolen KK, Fragiadakis GK, Becker PM, Augustine AD, Sekaly RP, Ehrlich LIR, Fourati S, Peters B, Kleinstein SH, Guan L

Preprint; Journal Article , 2023

A supervised Bayesian factor model for the identification of multi-omics signatures.

Gygi JP, Konstorum A, Pawar S, Aron E, Kleinstein SH, Guan L

Preprint; Journal Article , 2023

A systems vaccinology resource to develop and test computational models of immunity.

Shinde P; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA., Soldevila F; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA., Reyna J; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, CA, USA., Aoki M; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA., Rasmussen M; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.; Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark., Willemsen L; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA., Kojima M; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA., Ha B; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA., Greenbaum JA; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA., Overton JA; Knocean Inc., 107 Quebec Ave. Toronto, Ontario, M6P 2T3, Canada., Guzman-Orozco H; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA., Nili S; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA., Orfield S; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA., Gygi JP; Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, USA., da Silva Antunes R; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA., Sette A; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.; Department of Medicine, University of California, San Diego, San Diego, CA, USA., Grant B; Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, California, USA., Olsen LR; Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark., Konstorum A; Department of Pathology, Yale University School of Medicine, New Haven, CT, USA., Guan L; Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA., Ay F; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.; Department of Medicine, University of California, San Diego, San Diego, CA, USA., Kleinstein SH; Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, USA.; Department of Pathology, Yale University School of Medicine, New Haven, CT, USA., Peters B; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.; Department of Medicine, University of California, San Diego, San Diego, CA, USA.

Preprint; Journal Article , 2023

Predictive overfitting in immunological applications: Pitfalls and solutions.

Gygi JP; Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, USA., Kleinstein SH; Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, USA.; Department of Pathology, Yale School of Medicine, New Haven, CT, USA.; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA., Guan L; Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, USA.; Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA.

Journal Article; Review; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S. , 2023

Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients.

Diray-Arce J; Clinical and Data Coordinating Center, Boston Children's Hospital, Boston, MA 02115, USA; Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA. Electronic address: joann.arce@childrens.harvard.edu., Fourati S; Emory School of Medicine, Atlanta, GA 30322, USA., Doni Jayavelu N; Benaroya Research Institute, University of Washington, Seattle, WA 98101, USA., Patel R; University of California San Francisco, San Francisco, CA 94115, USA., Maguire C; The University of Texas at Austin, Austin, TX 78712, USA., Chang AC; Clinical and Data Coordinating Center, Boston Children's Hospital, Boston, MA 02115, USA., Dandekar R; University of California San Francisco, San Francisco, CA 94115, USA., Qi J; Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Lee BH; Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., van Zalm P; Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA., Schroeder A; University of California San Francisco, San Francisco, CA 94115, USA., Chen E; Yale School of Medicine, New Haven, CT 06510, USA., Konstorum A; Yale School of Medicine, New Haven, CT 06510, USA., Brito A; Yale School of Public Health, New Haven, CT 06510, USA., Gygi JP; Yale School of Medicine, New Haven, CT 06510, USA., Kho A; Clinical and Data Coordinating Center, Boston Children's Hospital, Boston, MA 02115, USA., Chen J; Clinical and Data Coordinating Center, Boston Children's Hospital, Boston, MA 02115, USA; Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA., Pawar S; Yale School of Medicine, New Haven, CT 06510, USA., Gonzalez-Reiche AS; Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Hoch A; Clinical and Data Coordinating Center, Boston Children's Hospital, Boston, MA 02115, USA; Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA., Milliren CE; Clinical and Data Coordinating Center, Boston Children's Hospital, Boston, MA 02115, USA., Overton JA; Knocean, Inc., Toronto, ON M6P 2T3, Canada., Westendorf K; La Jolla Institute for Immunology, La Jolla, CA 92037, USA., Cairns CB; Drexel University, Tower Health Hospital, Philadelphia, PA 19104, USA., Rouphael N; Emory School of Medicine, Atlanta, GA 30322, USA., Bosinger SE; Emory School of Medicine, Atlanta, GA 30322, USA., Kim-Schulze S; Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Krammer F; Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Rosen L; National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD 20814, USA., Grubaugh ND; Yale School of Public Health, New Haven, CT 06510, USA., van Bakel H; Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Wilson M; University of California San Francisco, San Francisco, CA 94115, USA., Rajan J; University of California San Francisco, San Francisco, CA 94115, USA., Steen H; Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA., Eckalbar W; University of California San Francisco, San Francisco, CA 94115, USA., Cotsapas C; Yale School of Medicine, New Haven, CT 06510, USA; Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA., Langelier CR; University of California San Francisco, San Francisco, CA 94115, USA., Levy O; Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA., Altman MC; Benaroya Research Institute, University of Washington, Seattle, WA 98101, USA., Maecker H; Stanford University School of Medicine, Palo Alto, CA 94305, USA., Montgomery RR; Yale School of Medicine, New Haven, CT 06510, USA., Haddad EK; Drexel University, Tower Health Hospital, Philadelphia, PA 19104, USA., Sekaly RP; Emory School of Medicine, Atlanta, GA 30322, USA., Esserman D; Yale School of Public Health, New Haven, CT 06510, USA., Ozonoff A; Clinical and Data Coordinating Center, Boston Children's Hospital, Boston, MA 02115, USA; Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA., Becker PM; National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD 20814, USA., Augustine AD; National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD 20814, USA., Guan L; Yale School of Public Health, New Haven, CT 06510, USA., Peters B; La Jolla Institute for Immunology, La Jolla, CA 92037, USA., Kleinstein SH; Yale School of Medicine, New Haven, CT 06510, USA. Electronic address: steven.kleinstein@yale.edu.

IMPACC Network

Journal Article; Research Support, N.I.H., Extramural , 2023

Assessing interference in isobaric tag-based sample multiplexing using an 18-plex interference standard.

Navarrete-Perea J; Department of Cell Biology, Harvard Medical School, Boston, MA, USA., Liu X; Department of Cell Biology, Harvard Medical School, Boston, MA, USA., Rad R; Department of Cell Biology, Harvard Medical School, Boston, MA, USA., Gygi JP; Department of Cell Biology, Harvard Medical School, Boston, MA, USA., Gygi SP; Department of Cell Biology, Harvard Medical School, Boston, MA, USA., Paulo JA; Department of Cell Biology, Harvard Medical School, Boston, MA, USA.

Journal Article; Research Support, N.I.H., Extramural , 2022

A Triple Knockout Isobaric-Labeling Quality Control Platform with an Integrated Online Database Search.

Gygi JP; Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States., Ramin Rad; Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States., Navarrete-Perea J; Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States., Younesi S; Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States., Gygi SP; Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States., Paulo JA; Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States.

Journal Article , 2020

Web-Based Search Tool for Visualizing Instrument Performance Using the Triple Knockout (TKO) Proteome Standard.

Gygi JP; Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States., Yu Q; Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States., Navarrete-Perea J; Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States., Rad R; Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States., Gygi SP; Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States., Paulo JA; Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States.

Journal Article; Research Support, N.I.H., Extramural , 2019

ACP Acylation Is an Acetyl-CoA-Dependent Modification Required for Electron Transport Chain Assembly.

Van Vranken JG; Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84132, USA., Nowinski SM; Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84132, USA., Clowers KJ; Department of Cell Biology, Harvard University School of Medicine, Boston, MA 02115, USA., Jeong MY; Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84132, USA; Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT 84132, USA., Ouyang Y; Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84132, USA., Berg JA; Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84132, USA., Gygi JP; Department of Cell Biology, Harvard University School of Medicine, Boston, MA 02115, USA., Gygi SP; Department of Cell Biology, Harvard University School of Medicine, Boston, MA 02115, USA., Winge DR; Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84132, USA; Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT 84132, USA., Rutter J; Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84132, USA; Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84132, USA. Electronic address: rutter@biochem.utah.edu.

Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't , 2018