Search Results - "Fragiadakis GK"

Single-cell omics technologies - Fundamentals on how to create single-cell looking glasses for reproductive health.

Diop M; Program in Immunology, Stanford University School of Medicine, Stanford, CA; Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA., Davidson BR; UCSF CoLabs, University of California, San Francisco, CA., Fragiadakis GK; UCSF CoLabs, University of California, San Francisco, CA; Bakar ImmunoX Initiative, University of California, San Francisco, CA; Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA. Electronic address: Gabriela.Fragiadakis@ucsf.edu., Sirota M; Bakar Computational Health Sciences Institute, University of California, San Francisco, CA; Department of Pediatrics, University of California, San Francisco, CA. Electronic address: marina.sirota@ucsf.edu., Gaudillière B; Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA. Electronic address: gbrice@stanford.edu., Combes AJ; UCSF CoLabs, University of California, San Francisco, CA; Department of Pathology, University of California, San Francisco, CA; Bakar ImmunoX Initiative, University of California, San Francisco, CA; Division of Gastroenterology, Department of Medicine, University of California, San Francisco, CA. Electronic address: Alexis.Combes@ucsf.edu.

Journal Article; Review , 2025

Coordinated variation in the immune systems and microbiomes of healthy humans is linked to tonic interferon states.

Babdor J, Patel RK, Davidson B, Noecker C, Rahim M, Bisanz JE, Tenvooren I, Marquez D, Calvo M, Johri V, McCarthy E, Shaheed A, Ekstrand C, Weakley AM, Yu FB, Fiehn O, Turnbaugh PJ, Combes AJ, Fragiadakis GK, Spitzer MH

Journal Article; Preprint , 2024

Single-cell spatial transcriptomics of fixed, paraffin-embedded biopsies reveals colitis-associated cell networks.

Mennillo E; Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA., Lotstein ML; Biomedical Sciences graduate program, University of California, San Francisco, San Francisco, CA 94143, USA.; UCSF CoLabs Initiative, University of California, San Francisco, San Francisco, CA 94143, USA., Lee G; Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA., Johri V; UCSF CoLabs Initiative, University of California, San Francisco, San Francisco, CA 94143, USA., Ekstrand C; Biomedical Sciences graduate program, University of California, San Francisco, San Francisco, CA 94143, USA.; UCSF CoLabs Initiative, University of California, San Francisco, San Francisco, CA 94143, USA., Tsui J; UCSF CoLabs Initiative, University of California, San Francisco, San Francisco, CA 94143, USA., Hou J; Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA., Leet DE; Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA., He JY; Division of Hematology/Oncology, University of California, San Francisco, San Francisco, CA 94143, USA.; UCSF Bakar ImmunoX Initiative, University of California, San Francisco, San Francisco, CA 94143, USA., Mahadevan U; Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA., Eckalbar W; UCSF CoLabs Initiative, University of California, San Francisco, San Francisco, CA 94143, USA.; Division of pulmonary and intensive care, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA., Oh DY; Division of Hematology/Oncology, University of California, San Francisco, San Francisco, CA 94143, USA.; UCSF Bakar ImmunoX Initiative, University of California, San Francisco, San Francisco, CA 94143, USA., Fragiadakis GK; Biomedical Sciences graduate program, University of California, San Francisco, San Francisco, CA 94143, USA.; UCSF CoLabs Initiative, University of California, San Francisco, San Francisco, CA 94143, USA.; Division of Rheumatology, University of California, San Francisco, San Francisco, CA 94143, USA.; UCSF Bakar ImmunoX Initiative, University of California, San Francisco, San Francisco, CA 94143, USA., Kattah MG; Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.; Biomedical Sciences graduate program, University of California, San Francisco, San Francisco, CA 94143, USA.; UCSF Bakar ImmunoX Initiative, University of California, San Francisco, San Francisco, CA 94143, USA., Combes AJ; Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.; Biomedical Sciences graduate program, University of California, San Francisco, San Francisco, CA 94143, USA.; UCSF CoLabs Initiative, University of California, San Francisco, San Francisco, CA 94143, USA.; UCSF Bakar ImmunoX Initiative, University of California, San Francisco, San Francisco, CA 94143, USA.; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA.

Journal Article; Preprint , 2024

Cell-Specific Transposable Element and Gene Expression Analysis Across Systemic Lupus Erythematosus Phenotypes.

Cutts Z; University of California, San Francisco, San Francisco., Patterson S; University of California, San Francisco, San Francisco., Maliskova L; University of California, San Francisco, San Francisco., Taylor KE; University of California, San Francisco, San Francisco., Ye CJ; University of California, San Francisco, San Francisco., Dall'Era M; University of California, San Francisco, San Francisco., Yazdany J; University of California, San Francisco, San Francisco., Criswell LA; National Human Genome Research Institute, NIH, Bethesda, Maryland., Fragiadakis GK; University of California, San Francisco, San Francisco., Langelier C; University of California, San Francisco, San Francisco., Capra JA; University of California, San Francisco, San Francisco., Sirota M; University of California, San Francisco, San Francisco., Lanata CM; National Human Genome Research Institute, NIH, Bethesda, Maryland.

Journal Article , 2024

Single-cell RNA-Seq analysis reveals cell subsets and gene signatures associated with rheumatoid arthritis disease activity.

Binvignat M; Bakar Computational Health Sciences Institute, UCSF, San Francisco, California, USA.; Immunology Immunopathology Immunotherapy, Pitie Salpetriere Hospital UMRS 959, Sorbonne University, Paris, France.; Department of Rheumatology, Research Center Saint Antoine, UMRS 938, Sorbonne University, AP-HP, Saint-Antoine Hospital, Inserm UMRS 938, Paris, France., Miao BY; Bakar Computational Health Sciences Institute, UCSF, San Francisco, California, USA., Wibrand C; Bakar Computational Health Sciences Institute, UCSF, San Francisco, California, USA.; Aarhus University, Aarhus, Denmark., Yang MM; Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, and., Rychkov D; Bakar Computational Health Sciences Institute, UCSF, San Francisco, California, USA., Flynn E; Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, and.; CoLabs, UCSF, San Francisco, California, USA., Nititham J; Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, and., Tamaki W; Bakar Computational Health Sciences Institute, UCSF, San Francisco, California, USA., Khan U; Bakar Computational Health Sciences Institute, UCSF, San Francisco, California, USA., Carvidi A; Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, and., Krueger M; Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA., Niemi E; Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, and., Sun Y; Department of Human Genetics and., Fragiadakis GK; Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, and.; CoLabs, UCSF, San Francisco, California, USA., Sellam J; Department of Rheumatology, Research Center Saint Antoine, UMRS 938, Sorbonne University, AP-HP, Saint-Antoine Hospital, Inserm UMRS 938, Paris, France., Mariotti-Ferrandiz E; Immunology Immunopathology Immunotherapy, Pitie Salpetriere Hospital UMRS 959, Sorbonne University, Paris, France., Klatzmann D; Immunology Immunopathology Immunotherapy, Pitie Salpetriere Hospital UMRS 959, Sorbonne University, Paris, France., Gross AJ; Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, and., Ye CJ; Department of Human Genetics and., Butte AJ; Bakar Computational Health Sciences Institute, UCSF, San Francisco, California, USA.; Department of Pediatrics, UCSF, San Francisco, California, USA., Criswell LA; Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, and.; National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA., Nakamura MC; Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, and.; San Francisco VA Health Care System, San Francisco, California, USA., Sirota M; Bakar Computational Health Sciences Institute, UCSF, San Francisco, California, USA.

Journal Article , 2024

Distinct pulmonary and systemic effects of dexamethasone in severe COVID-19.

Neyton LPA; Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA., Patel RK; UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA., Sarma A; Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA., Willmore A; Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA., Haller SC; Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA., Kangelaris KN; Division of Hospital Medicine, University of California, San Francisco, CA, USA., Eckalbar WL; Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA.; UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA., Erle DJ; Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA.; UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA.; Department of Medicine, University of California, San Francisco, CA, USA.; Lung Biology Center, University of California, San Francisco, CA, USA., Krummel MF; Department of Pathology, University of California, San Francisco, CA, USA., Hendrickson CM; Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA., Woodruff PG; Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA., Langelier CR; Chan Zuckerberg Biohub, San Francisco, CA, USA.; Division of Infectious Diseases, University of California, San Francisco, CA, USA., Calfee CS; Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA.; Department of Medicine, University of California, San Francisco, CA, USA.; Department of Anesthesia, University of California, San Francisco, CA, USA., Fragiadakis GK; UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA. gabriela.fragiadakis@ucsf.edu.; Division of Rheumatology, University of California, San Francisco, CA, USA. gabriela.fragiadakis@ucsf.edu.

UCSF COMET Consortium

Journal Article , 2024

Coordinated immune dysregulation in juvenile dermatomyositis revealed by single-cell genomics.

Rabadam G; UC Berkeley-UC San Francisco Graduate Program in Bioengineering, and.; Department of Pharmaceutical Chemistry, UCSF, San Francisco, California, USA., Wibrand C; Aarhus University, Aarhus, Denmark.; Division of Pediatric Rheumatology, Department of Pediatrics., Flynn E; CoLabs., Hartoularos GC; Graduate Program in Biological and Medical Informatics.; Division of Rheumatology, Department of Medicine.; Institute for Human Genetics., Sun Y; Division of Rheumatology, Department of Medicine., Madubata C; Division of Pediatric Rheumatology, Department of Pediatrics.; CoLabs., Fragiadakis GK; CoLabs.; Division of Rheumatology, Department of Medicine., Ye CJ; Division of Rheumatology, Department of Medicine.; Institute for Human Genetics.; Department of Epidemiology and Biostatistics, and.; Bakar Computational Health Sciences Institute, UCSF, San Francisco, California, USA.; Chan Zuckerberg Biohub, San Francisco, California, USA.; Parker Institute for Cancer Immunotherapy, San Francisco, California, USA., Kim S; Division of Pediatric Rheumatology, Department of Pediatrics., Gartner ZJ; Department of Pharmaceutical Chemistry, UCSF, San Francisco, California, USA.; Chan Zuckerberg Biohub, San Francisco, California, USA., Sirota M; Bakar Computational Health Sciences Institute, UCSF, San Francisco, California, USA.; Department of Pediatrics, UCSF, San Francisco, California, USA., Neely J; Division of Pediatric Rheumatology, Department of Pediatrics.

Journal Article , 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

Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis.

Mennillo E; Department of Medicine, University of California San Francisco, San Francisco, CA, USA., Kim YJ; Chan Zuckerberg Biohub, San Francisco, CA, USA., Lee G; Department of Medicine, University of California San Francisco, San Francisco, CA, USA., Rusu I; Department of Medicine, University of California San Francisco, San Francisco, CA, USA., Patel RK; Department of Medicine, University of California San Francisco, San Francisco, CA, USA.; CoLabs, University of California San Francisco, San Francisco, CA, USA., Dorman LC; Chan Zuckerberg Biohub, San Francisco, CA, USA., Flynn E; CoLabs, University of California San Francisco, San Francisco, CA, USA., Li S; Department of Medicine, University of California San Francisco, San Francisco, CA, USA., Bain JL; Department of Medicine, University of California San Francisco, San Francisco, CA, USA., Andersen C; Department of Medicine, University of California San Francisco, San Francisco, CA, USA.; CoLabs, University of California San Francisco, San Francisco, CA, USA., Rao A; Department of Medicine, University of California San Francisco, San Francisco, CA, USA.; CoLabs, University of California San Francisco, San Francisco, CA, USA., Tamaki S; CoLabs, University of California San Francisco, San Francisco, CA, USA., Tsui J; Department of Medicine, University of California San Francisco, San Francisco, CA, USA.; CoLabs, University of California San Francisco, San Francisco, CA, USA.; Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA., Shen A; Department of Medicine, University of California San Francisco, San Francisco, CA, USA.; CoLabs, University of California San Francisco, San Francisco, CA, USA.; Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA., Lotstein ML; Department of Medicine, University of California San Francisco, San Francisco, CA, USA.; CoLabs, University of California San Francisco, San Francisco, CA, USA., Rahim M; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, 94143, USA., Naser M; Biological Imaging Development CoLab, University of California San Francisco, San Francisco, CA, USA., Bernard-Vazquez F; Department of Medicine, University of California San Francisco, San Francisco, CA, USA., Eckalbar W; CoLabs, University of California San Francisco, San Francisco, CA, USA., Cho SJ; Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA., Beck K; Department of Medicine, University of California San Francisco, San Francisco, CA, USA., El-Nachef N; Department of Medicine, University of California San Francisco, San Francisco, CA, USA., Lewin S; Department of Medicine, University of California San Francisco, San Francisco, CA, USA., Selvig DR; Department of Medicine, University of California San Francisco, San Francisco, CA, USA., Terdiman JP; Department of Medicine, University of California San Francisco, San Francisco, CA, USA., Mahadevan U; Department of Medicine, University of California San Francisco, San Francisco, CA, USA., Oh DY; Department of Medicine, University of California San Francisco, San Francisco, CA, USA.; Division of Hematology/Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA., Fragiadakis GK; Department of Medicine, University of California San Francisco, San Francisco, CA, USA.; CoLabs, University of California San Francisco, San Francisco, CA, USA., Pisco A; Chan Zuckerberg Biohub, San Francisco, CA, USA., Combes AJ; Department of Medicine, University of California San Francisco, San Francisco, CA, USA.; CoLabs, University of California San Francisco, San Francisco, CA, USA.; Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA., Kattah MG; Department of Medicine, University of California San Francisco, San Francisco, CA, USA. michael.kattah@ucsf.edu.

Journal Article , 2024

Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis.

Mennillo E, Kim YJ, Lee G, Rusu I, Patel RK, Dorman LC, Flynn E, Li S, Bain JL, Andersen C, Rao A, Tamaki S, Tsui J, Shen A, Lotstein ML, Rahim M, Naser M, Bernard-Vazquez F, Eckalbar W, Cho SJ, Beck K, El-Nachef N, Lewin S, Selvig DR, Terdiman JP, Mahadevan U, Oh DY, Fragiadakis GK, Pisco A, Combes AJ, Kattah MG

Preprint; Journal Article , 2024

Cell-Specific Transposable Element Gene Expression Analysis Identifies Associations with Systemic Lupus Erythematosus Phenotypes.

Cutts Z, Patterson S, Maliskova L, Taylor KE, Ye C, Dall'Era M, Yazdany J, Criswell L, Fragiadakis GK, Langelier C, Capra JA, Sirota M, Lanata CM

Preprint; Journal Article , 2023

Homeostatic cytokines reciprocally modulate the emergence of prenatal effector PLZF+CD4+ T cells in humans.

Locher V; Division of Neonatology, Department of Pediatrics, and.; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, California, USA.; Committee on Immunology, University of Chicago, Chicago, Illinois, USA., Park S; Division of Neonatology, Department of Pediatrics, and.; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, California, USA., Bunis DG; Bakar ImmunoX Initiative and.; CoLabs, UCSF, San Francisco, California, USA., Makredes S; Division of Neonatology, Department of Pediatrics, and.; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, California, USA., Mayer M; Division of Neonatology, Department of Pediatrics, and.; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, California, USA., Burt TD; Division of Neonatology and the Children's Health & Discovery Initiative, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA., Fragiadakis GK; Bakar ImmunoX Initiative and.; CoLabs, UCSF, San Francisco, California, USA.; Division of Rheumatology, Department of Medicine, UCSF, San Francisco, California, USA., Halkias J; Division of Neonatology, Department of Pediatrics, and.; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, California, USA.; Bakar ImmunoX Initiative and.

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

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

Cyclone: an accessible pipeline to analyze, evaluate, and optimize multiparametric cytometry data.

Patel RK; UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States., Jaszczak RG; UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States., Im K; UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States.; Department of Pathology, University of California San Francisco, San Francisco, CA, United States.; ImmunoX Initiative, University of California San Francisco, San Francisco, CA, United States., Carey ND; UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States.; Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, United States.; UCSF Liver Center, University of California San Francisco, San Francisco, CA, United States., Courau T; UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States.; Department of Pathology, University of California San Francisco, San Francisco, CA, United States.; ImmunoX Initiative, University of California San Francisco, San Francisco, CA, United States.; UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA, United States., Bunis DG; UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States., Samad B; UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States., Avanesyan L; Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, United States.; UCSF Liver Center, University of California San Francisco, San Francisco, CA, United States.; The Ibrahim El-Hefni Liver Biorepository at California Pacific Medical Center (IELBC), San Francisco, CA, United States.; Division of General and Transplant Hepatology, California Pacific Medical Center & Research Institute, San Francisco, CA, United States., Chew NW; UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States.; Department of Pathology, University of California San Francisco, San Francisco, CA, United States.; ImmunoX Initiative, University of California San Francisco, San Francisco, CA, United States., Stenske S; Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, United States.; UCSF Liver Center, University of California San Francisco, San Francisco, CA, United States., Jespersen JM; Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, United States.; UCSF Liver Center, University of California San Francisco, San Francisco, CA, United States., Publicover J; Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, United States.; UCSF Liver Center, University of California San Francisco, San Francisco, CA, United States., Edwards AW; UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States., Naser M; UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States., Rao AA; UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States., Lupin-Jimenez L; UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States., Krummel MF; Department of Pathology, University of California San Francisco, San Francisco, CA, United States.; ImmunoX Initiative, University of California San Francisco, San Francisco, CA, United States.; UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA, United States., Cooper S; UCSF Liver Center, University of California San Francisco, San Francisco, CA, United States.; The Ibrahim El-Hefni Liver Biorepository at California Pacific Medical Center (IELBC), San Francisco, CA, United States.; Division of General and Transplant Hepatology, California Pacific Medical Center & Research Institute, San Francisco, CA, United States., Baron JL; Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, United States.; UCSF Liver Center, University of California San Francisco, San Francisco, CA, United States.; The Ibrahim El-Hefni Liver Biorepository at California Pacific Medical Center (IELBC), San Francisco, CA, United States., Combes AJ; UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States.; Department of Pathology, University of California San Francisco, San Francisco, CA, United States.; ImmunoX Initiative, University of California San Francisco, San Francisco, CA, United States.; Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, United States.; UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA, United States., Fragiadakis GK; UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States.; Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States.

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

A myeloid program associated with COVID-19 severity is decreased by therapeutic blockade of IL-6 signaling.

Hackney JA; Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA., Shivram H; Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA., Vander Heiden J; Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA., Overall C; Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA., Orozco L; Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA., Gao X; Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA., Kim E; Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA., West N; Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA., Qamra A; Hoffman-La Roche Limited, 7070 Mississauga Road, Mississauga, ON L5N 5M8, Canada., Chang D; Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA., Chakrabarti A; Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA., Choy DF; Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA., Combes AJ; University of California San Francisco, San Francisco, CA, USA., Courau T; University of California San Francisco, San Francisco, CA, USA., Fragiadakis GK; University of California San Francisco, San Francisco, CA, USA., Rao AA; University of California San Francisco, San Francisco, CA, USA., Ray A; University of California San Francisco, San Francisco, CA, USA., Tsui J; University of California San Francisco, San Francisco, CA, USA., Hu K; University of California San Francisco, San Francisco, CA, USA., Kuhn NF; University of California San Francisco, San Francisco, CA, USA., Krummel MF; University of California San Francisco, San Francisco, CA, USA., Erle DJ; University of California San Francisco, San Francisco, CA, USA., Kangelaris K; University of California San Francisco, San Francisco, CA, USA., Sarma A; University of California San Francisco, San Francisco, CA, USA., Lyon Z; University of California San Francisco, San Francisco, CA, USA., Calfee CS; University of California San Francisco, San Francisco, CA, USA., Woodruff PG; University of California San Francisco, San Francisco, CA, USA., Ghale R; University of California San Francisco, San Francisco, CA, USA., Mick E; University of California San Francisco, San Francisco, CA, USA., Byrne A; University of California San Francisco, San Francisco, CA, USA., Zha BS; University of California San Francisco, San Francisco, CA, USA., Langelier C; University of California San Francisco, San Francisco, CA, USA., Hendrickson CM; University of California San Francisco, San Francisco, CA, USA., van der Wijst MGP; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands., Hartoularos GC; University of California San Francisco, San Francisco, CA, USA., Grant T; University of California San Francisco, San Francisco, CA, USA., Bueno R; University of California San Francisco, San Francisco, CA, USA., Lee DS; University of California San Francisco, San Francisco, CA, USA., Greenland JR; University of California San Francisco, San Francisco, CA, USA., Sun Y; University of California San Francisco, San Francisco, CA, USA., Perez R; University of California San Francisco, San Francisco, CA, USA., Ogorodnikov A; University of California San Francisco, San Francisco, CA, USA., Ward A; University of California San Francisco, San Francisco, CA, USA., Ye CJ; University of California San Francisco, San Francisco, CA, USA., Ramalingam T; Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA., McBride JM; Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA., Cai F; Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA., Teterina A; Hoffman-La Roche Limited, 7070 Mississauga Road, Mississauga, ON L5N 5M8, Canada., Bao M; Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA., Tsai L; Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA., Rosas IO; Baylor College of Medicine, 7200 Cambridge St, Houston, TX 77030, USA., Regev A; Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA., Kapadia SB; Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA., Bauer RN; Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA., Rosenberger CM; Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA.

UCSF COMET Consortium

Journal Article , 2023

Single-Cell Multiomics.

Flynn E; CoLabs, University of California, San Francisco, California, USA; email: gabriela.fragiadakis@ucsf.edu., Almonte-Loya A; CoLabs, University of California, San Francisco, California, USA; email: gabriela.fragiadakis@ucsf.edu.; Biomedical Informatics Program, University of California, San Francisco, California, USA., Fragiadakis GK; CoLabs, University of California, San Francisco, California, USA; email: gabriela.fragiadakis@ucsf.edu.; Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA.

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

SARS-CoV-2 infection of airway organoids reveals conserved use of Tetraspanin-8 by Ancestral, Delta, and Omicron variants.

Hysenaj L; Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA., Little S; Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA., Kulhanek K; Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA., Magnen M; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA., Bahl K; Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA., Gbenedio OM; Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA., Prinz M; Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA., Rodriguez L; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA., Andersen C; UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA., Rao AA; UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA., Shen A; UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA., Lone JC; School of Life Science, University of Essex, C04 3SQ Colchester, UK., Lupin-Jimenez LC; UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA., Bonser LR; Lung Biology Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA., Serwas NK; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA., Mick E; Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA; Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA., Khalid MM; Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA., Taha TY; Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA., Kumar R; Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA., Li JZ; Department of Surgery, Division of Cardiothoracic Surgery, University of California, San Francisco, San Francisco, CA, USA., Ding VW; Department of Surgery, Division of Cardiothoracic Surgery, University of California, San Francisco, San Francisco, CA, USA., Matsumoto S; Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, CA 94143, USA., Maishan M; Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, CA 94143, USA., Sreekumar B; Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA., Simoneau C; Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA., Nazarenko I; Institute for Infection Prevention and Hospital Epidemiology, University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; German Cancer Consortium, Partner Site Freiburg and German Cancer Research Center, Heidelberg, Germany., Tomlinson MG; School of Biosciences, University of Birmingham, Birmingham, UK; Centre of Membrane Proteins and Receptors, Universities of Birmingham and Nottingham, Midlands, UK., Khan K; Africa Health Research Institute, Durban, South Africa; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa., von Gottberg A; National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; SAMRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, South Africa., Sigal A; Africa Health Research Institute, Durban, South Africa; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; Max Planck Institute for Infection Biology, Berlin, Germany; Centre for the AIDS Program of Research, Durban, South Africa., Looney MR; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA., Fragiadakis GK; UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, Division of Rheumatology, University of California, San Francisco, San Francisco, CA 94143, USA., Jablons DM; Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA; Department of Surgery, Division of Cardiothoracic Surgery, University of California, San Francisco, San Francisco, CA, USA; Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, CA 94143, USA., Langelier CR; Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA; Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA; Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA., Matthay M; Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA; Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, CA 94143, USA., Krummel M; Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA., Erle DJ; UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Lung Biology Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA., Combes AJ; UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA., Sil A; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA., Ott M; Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, Division of Rheumatology, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute COVID-19 Research Group, University of California, San Francisco, San Francisco, CA, USA., Kratz JR; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Surgery, Division of Cardiothoracic Surgery, University of California, San Francisco, San Francisco, CA, USA., Roose JP; Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA. Electronic address: jeroen.roose@ucsf.edu.

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

Cyclone: an accessible pipeline to analyze, evaluate and optimize multiparametric cytometry data.

Patel RK, Jaszczak RG, Kwok I, Carey ND, Courau T, Bunis D, Samad B, Avanesyan L, Chew NW, Stenske S, Jespersen JM, Publicover J, Edwards A, Naser M, Rao AA, Lupin-Jimenez L, Krummel MF, Cooper S, Baron J, Combes AJ, Fragiadakis GK

Preprint; Journal Article , 2023

Randomized controlled trial demonstrates response to a probiotic intervention for metabolic syndrome that may correspond to diet.

Wastyk HC; Department of Bioengineering, Stanford School of Medicine, Stanford, CA, USA., Perelman D; Stanford Prevention Research Center, Department of Medicine, Stanford School of 4Medicine, Stanford, CA, USA., Topf M; Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, USA., Fragiadakis GK; Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, USA., Robinson JL; Stanford Prevention Research Center, Department of Medicine, Stanford School of 4Medicine, Stanford, CA, USA., Sonnenburg JL; Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, USA.; Center for Human Microbiome Studies, Stanford School of Medicine, Stanford University, Stanford, CA, USA.; Chan Zuckerberg Biohub, San Francisco, CA, USA., Gardner CD; Stanford Prevention Research Center, Department of Medicine, Stanford School of 4Medicine, Stanford, CA, USA., Sonnenburg ED; Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, USA.; Center for Human Microbiome Studies, Stanford School of Medicine, Stanford University, Stanford, CA, USA.

Randomized Controlled Trial; Journal Article; Research Support, Non-U.S. Gov't , 2023

Bioinformatics Analysis of Publicly Available Single-Nuclei Transcriptomics Alzheimer's Disease Datasets Reveals APOE Genotype-Specific Changes Across Cell Types in Two Brain Regions.

Belonwu SA; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States.; Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, United States., Li Y; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States.; Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, United States., Bunis DG; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States.; CoLabs, University of California, San Francisco, San Francisco, CA, United States.; Bakar ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, United States., Rao AA; CoLabs, University of California, San Francisco, San Francisco, CA, United States.; Bakar ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, United States.; Department of Pathology, University of California, San Francisco, San Francisco, CA, United States., Solsberg CW; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States.; Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, United States.; Memory and Aging Center, University of California, San Francisco, San Francisco, CA, United States.; Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States., Oskotsky T; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States.; Department of Pediatrics, University of California, San Francisco, San Francisco, CA, United States., Taubes AL; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States.; Gladstone Institute of Neurological Disease, San Francisco, CA, United States., Grone B; Gladstone Institute of Neurological Disease, San Francisco, CA, United States., Zalocusky KA; Gladstone Institute of Neurological Disease, San Francisco, CA, United States., Fragiadakis GK; CoLabs, University of California, San Francisco, San Francisco, CA, United States.; Bakar ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, United States.; Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States., Huang Y; Department of Pathology, University of California, San Francisco, San Francisco, CA, United States.; Gladstone Institute of Neurological Disease, San Francisco, CA, United States.; Department of Neurology, University of California, San Francisco, San Francisco, CA, United States., Sirota M; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States.; Department of Pediatrics, University of California, San Francisco, San Francisco, CA, United States.

Journal Article , 2022