Gabriela Fragiadakis, PhD
Assistant Professor
Medicine
School of Medicine

Through CoLabs I have established partnerships to study systems-level immunity in viral infection, cancer, autoimmunity, and steady-state. From these projects I then pursue questions in immune phenotypes across contexts using high-dimensional analysis, data integration, and novel computational methods. In addition, I study immune-microbiome interactions at steady-state and in response to perturbation.

In the lab we have a sub-team that builds and develops the UCSF Data Library project, a web-based platform to store, curate, share and analyze high-dimensional data.

• Coordinated variation in the immune systems and microbiomes of healthy humans is linked to tonic interferon states.
  bioRxiv : the preprint server for biology 2024 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, …
• Single-cell spatial transcriptomics of fixed, paraffin-embedded biopsies reveals colitis-associated cell networks.
  bioRxiv : the preprint server for biology 2024 Mennillo E, Lotstein ML, Lee G, Johri V, Ekstrand C, Tsui J, Hou J, Leet DE, He JY, Mahadevan U, Eckalbar W, Oh DY, Fragiadakis GK, Kattah MG, Combes AJ
• A positive ReceptivaDx result for BCL6 does not correlate with abnormal ERA results or decreased expression of receptivity-associated markers: two sides of the endometrial receptivity coin in fertility evaluation and treatment.
  F&S science 2024 Huang D, Flynn E, Almonte-Loya A, Davidson B, Chan M, Casillas A, Irwin JC, Fragiadakis GK, Cakmak H, Combes AJ, Cedars MI, Sirota M, Giudice LC
• Cell-Specific Transposable Element and Gene Expression Analysis Across Systemic Lupus Erythematosus Phenotypes.
  ACR open rheumatology 2024 Cutts Z, Patterson S, Maliskova L, Taylor KE, Ye CJ, Dall'Era M, Yazdany J, Criswell LA, Fragiadakis GK, Langelier C, Capra JA, Sirota M, Lanata CM
• Single-cell RNA-Seq analysis reveals cell subsets and gene signatures associated with rheumatoid arthritis disease activity.
  JCI insight 2024 Binvignat M, Miao BY, Wibrand C, Yang MM, Rychkov D, Flynn E, Nititham J, Tamaki W, Khan U, Carvidi A, Krueger M, Niemi E, Sun Y, Fragiadakis GK, Sellam J, Mariotti-Ferrandiz E, Klatzmann D, Gross AJ,…
• Distinct pulmonary and systemic effects of dexamethasone in severe COVID-19.
  Nature communications 2024 Neyton LPA, Patel RK, Sarma A, UCSF COMET Consortium, Willmore A, Haller SC, Kangelaris KN, Eckalbar WL, Erle DJ, Krummel MF, Hendrickson CM, Woodruff PG, Langelier CR, Calfee CS, Fragiadakis GK
• Coordinated immune dysregulation in juvenile dermatomyositis revealed by single-cell genomics.
  JCI insight 2024 Rabadam G, Wibrand C, Flynn E, Hartoularos GC, Sun Y, Madubata C, Fragiadakis GK, Ye CJ, Kim S, Gartner ZJ, Sirota M, Neely J
• Integrated longitudinal multiomics study identifies immune programs associated with acute COVID-19 severity and mortality.
  The Journal of clinical investigation 2024 Gygi JP, Maguire C, Patel RK, Shinde P, Konstorum A, Shannon CP, Xu L, Hoch A, Jayavelu ND, Haddad EK, IMPACC Network, Reed EF, Kraft M, McComsey GA, Metcalf JP, Ozonoff A, Esserman D, Cairns CB, …
• Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis.
  Nature communications 2024 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 …
• Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis.
  bioRxiv : the preprint server for biology 2024 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 …
• Cell-Specific Transposable Element Gene Expression Analysis Identifies Associations with Systemic Lupus Erythematosus Phenotypes.
  bioRxiv : the preprint server for biology 2023 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
• Homeostatic cytokines reciprocally modulate the emergence of prenatal effector PLZF+CD4+ T cells in humans.
  JCI insight 2023 Locher V, Park S, Bunis DG, Makredes S, Mayer M, Burt TD, Fragiadakis GK, Halkias J
• Integrated longitudinal multi-omics study identifies immune programs associated with COVID-19 severity and mortality in 1152 hospitalized participants.
  bioRxiv : the preprint server for biology 2023 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…
• Cyclone: an accessible pipeline to analyze, evaluate, and optimize multiparametric cytometry data.
  Frontiers in immunology 2023 Patel RK, Jaszczak RG, Im K, Carey ND, Courau T, Bunis DG, Samad B, Avanesyan L, Chew NW, Stenske S, Jespersen JM, Publicover J, Edwards AW, Naser M, Rao AA, Lupin-Jimenez L, Krummel MF, Cooper S, …
• A myeloid program associated with COVID-19 severity is decreased by therapeutic blockade of IL-6 signaling.
  iScience 2023 Hackney JA, Shivram H, Vander Heiden J, Overall C, Orozco L, Gao X, Kim E, West N, Qamra A, Chang D, Chakrabarti A, Choy DF, Combes AJ, Courau T, Fragiadakis GK, Rao AA, Ray A, Tsui J, Hu K, Kuhn NF, …
• Distinct pulmonary and systemic effects of dexamethasone in severe COVID-19.
  Research square 2023 Neyton LPA, Patel RK, Sarma A, UCSF COMET Consortium, Willmore A, Haller SC, Kangelaris KN, Eckalbar WL, Erle DJ, Krummel MF, Hendrickson CM, Woodruff PG, Langelier CR, Calfee CS, Fragiadakis GK
• Single-Cell Multiomics.
  Annual review of biomedical data science 2023 Flynn E, Almonte-Loya A, Fragiadakis GK
• Cyclone: an accessible pipeline to analyze, evaluate and optimize multiparametric cytometry data.
  bioRxiv : the preprint server for biology 2023 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, …
• SARS-CoV-2 infection of airway organoids reveals conserved use of Tetraspanin-8 by Ancestral, Delta, and Omicron variants.
  Stem cell reports 2023 Hysenaj L, Little S, Kulhanek K, Magnen M, Bahl K, Gbenedio OM, Prinz M, Rodriguez L, Andersen C, Rao AA, Shen A, Lone JC, Lupin-Jimenez LC, Bonser LR, Serwas NK, Mick E, Khalid MM, Taha TY, Kumar R, …
• Randomized controlled trial demonstrates response to a probiotic intervention for metabolic syndrome that may correspond to diet.
  Gut microbes 2023 Wastyk HC, Perelman D, Topf M, Fragiadakis GK, Robinson JL, Sonnenburg JL, Gardner CD, Sonnenburg ED
• Distinct factors associated with short-term and long-term weight loss induced by low-fat or low-carbohydrate diet intervention.
  Cell reports. Medicine 2022 Li X, Perelman D, Leong AK, Fragiadakis G, Gardner CD, Snyder MP
• Bioinformatics Analysis of Publicly Available Single-Nuclei Transcriptomics Alzheimer's Disease Datasets Reveals APOE Genotype-Specific Changes Across Cell Types in Two Brain Regions.
  Frontiers in aging neuroscience 2022 Belonwu SA, Li Y, Bunis DG, Rao AA, Solsberg CW, Oskotsky T, Taubes AL, Grone B, Zalocusky KA, Fragiadakis GK, Huang Y, Sirota M
• Discovering dominant tumor immune archetypes in a pan-cancer census.
  Cell 2021 Combes AJ, Samad B, Tsui J, Chew NW, Yan P, Reeder GC, Kushnoor D, Shen A, Davidson B, Barczak AJ, Adkisson M, Edwards A, Naser M, Barry KC, Courau T, Hammoudi T, Argüello RJ, Rao AA, Olshen AB, …
• Sex-Stratified Single-Cell RNA-Seq Analysis Identifies Sex-Specific and Cell Type-Specific Transcriptional Responses in Alzheimer's Disease Across Two Brain Regions.
  Molecular neurobiology 2021 Belonwu SA, Li Y, Bunis D, Rao AA, Solsberg CW, Tang A, Fragiadakis GK, Dubal DB, Oskotsky T, Sirota M
• Increased risk of severe clinical course of COVID-19 in carriers of HLA-C*04:01.
  EClinicalMedicine 2021 Weiner J, Suwalski P, Holtgrewe M, Rakitko A, Thibeault C, Müller M, Patriki D, Quedenau C, Krüger U, Ilinsky V, Popov I, Balnis J, Jaitovich A, Helbig ET, Lippert LJ, Stubbemann P, Real LM, Macías J,…
• Type I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19.
  Science translational medicine 2021 van der Wijst MGP, Vazquez SE, Hartoularos GC, Bastard P, Grant T, Bueno R, Lee DS, Greenland JR, Sun Y, Perez R, Ogorodnikov A, Ward A, Mann SA, Lynch KL, Yun C, Havlir DV, Chamie G, Marquez C, …
• Inhibition of MET Signaling with Ficlatuzumab in Combination with Chemotherapy in Refractory AML: Clinical Outcomes and High-Dimensional Analysis.
  Blood cancer discovery 2021 Wang VE, Blaser BW, Patel RK, Behbehani GK, Rao AA, Durbin-Johnson B, Jiang T, Logan AC, Settles M, Mannis GN, Olin R, Damon LE, Martin TG, Sayre PH, Gaensler KM, McMahon E, Flanders M, Weinberg V, Ye…
• SARS-CoV-2 infection studies in lung organoids identify TSPAN8 as novel mediator.
  bioRxiv : the preprint server for biology 2021 Hysenaj L, Little S, Kulhanek K, Gbenedio OM, Rodriguez L, Shen A, Lone JC, Lupin-Jimenez LC, Bonser LR, Serwas NK, Bahl K, Mick E, Li JZ, Ding VW, Matsumoto S, Maishan M, Simoneau C, Fragiadakis G, …
• Single-cell transcriptome analysis defines heterogeneity of the murine pancreatic ductal tree.
  eLife 2021 Hendley AM, Rao AA, Leonhardt L, Ashe S, Smith JA, Giacometti S, Peng XL, Jiang H, Berrios DI, Pawlak M, Li LY, Lee J, Collisson EA, Anderson MS, Fragiadakis GK, Yeh JJ, Ye CJ, Kim GE, Weaver VM, …
• Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19: Anti-IFN antibodies in critical COVID-19 correlate with poor ISG response and upregulation of LAIR1 surface protein in PBMCs.
  bioRxiv : the preprint server for biology 2021 van der Wijst MGP, Vazquez SE, Hartoularos GC, Bastard P, Grant T, Bueno R, Lee DS, Greenland JR, Sun Y, Perez R, Ogorodnikov A, Ward A, Mann SA, Lynch KL, Yun C, Havlir DV, Chamie G, Marquez C, …
• Global absence and targeting of protective immune states in severe COVID-19.
  Nature 2021 Combes AJ, Courau T, Kuhn NF, Hu KH, Ray A, Chen WS, Chew NW, Cleary SJ, Kushnoor D, Reeder GC, Shen A, Tsui J, Hiam-Galvez KJ, Muñoz-Sandoval P, Zhu WS, Lee DS, Sun Y, You R, Magnen M, Rodriguez L, …
• Landscape of coordinated immune responses to H1N1 challenge in humans.
  The Journal of clinical investigation 2020 Rahil Z, Leylek R, Schürch CM, Chen H, Bjornson-Hooper Z, Christensen SR, Gherardini PF, Bhate SS, Spitzer MH, Fragiadakis GK, Mukherjee N, Kim N, Jiang S, Yo J, Gaudilliere B, Affrime M, Bock B, …
• Global Absence and Targeting of Protective Immune States in Severe COVID-19.
  bioRxiv : the preprint server for biology 2020 Combes AJ, Courau T, Kuhn NF, Hu KH, Ray A, Chen WS, Cleary SJ, Chew NW, Kushnoor D, Reeder GC, Shen A, Tsui J, Hiam-Galvez KJ, Muñoz-Sandoval P, Zhu WS, Lee DS, Sun Y, You R, Magnen M, Rodriguez L, …
• Global Absence and Targeting of Protective Immune States in Severe COVID-19.
  Research square 2020 Combes AJ, Courau T, Kuhn NF, Hu KH, Ray A, Chen WS, Cleary SJ, Chew NW, Kushnoor D, Reeder GC, Shen A, Tsui J, Hiam-Galvez KJ, Muñoz-Sandoval P, Zhu WS, Lee DS, Sun Y, You R, Magnen M, Rodriguez L, …
• FLOW-MAP: a graph-based, force-directed layout algorithm for trajectory mapping in single-cell time course datasets.
  Nature protocols 2020 Ko ME, Williams CM, Fread KI, Goggin SM, Rustagi RS, Fragiadakis GK, Nolan GP, Zunder ER
• Sex Differences in the Blood Transcriptome Identify Robust Changes in Immune Cell Proportions with Aging and Influenza Infection.
  Cell reports 2019 Bongen E, Lucian H, Khatri A, Fragiadakis GK, Bjornson ZB, Nolan GP, Utz PJ, Khatri P
• GateFinder: projection-based gating strategy optimization for flow and mass cytometry.
  Bioinformatics (Oxford, England) 2018 Aghaeepour N, Simonds EF, Knapp DJHF, Bruggner RV, Sachs K, Culos A, Gherardini PF, Samusik N, Fragiadakis GK, Bendall SC, Gaudilliere B, Angst MS, Eaves CJ, Weiss WA, Fantl WJ, Nolan GP
• Gut microbiome transition across a lifestyle gradient in Himalaya.
  PLoS biology 2018 Jha AR, Davenport ER, Gautam Y, Bhandari D, Tandukar S, Ng KM, Fragiadakis GK, Holmes S, Gautam GP, Leach J, Sherchand JB, Bustamante CD, Sonnenburg JL
• Multicenter Systems Analysis of Human Blood Reveals Immature Neutrophils in Males and During Pregnancy.
  Journal of immunology (Baltimore, Md. : 1950) 2017 Blazkova J, Gupta S, Liu Y, Gaudilliere B, Ganio EA, Bolen CR, Saar-Dover R, Fragiadakis GK, Angst MS, Hasni S, Aghaeepour N, Stevenson D, Baldwin N, Anguiano E, Chaussabel D, Altman MC, Kaplan MJ, …
• Expression of specific inflammasome gene modules stratifies older individuals into two extreme clinical and immunological states.
  Nature medicine 2017 Furman D, Chang J, Lartigue L, Bolen CR, Haddad F, Gaudilliere B, Ganio EA, Fragiadakis GK, Spitzer MH, Douchet I, Daburon S, Moreau JF, Nolan GP, Blanco P, Déchanet-Merville J, Dekker CL, Jojic V, …
• Biosynthesis and Regulation of Sulfomenaquinone, a Metabolite Associated with Virulence in Mycobacterium tuberculosis.
  ACS infectious diseases 2016 Sogi KM, Holsclaw CM, Fragiadakis GK, Nomura DK, Leary JA, Bertozzi CR
• In Reply.
  Anesthesiology 2016 Angst MS, Fragiadakis GK, Gaudillière B, Aghaeepour N, Nolan GP
• Patient-specific Immune States before Surgery Are Strong Correlates of Surgical Recovery.
  Anesthesiology 2015 Fragiadakis GK, Gaudillière B, Ganio EA, Aghaeepour N, Tingle M, Nolan GP, Angst MS
• The effect of microbial colonization on the host proteome varies by gastrointestinal location.
  The ISME journal 2015 Lichtman JS, Alsentzer E, Jaffe M, Sprockett D, Masutani E, Ikwa E, Fragiadakis GK, Clifford D, Huang BE, Sonnenburg JL, Huang KC, Elias JE
• Implementing Mass Cytometry at the Bedside to Study the Immunological Basis of Human Diseases: Distinctive Immune Features in Patients with a History of Term or Preterm Birth.
  Cytometry. Part A : the journal of the International Society for Analytical Cytology 2015 Gaudillière B, Ganio EA, Tingle M, Lancero HL, Fragiadakis GK, Baca QJ, Aghaeepour N, Wong RJ, Quaintance C, El-Sayed YY, Shaw GM, Lewis DB, Stevenson DK, Nolan GP, Angst MS
• IMMUNOLOGY. An interactive reference framework for modeling a dynamic immune system.
  Science (New York, N.Y.) 2015 Spitzer MH, Gherardini PF, Fragiadakis GK, Bhattacharya N, Yuan RT, Hotson AN, Finck R, Carmi Y, Zunder ER, Fantl WJ, Bendall SC, Engleman EG, Nolan GP
• Transient partial permeabilization with saponin enables cellular barcoding prior to surface marker staining.
  Cytometry. Part A : the journal of the International Society for Analytical Cytology 2014 Behbehani GK, Thom C, Zunder ER, Finck R, Gaudilliere B, Fragiadakis GK, Fantl WJ, Nolan GP
• Clinical recovery from surgery correlates with single-cell immune signatures.
  Science translational medicine 2014 Gaudillière B, Fragiadakis GK, Bruggner RV, Nicolau M, Finck R, Tingle M, Silva J, Ganio EA, Yeh CG, Maloney WJ, Huddleston JI, Goodman SB, Davis MM, Bendall SC, Fantl WJ, Angst MS, Nolan GP