Gabriela Fragiadakis, PhD
CFAR Bioinformatics Subcore Co-Director
Assistant Professor, School of Medicine
Biography
I lead a computational immunology lab studying states of the human immune system across disease contexts using single-cell methods and data integration. We work with a variety of data types, including bulk- and single-cell sequencing and CyTOF. My research program is built from a foundation of collaborations as Director of the Data Science CoLab. 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.
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- Spencer SP, Fragiadakis GK, Sonnenburg JL. Pursuing Human-Relevant Gut Microbiota-Immune Interactions. Immunity. 2019 08 20; 51(2):225-239.
- 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. GateFinder: projection-based gating strategy optimization for flow and mass cytometry. Bioinformatics. 2018 12 01; 34(23):4131-4133.
- 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. Gut microbiome transition across a lifestyle gradient in Himalaya. PLoS Biol. 2018 11; 16(11):e2005396.
- Fragiadakis GK, Smits SA, Sonnenburg ED, Van Treuren W, Reid G, Knight R, Manjurano A, Changalucha J, Dominguez-Bello MG, Leach J, Sonnenburg JL. Links between environment, diet, and the hunter-gatherer microbiome. Gut Microbes. 2019; 10(2):216-227.
- 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, Davis MM, Furman D. Multicenter Systems Analysis of Human Blood Reveals Immature Neutrophils in Males and During Pregnancy. J Immunol. 2017 03 15; 198(6):2479-2488.
- 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, Kuo CJ, Davis MM, Faustin B. Expression of specific inflammasome gene modules stratifies older individuals into two extreme clinical and immunological states. Nat Med. 2017 Feb; 23(2):174-184.
- Fragiadakis GK, Baca QJ, Gherardini PF, Ganio EA, Gaudilliere DK, Tingle M, Lancero HL, McNeil LS, Spitzer MH, Wong RJ, Shaw GM, Darmstadt GL, Sylvester KG, Winn VD, Carvalho B, Lewis DB, Stevenson DK, Nolan GP, Aghaeepour N, Angst MS, Gaudilliere BL. Mapping the Fetomaternal Peripheral Immune System at Term Pregnancy. J Immunol. 2016 12 01; 197(11):4482-4492.
- Sogi KM, Holsclaw CM, Fragiadakis GK, Nomura DK, Leary JA, Bertozzi CR. Biosynthesis and Regulation of Sulfomenaquinone, a Metabolite Associated with Virulence in Mycobacterium tuberculosis. ACS Infect Dis. 2016 11 11; 2(11):800-806.
- Angst MS, Fragiadakis GK, Gaudillière B, Aghaeepour N, Nolan GP. In Reply. Anesthesiology. 2016 06; 124(6):1414-5.
- Fragiadakis GK, Gaudillière B, Ganio EA, Aghaeepour N, Tingle M, Nolan GP, Angst MS. Patient-specific Immune States before Surgery Are Strong Correlates of Surgical Recovery. Anesthesiology. 2015 Dec; 123(6):1241-55.
- Lichtman JS, Alsentzer E, Jaffe M, Sprockett D, Masutani E, Ikwa E, Fragiadakis GK, Clifford D, Huang BE, Sonnenburg JL, Huang KC, Elias JE. The effect of microbial colonization on the host proteome varies by gastrointestinal location. ISME J. 2016 May; 10(5):1170-81.
- 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. 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 A. 2015 Sep; 87(9):817-29.
- 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. IMMUNOLOGY. An interactive reference framework for modeling a dynamic immune system. Science. 2015 Jul 10; 349(6244):1259425.
- Behbehani GK, Thom C, Zunder ER, Finck R, Gaudilliere B, Fragiadakis GK, Fantl WJ, Nolan GP. Transient partial permeabilization with saponin enables cellular barcoding prior to surface marker staining. Cytometry A. 2014 Dec; 85(12):1011-9.
- 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. Clinical recovery from surgery correlates with single-cell immune signatures. Sci Transl Med. 2014 Sep 24; 6(255):255ra131.