Gabriela Fragiadakis, PhD

Title(s)Assistant Professor, Medicine
SchoolSchool of Medicine
Address533 Parnassus Avenue
San Francisco CA 94117
Phone--
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    Collapse Biography 
    Collapse Education and Training
    Stanford School of Medicine, Stanford, CA08/2019Postdoctoral training
    Stanford School of Medicine, Stanford, CAPhD08/2016Microbiology & Immunology
    University of California, Berkeley, Berkeley, CABA05/2011Molecular and Cellular Biology

    Collapse Overview 
    Collapse Overview
    Dr. Fragiadakis uses single-cell technologies to study systems-level human immunity and immune-microbiome interactions. She's the Director of the Data Science CoLab and leads the UCSF Data Library project.

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Increased risk of severe clinical course of COVID-19 in carriers of HLA-C*04:01. EClinicalMedicine. 2021 Sep 02; 101099. 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, Pineda JA, Fernandez-Fuertes M, Wang X, Karadeniz Z, Saccomanno J, Doehn JM, Hübner RH, Hinzmann B, Salvo M, Blueher A, Siemann S, Jurisic S, Beer JH, Rutishauser J, Wiggli B, Schmid H, Danninger K, Binder R, Corman VM, Mühlemann B, Arjun Arkal R, Fragiadakis GK, Mick E, Comet C, Calfee CS, Erle DJ, Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Langelier CR, Venkataramani U, García F, Zyla J, Drosten C, Alice B, Jones TC, Suttorp N, Witzenrath M, Hippenstiel S, Zemojtel T, Skurk C, Wolfgang P, Borodina T, Pa-Covid SG, Ripke S, Sander LE, Beule D, Landmesser U, Guettouche T, Kurth F, Heidecker B. PMID: 34490415.
      View in: PubMed   Mentions:
    2. Type I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19. Sci Transl Med. 2021 09 22; 13(612):eabh2624. 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, Greenhouse B, Lionakis MS, Norris PJ, Dumont LJ, Kelly K, Zhang P, Zhang Q, Gervais A, Le Voyer T, Whatley A, Si Y, Byrne A, Combes AJ, Rao AA, Song YS, Fragiadakis GK, Kangelaris K, Calfee CS, Erle DJ, Hendrickson C, Krummel MF, Woodruff PG, Langelier CR, Casanova JL, Derisi JL, Anderson MS, Ye CJ, UCSF COMET consortium . PMID: 34429372.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    3. Publisher Correction: Global absence and targeting of protective immune states in severe COVID-19. Nature. 2021 Aug; 596(7872):E8. 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, Im KW, Serwas NK, Leligdowicz A, Zamecnik CR, Loudermilk RP, Wilson MR, Ye CJ, Fragiadakis GK, Looney MR, Chan V, Ward A, Carrillo S, UCSF COMET Consortium , Matthay M, Erle DJ, Woodruff PG, Langelier C, Kangelaris K, Hendrickson CM, Calfee C, Rao AA, Krummel MF. PMID: 34341540.
      View in: PubMed   Mentions:    Fields:    
    4. Inhibition of MET Signaling with Ficlatuzumab in Combination with Chemotherapy in Refractory AML: Clinical Outcomes and High-Dimensional Analysis. Blood Cancer Discov. 2021 Sep; 2(5):434-449. 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 CJ, Carbone DP, Munster PN, Fragiadakis GK, McCormick F, Andreadis C. PMID: 34514432.
      View in: PubMed   Mentions:
    5. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021 Aug 05; 184(16):4137-4153.e14. Wastyk HC, Fragiadakis GK, Perelman D, Dahan D, Merrill BD, Yu FB, Topf M, Gonzalez CG, Van Treuren W, Han S, Robinson JL, Elias JE, Sonnenburg ED, Gardner CD, Sonnenburg JL. PMID: 34256014.
      View in: PubMed   Mentions: 2     Fields:    
    6. SARS-CoV-2 infection studies in lung organoids identify TSPAN8 as novel mediator. bioRxiv. 2021 Jun 02. 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, Jablons DM, Langelier CR, Matthay M, Ott M, Krummel M, Combes AJ, Sil A, Erle DJ, Kratz JR, Roose JP. PMID: 34100012.
      View in: PubMed   Mentions:
    7. Single-cell transcriptome analysis defines heterogeneity of the murine pancreatic ductal tree. Elife. 2021 05 19; 10. 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, Hebrok M. PMID: 34009124.
      View in: PubMed   Mentions:    Fields:    
    8. Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19. bioRxiv. 2021 Mar 10. 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, Greenhouse B, Lionakis MS, Norris PJ, Dumont LJ, Kelly K, Zhang P, Zhang Q, Gervais A, Voyer TL, Whatley A, Si Y, Byrne A, Combes AJ, Rao AA, Song YS, UCSF COMET consortium , Fragiadakis GK, Kangelaris K, Calfee CS, Erle DJ, Hendrickson C, Krummel MF, Woodruff PG, Langelier CR, Casanova JL, Derisi JL, Anderson MS, Ye CJ. PMID: 33758859.
      View in: PubMed   Mentions:
    9. A "data sharing trust" model for rapid, collaborative science. Cell. 2021 02 04; 184(3):566-570. Chan V, Gherardini PF, Krummel MF, Fragiadakis GK. PMID: 33545032.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    10. Global absence and targeting of protective immune states in severe COVID-19. Nature. 2021 03; 591(7848):124-130. 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, Im KW, Serwas NK, Leligdowicz A, Zamecnik CR, Loudermilk RP, Wilson MR, Ye CJ, Fragiadakis GK, Looney MR, Chan V, Ward A, Carrillo S, UCSF COMET Consortium , Matthay M, Erle DJ, Woodruff PG, Langelier C, Kangelaris K, Hendrickson CM, Calfee C, Rao AA, Krummel MF. PMID: 33494096.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansCells
    11. dittoSeq: Universal User-Friendly Single-Cell and Bulk RNA Sequencing Visualization Toolkit. Bioinformatics. 2020 Dec 12. Bunis DG, Andrews J, Fragiadakis GK, Burt TD, Sirota M. PMID: 33313640.
      View in: PubMed   Mentions:    Fields:    
    12. Landscape of coordinated immune responses to H1N1 challenge in humans. J Clin Invest. 2020 11 02; 130(11):5800-5816. 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, Hensley SE, Idoyaga J, Aghaeepour N, Kim K, Nolan GP, McIlwain DR. PMID: 33044226.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCellsCTClinical Trials
    13. Global Absence and Targeting of Protective Immune States in Severe COVID-19. bioRxiv. 2020 Oct 29. 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, Leligdowicz A, Zamecnik CR, Loudermilk RP, Wilson MR, Ye CJ, Fragiadakis GK, Looney MR, Chan V, Ward A, Carrillo S, Matthay M, Erle DJ, Woodruff PG, Langelier C, Kangelaris K, Hendrickson CM, Calfee C, Rao AA, Krummel MF. PMID: 33140050.
      View in: PubMed   Mentions:
    14. Global Absence and Targeting of Protective Immune States in Severe COVID-19. Res Sq. 2020 Oct 28. 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, Leligdowicz A, Zamecnik CR, Loudermilk RP, Wilson MR, Ye CJ, Fragiadakis GK, Looney MR, Chan V, Ward A, Carrillo S, UCSF COMET Consortium , Matthay M, Erle DJ, Woodruff PG, Langelier C, Kangelaris K, Hendrickson CM, Calfee C, Rao AA, Krummel MF. PMID: 33140041.
      View in: PubMed   Mentions:
    15. Long-term dietary intervention reveals resilience of the gut microbiota despite changes in diet and weight. Am J Clin Nutr. 2020 06 01; 111(6):1127-1136. Fragiadakis GK, Wastyk HC, Robinson JL, Sonnenburg ED, Sonnenburg JL, Gardner CD. PMID: 32186326.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
    16. FLOW-MAP: a graph-based, force-directed layout algorithm for trajectory mapping in single-cell time course datasets. Nat Protoc. 2020 02; 15(2):398-420. Ko ME, Williams CM, Fread KI, Goggin SM, Rustagi RS, Fragiadakis GK, Nolan GP, Zunder ER. PMID: 31932774.
      View in: PubMed   Mentions: 2     Fields:    
    17. Sex Differences in the Blood Transcriptome Identify Robust Changes in Immune Cell Proportions with Aging and Influenza Infection. Cell Rep. 2019 11 12; 29(7):1961-1973.e4. Bongen E, Lucian H, Khatri A, Fragiadakis GK, Bjornson ZB, Nolan GP, Utz PJ, Khatri P. PMID: 31722210.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCells
    18. Pursuing Human-Relevant Gut Microbiota-Immune Interactions. Immunity. 2019 08 20; 51(2):225-239. Spencer SP, Fragiadakis GK, Sonnenburg JL. PMID: 31433970.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansAnimals
    19. GateFinder: projection-based gating strategy optimization for flow and mass cytometry. Bioinformatics. 2018 12 01; 34(23):4131-4133. 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. PMID: 29850785.
      View in: PubMed   Mentions: 9     Fields:    
    20. Gut microbiome transition across a lifestyle gradient in Himalaya. PLoS Biol. 2018 11; 16(11):e2005396. 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. PMID: 30439937.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    21. Links between environment, diet, and the hunter-gatherer microbiome. Gut Microbes. 2019; 10(2):216-227. Fragiadakis GK, Smits SA, Sonnenburg ED, Van Treuren W, Reid G, Knight R, Manjurano A, Changalucha J, Dominguez-Bello MG, Leach J, Sonnenburg JL. PMID: 30118385.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansAnimalsPHPublic Health
    22. Multicenter Systems Analysis of Human Blood Reveals Immature Neutrophils in Males and During Pregnancy. J Immunol. 2017 03 15; 198(6):2479-2488. 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. PMID: 28179497.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
    23. Expression of specific inflammasome gene modules stratifies older individuals into two extreme clinical and immunological states. Nat Med. 2017 Feb; 23(2):174-184. 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. PMID: 28092664.
      View in: PubMed   Mentions: 94     Fields:    Translation:HumansAnimalsCells
    24. Mapping the Fetomaternal Peripheral Immune System at Term Pregnancy. J Immunol. 2016 12 01; 197(11):4482-4492. 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. PMID: 27793998.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
    25. Biosynthesis and Regulation of Sulfomenaquinone, a Metabolite Associated with Virulence in Mycobacterium tuberculosis. ACS Infect Dis. 2016 11 11; 2(11):800-806. Sogi KM, Holsclaw CM, Fragiadakis GK, Nomura DK, Leary JA, Bertozzi CR. PMID: 27933784.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    26. In Reply. Anesthesiology. 2016 06; 124(6):1414-5. Angst MS, Fragiadakis GK, Gaudillière B, Aghaeepour N, Nolan GP. PMID: 27187126.
      View in: PubMed   Mentions:    Fields:    
    27. Patient-specific Immune States before Surgery Are Strong Correlates of Surgical Recovery. Anesthesiology. 2015 Dec; 123(6):1241-55. Fragiadakis GK, Gaudillière B, Ganio EA, Aghaeepour N, Tingle M, Nolan GP, Angst MS. PMID: 26655308.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansCells
    28. The effect of microbial colonization on the host proteome varies by gastrointestinal location. ISME J. 2016 May; 10(5):1170-81. Lichtman JS, Alsentzer E, Jaffe M, Sprockett D, Masutani E, Ikwa E, Fragiadakis GK, Clifford D, Huang BE, Sonnenburg JL, Huang KC, Elias JE. PMID: 26574685.
      View in: PubMed   Mentions: 12     Fields:    Translation:Animals
    29. 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. 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. PMID: 26190063.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    30. IMMUNOLOGY. An interactive reference framework for modeling a dynamic immune system. Science. 2015 Jul 10; 349(6244):1259425. 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. PMID: 26160952.
      View in: PubMed   Mentions: 80     Fields:    Translation:HumansAnimals
    31. Transient partial permeabilization with saponin enables cellular barcoding prior to surface marker staining. Cytometry A. 2014 Dec; 85(12):1011-9. Behbehani GK, Thom C, Zunder ER, Finck R, Gaudilliere B, Fragiadakis GK, Fantl WJ, Nolan GP. PMID: 25274027.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansCells
    32. Clinical recovery from surgery correlates with single-cell immune signatures. Sci Transl Med. 2014 Sep 24; 6(255):255ra131. 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. PMID: 25253674.
      View in: PubMed   Mentions: 105     Fields:    Translation:HumansCells
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