Gabriela Fragiadakis, PhD

Title(s)Assistant Professor, Medicine
SchoolSchool of Medicine
Address513 Parnassus Avenue, MSB, #847C
San Francisco CA 94143
ORCID ORCID Icon0000-0001-9703-2591 Additional info
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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
    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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    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. Single-cell spatial transcriptomics of fixed, paraffin-embedded biopsies reveals colitis-associated cell networks. bioRxiv. 2024 Nov 11. 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. PMID: 39605355; PMCID: PMC11601222.
      View in: PubMed   Mentions:
    2. 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 Sci. 2024 Oct 15. 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. PMID: 39419175.
      View in: PubMed   Mentions:    Fields:    
    3. Cell-Specific Transposable Element and Gene Expression Analysis Across Systemic Lupus Erythematosus Phenotypes. ACR Open Rheumatol. 2024 Aug 14. 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. PMID: 39143499.
      View in: PubMed   Mentions:
    4. Single-cell RNA-Seq analysis reveals cell subsets and gene signatures associated with rheumatoid arthritis disease activity. JCI Insight. 2024 Jul 02; 9(16). 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, Ye CJ, Butte AJ, Criswell LA, Nakamura MC, Sirota M. PMID: 38954480; PMCID: PMC11343607.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    5. Distinct pulmonary and systemic effects of dexamethasone in severe COVID-19. Nat Commun. 2024 Jun 28; 15(1):5483. 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. PMID: 38942804; PMCID: PMC11213873.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    6. Coordinated immune dysregulation in juvenile dermatomyositis revealed by single-cell genomics. JCI Insight. 2024 May 14; 9(12). Rabadam G, Wibrand C, Flynn E, Hartoularos GC, Sun Y, Madubata C, Fragiadakis GK, Ye CJ, Kim S, Gartner ZJ, Sirota M, Neely J. PMID: 38743491; PMCID: PMC11383589.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    7. Integrated longitudinal multiomics study identifies immune programs associated with acute COVID-19 severity and mortality. J Clin Invest. 2024 May 01; 134(9). 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, Rouphael N, Bosinger SE, Kim-Schulze S, Krammer F, Rosen LB, van Bakel H, Wilson M, Eckalbar WL, Maecker HT, Langelier CR, Steen H, Altman MC, Montgomery RR, Levy O, Melamed E, Pulendran B, Diray-Arce J, Smolen KK, Fragiadakis GK, Becker PM, Sekaly RP, Ehrlich LI, Fourati S, Peters B, Kleinstein SH, Guan L. PMID: 38690733; PMCID: PMC11060740.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    8. Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis. Nat Commun. 2024 Feb 19; 15(1):1493. 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. PMID: 38374043; PMCID: PMC10876948.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    9. Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis. bioRxiv. 2024 Jan 03. 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. PMID: 36711576; PMCID: PMC9882264.
      View in: PubMed   Mentions:
    10. Cell-Specific Transposable Element Gene Expression Analysis Identifies Associations with Systemic Lupus Erythematosus Phenotypes. bioRxiv. 2023 Nov 28. 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. PMID: 38076936; PMCID: PMC10705239.
      View in: PubMed   Mentions:
    11. Homeostatic cytokines reciprocally modulate the emergence of prenatal effector PLZF+CD4+ T cells in humans. JCI Insight. 2023 Nov 22; 8(22). Locher V, Park S, Bunis DG, Makredes S, Mayer M, Burt TD, Fragiadakis GK, Halkias J. PMID: 37856221; PMCID: PMC10721317.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    12. Integrated longitudinal multi-omics study identifies immune programs associated with COVID-19 severity and mortality in 1152 hospitalized participants. bioRxiv. 2023 Nov 06. 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. PMID: 37986828; PMCID: PMC10659275.
      View in: PubMed   Mentions:
    13. Cyclone: an accessible pipeline to analyze, evaluate, and optimize multiparametric cytometry data. Front Immunol. 2023; 14:1167241. 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, Baron JL, Combes AJ, Fragiadakis GK. PMID: 37731497; PMCID: PMC10507399.
      View in: PubMed   Mentions: 2     Fields:    
    14. A myeloid program associated with COVID-19 severity is decreased by therapeutic blockade of IL-6 signaling. iScience. 2023 Oct 20; 26(10):107813. 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, Krummel MF, Erle DJ, Kangelaris K, Sarma A, Lyon Z, Calfee CS, Woodruff PG, Ghale R, Mick E, Byrne A, Zha BS, Langelier C, Hendrickson CM, van der Wijst MGP, Hartoularos GC, Grant T, Bueno R, Lee DS, Greenland JR, Sun Y, Perez R, Ogorodnikov A, Ward A, Ye CJ, UCSF COMET Consortium, Ramalingam T, McBride JM, Cai F, Teterina A, Bao M, Tsai L, Rosas IO, Regev A, Kapadia SB, Bauer RN, Rosenberger CM. PMID: 37810211; PMCID: PMC10551843.
      View in: PubMed   Mentions: 2  
    15. Distinct pulmonary and systemic effects of dexamethasone in severe COVID-19. Res Sq. 2023 Aug 03. 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. PMID: 37577607; PMCID: PMC10418533.
      View in: PubMed   Mentions:
    16. Single-Cell Multiomics. Annu Rev Biomed Data Sci. 2023 08 10; 6:313-337. Flynn E, Almonte-Loya A, Fragiadakis GK. PMID: 37159875; PMCID: PMC11146013.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    17. Cyclone: an accessible pipeline to analyze, evaluate and optimize multiparametric cytometry data. bioRxiv. 2023 Mar 11. 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. PMID: 36945648; PMCID: PMC10028883.
      View in: PubMed   Mentions:
    18. SARS-CoV-2 infection of airway organoids reveals conserved use of Tetraspanin-8 by Ancestral, Delta, and Omicron variants. Stem Cell Reports. 2023 03 14; 18(3):636-653. 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, Li JZ, Ding VW, Matsumoto S, Maishan M, Sreekumar B, Simoneau C, Nazarenko I, Tomlinson MG, Khan K, von Gottberg A, Sigal A, Looney MR, Fragiadakis GK, Jablons DM, Langelier CR, Matthay M, Krummel M, Erle DJ, Combes AJ, Sil A, Ott M, Kratz JR, Roose JP. PMID: 36827975; PMCID: PMC9948283.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    19. Randomized controlled trial demonstrates response to a probiotic intervention for metabolic syndrome that may correspond to diet. Gut Microbes. 2023 Jan-Dec; 15(1):2178794. Wastyk HC, Perelman D, Topf M, Fragiadakis GK, Robinson JL, Sonnenburg JL, Gardner CD, Sonnenburg ED. PMID: 36803658; PMCID: PMC9980610.
      View in: PubMed   Mentions: 10     Fields:    Translation:Humans
    20. Distinct factors associated with short-term and long-term weight loss induced by low-fat or low-carbohydrate diet intervention. Cell Rep Med. 2022 12 20; 3(12):100870. Li X, Perelman D, Leong AK, Fragiadakis G, Gardner CD, Snyder MP. PMID: 36516846; PMCID: PMC9798029.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    21. Bioinformatics Analysis of Publicly Available Single-Nuclei Transcriptomics Alzheimer's Disease Datasets Reveals APOE Genotype-Specific Changes Across Cell Types in Two Brain Regions. Front Aging Neurosci. 2022; 14:749991. Belonwu SA, Li Y, Bunis DG, Rao AA, Solsberg CW, Oskotsky T, Taubes AL, Grone B, Zalocusky KA, Fragiadakis GK, Huang Y, Sirota M. PMID: 35572130; PMCID: PMC9093608.
      View in: PubMed   Mentions: 2  
    22. Variation of Immune Cell Responses in Humans Reveals Sex-Specific Coordinated Signaling Across Cell Types. Front Immunol. 2022; 13:867016. Fragiadakis GK, Bjornson-Hooper ZB, Madhireddy D, Sachs K, Chen H, McIlwain DR, Spitzer MH, Bendall SC, Nolan GP. PMID: 35419006; PMCID: PMC8995898.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    23. A Comprehensive Atlas of Immunological Differences Between Humans, Mice, and Non-Human Primates. Front Immunol. 2022; 13:867015. Bjornson-Hooper ZB, Fragiadakis GK, Spitzer MH, Chen H, Madhireddy D, Hu K, Lundsten K, McIlwain DR, Nolan GP. PMID: 35359965; PMCID: PMC8962947.
      View in: PubMed   Mentions: 63     Fields:    Translation:HumansAnimalsCells
    24. Discovering dominant tumor immune archetypes in a pan-cancer census. Cell. 2022 01 06; 185(1):184-203.e19. 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, Immunoprofiler Consortium, Cai C, Zhan J, Davis KC, Kelley RK, Chapman JS, Atreya CE, Patel A, Daud AI, Ha P, Diaz AA, Kratz JR, Collisson EA, Fragiadakis GK, Erle DJ, Boissonnas A, Asthana S, Chan V, Krummel MF. PMID: 34963056; PMCID: PMC8862608.
      View in: PubMed   Mentions: 49     Fields:    Translation:HumansCells
    25. Sex-Stratified Single-Cell RNA-Seq Analysis Identifies Sex-Specific and Cell Type-Specific Transcriptional Responses in Alzheimer's Disease Across Two Brain Regions. Mol Neurobiol. 2022 Jan; 59(1):276-293. Belonwu SA, Li Y, Bunis D, Rao AA, Solsberg CW, Tang A, Fragiadakis GK, Dubal DB, Oskotsky T, Sirota M. PMID: 34669146; PMCID: PMC8786804.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    26. Increased risk of severe clinical course of COVID-19 in carriers of HLA-C*04:01. EClinicalMedicine. 2021 Oct; 40:101099. 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, Poller W, Borodina T, Pa-Covid SG, Ripke S, Sander LE, Beule D, Landmesser U, Guettouche T, Kurth F, Heidecker B. PMID: 34490415; PMCID: PMC8410317.
      View in: PubMed   Mentions: 48  
    27. Type I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19. Sci Transl Med. 2021 Sep 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; PMCID: PMC8601717.
      View in: PubMed   Mentions: 127     Fields:    Translation:Humans
    28. Inhibition of MET Signaling with Ficlatuzumab in Combination with Chemotherapy in Refractory AML: Clinical Outcomes and High-Dimensional Analysis. Blood Cancer Discov. 2021 09; 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; PMCID: PMC8425277.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    29. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021 08 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; PMCID: PMC9020749.
      View in: PubMed   Mentions: 337     Fields:    Translation:HumansCells
    30. 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; PMCID: PMC8183007.
      View in: PubMed   Mentions: 1  
    31. 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; PMCID: PMC8184217.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansAnimalsCells
    32. dittoSeq: universal user-friendly single-cell and bulk RNA sequencing visualization toolkit. Bioinformatics. 2021 Apr 01; 36(22-23):5535-5536. Bunis DG, Andrews J, Fragiadakis GK, Burt TD, Sirota M. PMID: 33313640; PMCID: PMC8016464.
      View in: PubMed   Mentions: 75     Fields:    
    33. 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. 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, Le Voyer T, 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; PMCID: PMC7987018.
      View in: PubMed   Mentions: 1  
    34. 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: 3     Fields:    Translation:Humans
    35. 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; PMCID: PMC8567458.
      View in: PubMed   Mentions: 143     Fields:    Translation:HumansCells
    36. 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; PMCID: PMC7598057.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCellsCTClinical Trials
    37. 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; PMCID: PMC7605559.
      View in: PubMed   Mentions:
    38. 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; PMCID: PMC7605560.
      View in: PubMed   Mentions:
    39. 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; PMCID: PMC7266695.
      View in: PubMed   Mentions: 56     Fields:    Translation:HumansCells
    40. 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; PMCID: PMC7897424.
      View in: PubMed   Mentions: 10     Fields:    
    41. 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; PMCID: PMC6856718.
      View in: PubMed   Mentions: 50     Fields:    Translation:HumansCells
    42. Pursuing Human-Relevant Gut Microbiota-Immune Interactions. Immunity. 2019 08 20; 51(2):225-239. Spencer SP, Fragiadakis GK, Sonnenburg JL. PMID: 31433970; PMCID: PMC7205593.
      View in: PubMed   Mentions: 47     Fields:    Translation:HumansAnimals
    43. 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; PMCID: PMC6247943.
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    44. 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; PMCID: PMC6237292.
      View in: PubMed   Mentions: 81     Fields:    Translation:HumansCells
    45. 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; PMCID: PMC6546328.
      View in: PubMed   Mentions: 64     Fields:    Translation:HumansAnimalsPHPublic Health
    46. 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; PMCID: PMC5337813.
      View in: PubMed   Mentions: 47     Fields:    Translation:HumansCells
    47. 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; PMCID: PMC5320935.
      View in: PubMed   Mentions: 192     Fields:    Translation:HumansAnimalsCells
    48. 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; PMCID: PMC5125527.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    49. 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; PMCID: PMC5505729.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansAnimalsCells
    50. In Reply. Anesthesiology. 2016 06; 124(6):1414-5. Angst MS, Fragiadakis GK, Gaudillière B, Aghaeepour N, Nolan GP. PMID: 27187126; PMCID: PMC4914362.
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    51. 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; PMCID: PMC4681408.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansCells
    52. 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; PMCID: PMC5029216.
      View in: PubMed   Mentions: 17     Fields:    Translation:Animals
    53. 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; PMCID: PMC4758855.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCells
    54. 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; PMCID: PMC4537647.
      View in: PubMed   Mentions: 116     Fields:    Translation:HumansAnimals
    55. 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; PMCID: PMC4361015.
      View in: PubMed   Mentions: 53     Fields:    Translation:HumansCells
    56. 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; PMCID: PMC4334126.
      View in: PubMed   Mentions: 171     Fields:    Translation:HumansCells
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