Gabriela Fragiadakis, PhD

Assistant Professor
Research Description: 

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.

Primary Thematic Area: 
Secondary Thematic Area: 
Virology & Microbial Pathogenesis
Research Summary: 
Profiling states of the human immune system and immune-microbiome interactions using single-cell methods


Featured Publications: 

Variation of Immune Cell Responses in Humans Reveals Sex-Specific Coordinated Signaling Across Cell Types.

Frontiers in immunology

Fragiadakis GK, Bjornson-Hooper ZB, Madhireddy D, Sachs K, Chen H, McIlwain DR, Spitzer MH, Bendall SC, Nolan GP

A Comprehensive Atlas of Immunological Differences Between Humans, Mice, and Non-Human Primates.

Frontiers in immunology

Bjornson-Hooper ZB, Fragiadakis GK, Spitzer MH, Chen H, Madhireddy D, Hu K, Lundsten K, McIlwain DR, Nolan GP

Gut-microbiota-targeted diets modulate human immune status.


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

Long-term dietary intervention reveals resilience of the gut microbiota despite changes in diet and weight.

The American journal of clinical nutrition

Fragiadakis GK, Wastyk HC, Robinson JL, Sonnenburg ED, Sonnenburg JL, Gardner CD

Pursuing Human-Relevant Gut Microbiota-Immune Interactions.


Spencer SP, Fragiadakis GK, Sonnenburg JL

Links between environment, diet, and the hunter-gatherer microbiome.

Gut microbes

Fragiadakis GK, Smits SA, Sonnenburg ED, Van Treuren W, Reid G, Knight R, Manjurano A, Changalucha J, Dominguez-Bello MG, Leach J, Sonnenburg JL

A "data sharing trust" model for rapid, collaborative science.


Chan V, Gherardini PF, Krummel MF, Fragiadakis GK

dittoSeq: Universal User-Friendly Single-Cell and Bulk RNA Sequencing Visualization Toolkit.

Bioinformatics (Oxford, England)

Bunis DG, Andrews J, Fragiadakis GK, Burt TD, Sirota M

Discovering dominant tumor immune archetypes in a pan-cancer census.


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

Global Absence and Targeting of Protective Immune States in Severe COVID-19.

bioRxiv : the preprint server for biology

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

Patient-specific Immune States before Surgery Are Strong Correlates of Surgical Recovery.


Fragiadakis GK, Gaudillière B, Ganio EA, Aghaeepour N, Tingle M, Nolan GP, Angst MS

Clinical recovery from surgery correlates with single-cell immune signatures.

Science translational medicine

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

Mapping the Fetomaternal Peripheral Immune System at Term Pregnancy.

Journal of immunology (Baltimore, Md. : 1950)

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