Publications

Published and in progress works
Links between environment, diet, and the hunter-gatherer microbiome
Fragiadakis GK, Smits SA, Sonnenburg ED, Van Treuren W, Reid G, Knight R, Manjurano A, Changalucha J, Dominguez-Bello MG, Leach J, Sonnenburg JL.
Gut Microbes 2018; Epub.
Mapping the Fetomaternal Peripheral Immune System at Term Pregnancy
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, Carvalho B, Lewis DB, Stevenson DK, Nolan GP, Aghaeepour N, Angst MA, Gaudilliere B.
Journal of Immunology 2016; 197: 4482-4492.
Patient-specific immune states before surgery are strong correlates of surgical recovery
Fragiadakis GK*, Gaudilliere, B*, Ganio EA, Aghaeepour N, Tingle M, Nolan GP, Angst MS.
Anethesiology 2015; 123: 1241-55.
Clinical recovery from surgery correlates with single-cell immune signatures
Gaudilliere 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
Sci Transl Med, cover article, 2014; 6: 255ra131
“Learning Biomolecular Pathways from Data.”
Sachs K*, Fragiadakis GK*.
A Bioinformatics Guide for Molecular Biologists. Ed. Aerni S, Sarota M. New York: Cold Spring Harbor Laboratory Press, 2014. 241-260. Print.
Gut microbiome transition across a lifestyle gradient in Himalaya.
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.
Plos Biol 2018
GateFinder: Projection-based Gating Strategy Optimization for Flow and Mass Cytometry.
Aghaeepour N, Simonds EF, Knapp DJHF, Bruggner R, Sachs K, Culos A, Gherardini PF, Samusik N, Fragiadakis GK, Bendall S, Gaudilliere B, Angst MS, Eaves CJ, Weiss WA, Fantl W, Nolan G.
Bioinformatics 2018; Epub.
Expression of specific inflammasome gene modules stratifies older individuals into two extreme clinical and immunological states.
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.
Nat Med 2017; 23(2): 174-184.
Multicenter Systems Analysis of Human Blood Reveals Immature Neutrophils in Males and During Pregnancy
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.
Journal of Immunology 2017; 198(6):2479- 2488.
The effect of microbial colonization on the host proteome varies by gastrointestinal location.
Elias J, Lichtman J, Emily Alsentzer, Jaffe M, Sprockett D, Masutani E, Ikwa E, Fragiadakis GK, Clifford D, Huang B, Sonnenburg J, Huang K.
ISMEJ 2016; 10: 1170-1181.
Biosynthesis and Regulation of Sulfomenaquinone, a Metabolite Associated with Virulence in Mycobacterium tuberculosis
Sogi KM, Holsclaw CM, Fragiadakis GK, Nomura DK, Leary JA, Bertozzi CR.
ACS Infect Dis. 2016; 2: 800-806.
IMMUNOLOGY. An interactive reference framework for modeling a dynamic immune system
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.
Science 2015; 349: 1259425
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
Gaudilliere 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.
Cytometry A 2015; 87: 817-29
Transient partial permeabilization with saponin enables cellular barcoding prior to surface marker staining
Behbehani GK, Thom C, Zunder ER, Finck R, Gaudilliere B, Fragiadakis GK, Fantl WJ, Nolan GP.
Cytometry A 2014; 85: 1011-9