Faculty & Scientific Staff
John Ray, PhD
Assistant Member; Principal Investigator, Ray Lab; Center for Systems Immunology
206.342.6920
Background Information
John Ray received his BS in Molecular, Cellular and Development Biology at the University of Washington in 2007 and his PhD in Immunobiology at Yale University in 2014, working in the laboratory of Joe Craft, MD. He completed his postdoctoral research at the Broad Institute of MIT and Harvard in the lab of Nir Hacohen, PhD, studying autoimmune disease genetic risk in non-coding regions and epigenetic regulation of immune cell subsets.
Dr. Ray joined the faculty of the Benaroya Research Institute in 2020 and is currently an Assistant Member. Dr. Ray has affiliate appointments at the University of Washington’s Departments of Immunology and Genome Sciences.
Featured Publications
Jul 2025
A haplotype-resolved view of human gene regulation.
bioRxiv
Vollger MR, Swanson EG, Neph SJ, Ranchalis J, Munson KM, Ho CH, Cheng YHH, Sedeno-Cortes AE, Fondrie WE, Bohaczuk SC, Dippel MA, Mao Y, Parmalee NL, Mallory BJ, Harvey WT, Kwon Y, Garcia GH, Hoekzema K, Meyer JG, Cicek M, Eichler EE, Noble WS, Witten DM, Bennett JT, Ray JP, Stergachis AB
Oct 2024
Linking candidate causal autoimmune variants to T cell networks using genetic and epigenetic screens in primary human T cells.
bioRxiv
Ho CH, Dippel MA, McQuade MS, Mishra A, Pribitzer S, Nguyen LP, Hardy S, Chandok H, Chardon F, McDiarmid TA, DeBerg HA, Buckner JH, Shendure J, de Boer CG, Guo MH, Tewhey R, Ray JP
Jun 2024
A haplotype-resolved view of human gene regulation.
bioRxiv
Vollger MR, Swanson EG, Neph SJ, Ranchalis J, Munson KM, Ho C-H, Sedeno-Cortes AE, Fondrie WE, Bohaczuk ST, Mao Y, Parmalee NL, Mallory BJ, Harvey WT, Kwon Y, Garcia GH, Hoekzema K, Meyer JG, Cicek M, Eichler EE, Noble WS, Witten DM, Bennett JT, Ray JP, Stergachis AB.
Jun 2022
Systematic identification of genomic elements that regulate FCGR2A expression and harbor variants linked with autoimmune disease.
Hum Mol Genet
Dahlqvist J, Fulco CP, Ray JP, Liechti T, de Boer CG, Lieb DJ, Eisenhaure TM, Engreitz JM, Roederer M, Hacohen N
May 2022
Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells.
Nat Genet
Mouri K, Guo MH, de Boer CG, Lissner MM, Harten IA, Newby GA, DeBerg HA, Platt WF, Gentili M, Liu DR, Campbell DJ, Hacohen N, Tewhey R, Ray JP
