faculty

John Ray

jray@benaroyaresearch.org
Assistant Member

Benaroya Research Institute

Gene Expression, Cell Cycle & Chromosome Biology

Genetics, Genomics & Evolution

Microbiology, Infection & Immunity

Using genomic approaches to study autoimmune disease susceptibility

Faculty Contact Information

Building: Benaroya Research Institute Box: Ray Lab Phone: 206-342-6920 https://www.benaroyaresearch.org/what-is-bri/scientists-laboratories/principal-scientist-labs/ray-laboratory

Research Summary

The Ray lab studies the mechanisms that contribute to variation in human immune responses. In particular, we determine how genetic variants and non-coding regulatory regions alter immune responses and confer autoimmune disease susceptibility. With a focus on T cells, we prioritize likely disease-causal genetic variants and enhancers, and, in human and mouse systems, we dissect their mechanisms of action. Understanding the mechanisms of inherited autoimmune disease susceptibility will inform efforts for personalized therapies and disease prevention.

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&query_key=1&WebEnv=MCID_60076d5d319476280b2b1aa9&retmode=json
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Publications

The following publications were retrieved from PubMed:

MAUDE: inferring expression changes in sorting-based CRISPR screens.

de Boer CG, Ray JP, Hacohen N, Regev A.

Genome Biol. 2020 Jun 3; 1(21)134

Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features.

Ray JP, de Boer CG, Fulco CP, Lareau CA, Kanai M, Ulirsch JC, Tewhey R, Ludwig LS, Reilly SK, Bergman DT, Engreitz JM, Issner R, Finucane HK, Lander ES, Regev A, Hacohen N.

Nat Commun. 2020 Mar 6; 1(11)1237

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma.

Sade-Feldman M, Yizhak K, Bjorgaard SL, Ray JP, de Boer CG, Jenkins RW, Lieb DJ, Chen JH, Frederick DT, Barzily-Rokni M, Freeman SS, Reuben A, Hoover PJ, Villani AC, Ivanova E, Portell A, Lizotte PH, Aref AR, Eliane JP, Hammond MR, Vitzthum H, Blackmon SM, Li B, Gopalakrishnan V, Reddy SM, Cooper ZA, Paweletz CP, Barbie DA, Stemmer-Rachamimov A, Flaherty KT, Wargo JA, Boland GM, Sullivan RJ, Getz G, Hacohen N.

Cell. 2019 Jan 10; 1-2(176)404

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma.

Sade-Feldman M, Yizhak K, Bjorgaard SL, Ray JP, de Boer CG, Jenkins RW, Lieb DJ, Chen JH, Frederick DT, Barzily-Rokni M, Freeman SS, Reuben A, Hoover PJ, Villani AC, Ivanova E, Portell A, Lizotte PH, Aref AR, Eliane JP, Hammond MR, Vitzthum H, Blackmon SM, Li B, Gopalakrishnan V, Reddy SM, Cooper ZA, Paweletz CP, Barbie DA, Stemmer-Rachamimov A, Flaherty KT, Wargo JA, Boland GM, Sullivan RJ, Getz G, Hacohen N.

Cell. 2018 Nov 1; 4(175)998-1013.e20

Positional specificity of different transcription factor classes within enhancers.

Grossman SR, Engreitz J, Ray JP, Nguyen TH, Hacohen N, Lander ES.

Proc Natl Acad Sci U S A. 2018 Jul 24; 30(115)E7222-E7230

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