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Oct 2024
Linking candidate causal autoimmune variants to T cell networks using genetic and epigenetic screens in primary human T cells.
bioRxivHo 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.
bioRxivVollger 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 GenetDahlqvist 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 GenetMouri 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 -
May 2022
Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells
Nat GenetMouri 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 -
May 2021
Genome-wide enhancer maps link risk variants to disease genes.
NatureNasser J, Bergman DT, Fulco CP, Guckelberger P, Doughty BR, Patwardhan TA, Jones TR, Nguyen TH, Ulirsch JC, Lekschas F, Mualim K, Natri HM, Weeks EM, Munson G, Kane M, Kang HY, Cui A, Ray JP, Eisenhaure TM, Collins RL, Dey K, Pfister H, Price AL, Epstein CB, Kundaje A, Xavier RJ, Daly MJ, Huang H, Finucane HK, Hacohen N, Lander ES, Engreitz JM -
Mar 2021
Global discovery of lupus genetic risk variant allelic enhancer activity.
Nat CommunLu X, Chen X, Forney C, Donmez O, Miller D, Parameswaran S, Hong T, Huang Y, Pujato M, Cazares T, Miraldi ER, Ray JP, de Boer CG, Harley JB, Weirauch MT, Kottyan LC -
Jun 2020
MAUDE: inferring expression changes in sorting-based CRISPR screens
Genome Biolde Boer CG, Ray JP, Hacohen N, Regev A -
Mar 2020
Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features
Nat CommunRay 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 -
Nov 2018
Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma
CellSade-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, Elaine 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 GS, Hacohen N -
Jul 2018
Positional specificity of different transcription factor classes within enhancers
Proc Natl Acad Sci U S AGrossman SR, Engreitz JM, Ray JP, Nguyen TH, Hacohen N, Lander ES -
Oct 2017
Resistance to checkpoint blockade therapy through inactivation of antigen presentation
Nat CommunSade-Feldman M, Jiao YJ, Chen JH, Rooney MS, Barzily-Rokni M, Eliane JP, Bjorgaard SL, Hammond MR, Vitzthum H, Blackmon SM, Frederick DT, Hazar-Rethinam M, Nadres BA, Van Seventer EE, Shukla SA, Yizhak K, Ray JP, Rosebrock D, Adalsteinsson V, Getz GS, Duncan LM, Li B, Corcoran RB, Lawrence DP, Stemmer-Rachamimov A, Boland GM, Landau DA, Flaherty KT, Sullivan RJ, Hacohen N -
Oct 2015
The Interleukin-2-mTORc1 Kinase Axis Defines the Signaling, Differentiation, and Metabolism of T Helper 1 and Follicular B Helper T Cells
ImmunityRay JP, Staron MM, Shyer JA, Ho PC, Marshall HD, Gray SM, Laidlaw BJ, Araki K, Ahmed R, Kaech SM, Craft J -
Jun 2015
Impact of autoimmune risk alleles on the immune system
Genome MedRay JP, Hacohen N -
Feb 2015
PTENtiating autoimmunity through Treg cell deregulation
Nat ImmunolRay JP, Craft J
