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High Shear Stress Reduces ERG Causing Endothelial-Mesenchymal Transition and Pulmonary Arterial Hypertension.
Shinohara T, Moonen JR, Chun YH, Lee-Yow YC, Okamura K, Szafron JM, Kaplan J, Cao A, Wang L, Guntur D, Taylor S, Isobe S, Dong M, Yang W, Guo K, Franco BD, Pacharinsak C, Pisani LJ, Saitoh S, Mitani Y, Marsden AL, Engreitz JM, Körbelin J, Rabinovitch M. Shinohara T, et al. Among authors: engreitz jm. Arterioscler Thromb Vasc Biol. 2024 Dec 26. doi: 10.1161/ATVBAHA.124.321092. Online ahead of print. Arterioscler Thromb Vasc Biol. 2024. PMID: 39723537
Small-cohort GWAS discovery with AI over massive functional genomics knowledge graph.
Huang K, Zeng T, Koc S, Pettet A, Zhou J, Jain M, Sun D, Ruiz C, Ren H, Howe L, Richardson TG, Cortes A, Aiello K, Branson K, Pfenning A, Engreitz JM, Zhang MJ, Leskovec J. Huang K, et al. Among authors: engreitz jm. medRxiv [Preprint]. 2024 Dec 5:2024.12.03.24318375. doi: 10.1101/2024.12.03.24318375. medRxiv. 2024. PMID: 39677475 Free PMC article. Preprint.
Single cell variant to enhancer to gene map for coronary artery disease.
Amrute JM, Lee PC, Eres I, Lee CJM, Bredemeyer A, Sheth MU, Yamawaki T, Gurung R, Anene-Nzelu C, Qiu WL, Kundu S, Li DY, Ramste M, Lu D, Tan A, Kang CJ, Wagoner RE, Alisio A, Cheng P, Zhao Q, Miller CL, Hall IM, Gupta RM, Hsu YH, Haldar SM, Lavine KJ, Jackson S, Andersson R, Engreitz JM, Foo RS, Li CM, Ason B, Quertermous T, Stitziel NO. Amrute JM, et al. Among authors: engreitz jm. medRxiv [Preprint]. 2024 Nov 13:2024.11.13.24317257. doi: 10.1101/2024.11.13.24317257. medRxiv. 2024. PMID: 39606421 Free PMC article. Preprint.
Molecular convergence of risk variants for congenital heart defects leveraging a regulatory map of the human fetal heart.
Ma XR, Conley SD, Kosicki M, Bredikhin D, Cui R, Tran S, Sheth MU, Qiu WL, Chen S, Kundu S, Kang HY, Amgalan D, Munger CJ, Duan L, Dang K, Rubio OM, Kany S, Zamirpour S, DePaolo J, Padmanabhan A; Birth Defects Research Laboratory; Olgin J, Damrauer S, Andersson R, Gu M, Priest JR, Quertermous T, Qiu X, Rabinovitch M, Visel A, Pennacchio L, Kundaje A, Glass IA, Gifford CA, Pirruccello JP, Goodyer WR, Engreitz JM. Ma XR, et al. Among authors: engreitz jm. medRxiv [Preprint]. 2024 Nov 22:2024.11.20.24317557. doi: 10.1101/2024.11.20.24317557. medRxiv. 2024. PMID: 39606363 Free PMC article. Preprint.
Mapping enhancer-gene regulatory interactions from single-cell data.
Sheth MU, Qiu WL, Rosa Ma X, Gschwind AR, Jagoda E, Tan AS, Einarsson H, Gorissen BL, Dubocanin D, McGinnis CS, Amgalan D, Satpathy AT, Jones TR, Steinmetz LM, Kundaje A, Ustun B, Engreitz JM, Andersson R. Sheth MU, et al. Among authors: engreitz jm. bioRxiv [Preprint]. 2024 Nov 24:2024.11.23.624931. doi: 10.1101/2024.11.23.624931. bioRxiv. 2024. PMID: 39605382 Free PMC article. Preprint.
Selective Enhancer Gain-of-Function Deregulates MYC Expression in Multiple Myeloma.
Rahmat M, Clement K, Alberge JB, Sklavenitis-Pistofidis R, Kodgule R, Fulco CP, Heilpern-Mallory D, Nilsson K, Dorfman D, Engreitz JM, Getz G, Pinello L, Ryan RJH, Ghobrial IM. Rahmat M, et al. Among authors: engreitz jm. Cancer Res. 2024 Dec 16;84(24):4173-4183. doi: 10.1158/0008-5472.CAN-24-1440. Cancer Res. 2024. PMID: 39312195
Genetic and functional analysis of Raynaud's syndrome implicates loci in vasculature and immunity.
Tervi A, Ramste M, Abner E, Cheng P, Lane JM, Maher M, Valliere J, Lammi V, Strausz S, Riikonen J, Nguyen T, Martyn GE, Sheth MU, Xia F, Docampo ML, Gu W; FinnGen, Estonian Biobank research team; Esko T, Saxena R, Pirinen M, Palotie A, Ripatti S, Sinnott-Armstrong N, Daly M, Engreitz JM, Rabinovitch M, Heckman CA, Quertermous T, Jones SE, Ollila HM. Tervi A, et al. Among authors: engreitz jm. Cell Genom. 2024 Sep 11;4(9):100630. doi: 10.1016/j.xgen.2024.100630. Epub 2024 Aug 13. Cell Genom. 2024. PMID: 39142284 Free PMC article.
Cohesin-mediated 3D contacts tune enhancer-promoter regulation.
Guckelberger P, Doughty BR, Munson G, Rao SSP, Tan Y, Cai XS, Fulco CP, Nasser J, Mualim KS, Bergman DT, Ray J, Jagoda E, Munger CJ, Gschwind AR, Sheth MU, Tan AS, Pulido SG, Mitra N, Weisz D, Shamim MS, Durand NC, Mahajan R, Khan R, Steinmetz LM, Kanemaki MT, Lander ES, Meissner A, Aiden EL, Engreitz JM. Guckelberger P, et al. Among authors: engreitz jm. bioRxiv [Preprint]. 2024 Jul 22:2024.07.12.603288. doi: 10.1101/2024.07.12.603288. bioRxiv. 2024. PMID: 39026740 Free PMC article. Preprint.
Multicenter integrated analysis of noncoding CRISPRi screens.
Yao D, Tycko J, Oh JW, Bounds LR, Gosai SJ, Lataniotis L, Mackay-Smith A, Doughty BR, Gabdank I, Schmidt H, Guerrero-Altamirano T, Siklenka K, Guo K, White AD, Youngworth I, Andreeva K, Ren X, Barrera A, Luo Y, Yardımcı GG, Tewhey R, Kundaje A, Greenleaf WJ, Sabeti PC, Leslie C, Pritykin Y, Moore JE, Beer MA, Gersbach CA, Reddy TE, Shen Y, Engreitz JM, Bassik MC, Reilly SK. Yao D, et al. Among authors: engreitz jm. Nat Methods. 2024 Apr;21(4):723-734. doi: 10.1038/s41592-024-02216-7. Epub 2024 Mar 19. Nat Methods. 2024. PMID: 38504114 Free PMC article.
61 results