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Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions.
Nat Genet. 2023 Aug;55(8):1336-1346. doi: 10.1038/s41588-023-01450-7. Epub 2023 Jul 24.
Nat Genet. 2023.
PMID: 37488417
Free PMC article.
An encyclopedia of enhancer-gene regulatory interactions in the human genome.
Gschwind AR, Mualim KS, Karbalayghareh A, Sheth MU, Dey KK, Jagoda E, Nurtdinov RN, Xi W, Tan AS, Jones H, Ma XR, Yao D, Nasser J, Avsec Ž, James BT, Shamim MS, Durand NC, Rao SSP, Mahajan R, Doughty BR, Andreeva K, Ulirsch JC, Fan K, Perez EM, Nguyen TC, Kelley DR, Finucane HK, Moore JE, Weng Z, Kellis M, Bassik MC, Price AL, Beer MA, Guigó R, Stamatoyannopoulos JA, Lieberman Aiden E, Greenleaf WJ, Leslie CS, Steinmetz LM, Kundaje A, Engreitz JM.
Gschwind AR, et al.
bioRxiv [Preprint]. 2023 Nov 13:2023.11.09.563812. doi: 10.1101/2023.11.09.563812.
bioRxiv. 2023.
PMID: 38014075
Free PMC article.
Preprint.
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The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity.
Reese F, Williams B, Balderrama-Gutierrez G, Wyman D, Çelik MH, Rebboah E, Rezaie N, Trout D, Razavi-Mohseni M, Jiang Y, Borsari B, Morabito S, Liang HY, McGill CJ, Rahmanian S, Sakr J, Jiang S, Zeng W, Carvalho K, Weimer AK, Dionne LA, McShane A, Bedi K, Elhajjajy SI, Upchurch S, Jou J, Youngworth I, Gabdank I, Sud P, Jolanki O, Strattan JS, Kagda MS, Snyder MP, Hitz BC, Moore JE, Weng Z, Bennett D, Reinholdt L, Ljungman M, Beer MA, Gerstein MB, Pachter L, Guigó R, Wold BJ, Mortazavi A.
Reese F, et al.
bioRxiv [Preprint]. 2023 May 16:2023.05.15.540865. doi: 10.1101/2023.05.15.540865.
bioRxiv. 2023.
PMID: 37292896
Free PMC article.
Preprint.
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Early transcriptional responses of human nasal epithelial cells to infection with Influenza A and SARS-CoV-2 virus differ and are influenced by physiological temperature.
Resnick JD, Beer MA, Pekosz A.
Resnick JD, et al.
bioRxiv [Preprint]. 2023 Mar 9:2023.03.07.531609. doi: 10.1101/2023.03.07.531609.
bioRxiv. 2023.
PMID: 36945583
Free PMC article.
Updated.
Preprint.
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Early Transcriptional Responses of Human Nasal Epithelial Cells to Infection with Influenza A and SARS-CoV-2 Virus Differ and Are Influenced by Physiological Temperature.
Resnick JD, Beer MA, Pekosz A.
Resnick JD, et al.
Pathogens. 2023 Mar 18;12(3):480. doi: 10.3390/pathogens12030480.
Pathogens. 2023.
PMID: 36986402
Free PMC article.
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