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Year Number of Results
2018 2
2019 2
2020 1
2021 2
2023 5
2024 1

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13 results

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Page 1
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. 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.
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.
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.
The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles.
Schreiber J, Boix C, Wook Lee J, Li H, Guan Y, Chang CC, Chang JC, Hawkins-Hooker A, Schölkopf B, Schweikert G, Carulla MR, Canakoglu A, Guzzo F, Nanni L, Masseroli M, Carman MJ, Pinoli P, Hong C, Yip KY, Spence JP, Batra SS, Song YS, Mahony S, Zhang Z, Tan W, Shen Y, Sun Y, Shi M, Adrian J, Sandstrom R, Farrell N, Halow J, Lee K, Jiang L, Yang X, Epstein C, Strattan JS, Bernstein B, Snyder M, Kellis M, Stafford W, Kundaje A; ENCODE Imputation Challenge Participants. Schreiber J, et al. Genome Biol. 2023 Apr 18;24(1):79. doi: 10.1186/s13059-023-02915-y. Genome Biol. 2023. PMID: 37072822 Free PMC article.
The ENCODE Uniform Analysis Pipelines.
Hitz BC, Jin-Wook L, Jolanki O, Kagda MS, Graham K, Sud P, Gabdank I, Strattan JS, Sloan CA, Dreszer T, Rowe LD, Podduturi NR, Malladi VS, Chan ET, Davidson JM, Ho M, Miyasato S, Simison M, Tanaka F, Luo Y, Whaling I, Hong EL, Lee BT, Sandstrom R, Rynes E, Nelson J, Nishida A, Ingersoll A, Buckley M, Frerker M, Kim DS, Boley N, Trout D, Dobin A, Rahmanian S, Wyman D, Balderrama-Gutierrez G, Reese F, Durand NC, Dudchenko O, Weisz D, Rao SSP, Blackburn A, Gkountaroulis D, Sadr M, Olshansky M, Eliaz Y, Nguyen D, Bochkov I, Shamim MS, Mahajan R, Aiden E, Gingeras T, Heath S, Hirst M, Kent WJ, Kundaje A, Mortazavi A, Wold B, Cherry JM. Hitz BC, et al. bioRxiv [Preprint]. 2023 Apr 6:2023.04.04.535623. doi: 10.1101/2023.04.04.535623. bioRxiv. 2023. PMID: 37066421 Free PMC article. Preprint.
The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models.
Rozowsky J, Gao J, Borsari B, Yang YT, Galeev T, Gürsoy G, Epstein CB, Xiong K, Xu J, Li T, Liu J, Yu K, Berthel A, Chen Z, Navarro F, Sun MS, Wright J, Chang J, Cameron CJF, Shoresh N, Gaskell E, Drenkow J, Adrian J, Aganezov S, Aguet F, Balderrama-Gutierrez G, Banskota S, Corona GB, Chee S, Chhetri SB, Cortez Martins GC, Danyko C, Davis CA, Farid D, Farrell NP, Gabdank I, Gofin Y, Gorkin DU, Gu M, Hecht V, Hitz BC, Issner R, Jiang Y, Kirsche M, Kong X, Lam BR, Li S, Li B, Li X, Lin KZ, Luo R, Mackiewicz M, Meng R, Moore JE, Mudge J, Nelson N, Nusbaum C, Popov I, Pratt HE, Qiu Y, Ramakrishnan S, Raymond J, Salichos L, Scavelli A, Schreiber JM, Sedlazeck FJ, See LH, Sherman RM, Shi X, Shi M, Sloan CA, Strattan JS, Tan Z, Tanaka FY, Vlasova A, Wang J, Werner J, Williams B, Xu M, Yan C, Yu L, Zaleski C, Zhang J, Ardlie K, Cherry JM, Mendenhall EM, Noble WS, Weng Z, Levine ME, Dobin A, Wold B, Mortazavi A, Ren B, Gillis J, Myers RM, Snyder MP, Choudhary J, Milosavljevic A, Schatz MC, Bernstein BE, Guigó R, Gingeras TR, Gerstein M. Rozowsky J, et al. Cell. 2023 Mar 30;186(7):1493-1511.e40. doi: 10.1016/j.cell.2023.02.018. Cell. 2023. PMID: 37001506 Free PMC article.
Swarm: A federated cloud framework for large-scale variant analysis.
Bahmani A, Ferriter K, Krishnan V, Alavi A, Alavi A, Tsao PS, Snyder MP, Pan C. Bahmani A, et al. PLoS Comput Biol. 2021 May 12;17(5):e1008977. doi: 10.1371/journal.pcbi.1008977. eCollection 2021 May. PLoS Comput Biol. 2021. PMID: 33979321 Free PMC article.
The ENCODE Portal as an Epigenomics Resource.
Jou J, Gabdank I, Luo Y, Lin K, Sud P, Myers Z, Hilton JA, Kagda MS, Lam B, O'Neill E, Adenekan P, Graham K, Baymuradov UK, R Miyasato S, Strattan JS, Jolanki O, Lee JW, Litton C, Y Tanaka F, Hitz BC, Cherry JM. Jou J, et al. Curr Protoc Bioinformatics. 2019 Dec;68(1):e89. doi: 10.1002/cpbi.89. Curr Protoc Bioinformatics. 2019. PMID: 31751002 Free PMC article.
New developments on the Encyclopedia of DNA Elements (ENCODE) data portal.
Luo Y, Hitz BC, Gabdank I, Hilton JA, Kagda MS, Lam B, Myers Z, Sud P, Jou J, Lin K, Baymuradov UK, Graham K, Litton C, Miyasato SR, Strattan JS, Jolanki O, Lee JW, Tanaka FY, Adenekan P, O'Neill E, Cherry JM. Luo Y, et al. Nucleic Acids Res. 2020 Jan 8;48(D1):D882-D889. doi: 10.1093/nar/gkz1062. Nucleic Acids Res. 2020. PMID: 31713622 Free PMC article.
13 results