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Page 1
Prevention of data duplication for high throughput sequencing repositories.
Gabdank I, Chan ET, Davidson JM, Hilton JA, Davis CA, Baymuradov UK, Narayanan A, Onate KC, Graham K, Miyasato SR, Dreszer TR, Strattan JS, Jolanki O, Tanaka FY, Hitz BC, Sloan CA, Cherry JM. Gabdank I, et al. Among authors: baymuradov uk. Database (Oxford). 2018 Jan 1;2018:bay008. doi: 10.1093/database/bay008. Database (Oxford). 2018. PMID: 29688363 Free PMC article.
The Encyclopedia of DNA elements (ENCODE): data portal update.
Davis CA, Hitz BC, Sloan CA, Chan ET, Davidson JM, Gabdank I, Hilton JA, Jain K, Baymuradov UK, Narayanan AK, Onate KC, Graham K, Miyasato SR, Dreszer TR, Strattan JS, Jolanki O, Tanaka FY, Cherry JM. Davis CA, et al. Among authors: baymuradov uk. Nucleic Acids Res. 2018 Jan 4;46(D1):D794-D801. doi: 10.1093/nar/gkx1081. Nucleic Acids Res. 2018. PMID: 29126249 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. Among authors: baymuradov uk. Nucleic Acids Res. 2020 Jan 8;48(D1):D882-D889. doi: 10.1093/nar/gkz1062. Nucleic Acids Res. 2020. PMID: 31713622 Free PMC article.
Expanded encyclopaedias of DNA elements in the human and mouse genomes.
ENCODE Project Consortium; Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. ENCODE Project Consortium, et al. Nature. 2020 Jul;583(7818):699-710. doi: 10.1038/s41586-020-2493-4. Epub 2020 Jul 29. Nature. 2020. PMID: 32728249 Free PMC article.
SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata.
Hitz BC, Rowe LD, Podduturi NR, Glick DI, Baymuradov UK, Malladi VS, Chan ET, Davidson JM, Gabdank I, Narayana AK, Onate KC, Hilton J, Ho MC, Lee BT, Miyasato SR, Dreszer TR, Sloan CA, Strattan JS, Tanaka FY, Hong EL, Cherry JM. Hitz BC, et al. Among authors: baymuradov uk. PLoS One. 2017 Apr 12;12(4):e0175310. doi: 10.1371/journal.pone.0175310. eCollection 2017. PLoS One. 2017. PMID: 28403240 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. Among authors: baymuradov uk. Curr Protoc Bioinformatics. 2019 Dec;68(1):e89. doi: 10.1002/cpbi.89. Curr Protoc Bioinformatics. 2019. PMID: 31751002 Free PMC article.
Perspectives on ENCODE.
ENCODE Project Consortium; Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, Cherry JM, Bernstein BE, Mendenhall EM, Zerbino DR, Frankish A, Flicek P, Myers RM. ENCODE Project Consortium, et al. Nature. 2020 Jul;583(7818):693-698. doi: 10.1038/s41586-020-2449-8. Epub 2020 Jul 29. Nature. 2020. PMID: 32728248 Free PMC article.
Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes.
ENCODE Project Consortium; Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. ENCODE Project Consortium, et al. Nature. 2022 May;605(7909):E3. doi: 10.1038/s41586-021-04226-3. Nature. 2022. PMID: 35474001 Free PMC article. No abstract available.
Author Correction: Perspectives on ENCODE.
ENCODE Project Consortium; Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, Cherry JM, Bernstein BE, Mendenhall EM, Zerbino DR, Frankish A, Flicek P, Myers RM. ENCODE Project Consortium, et al. Nature. 2022 May;605(7909):E4. doi: 10.1038/s41586-021-04213-8. Nature. 2022. PMID: 35474002 Free PMC article. No abstract available.