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Page 1
ENCODE data at the ENCODE portal.
Sloan CA, Chan ET, Davidson JM, Malladi VS, Strattan JS, Hitz BC, Gabdank I, Narayanan AK, Ho M, Lee BT, Rowe LD, Dreszer TR, Roe G, Podduturi NR, Tanaka F, Hong EL, Cherry JM. Sloan CA, et al. Among authors: chan et. Nucleic Acids Res. 2016 Jan 4;44(D1):D726-32. doi: 10.1093/nar/gkv1160. Epub 2015 Nov 2. Nucleic Acids Res. 2016. PMID: 26527727 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.
Saccharomyces Genome Database: the genomics resource of budding yeast.
Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED. Cherry JM, et al. Among authors: chan et. Nucleic Acids Res. 2012 Jan;40(Database issue):D700-5. doi: 10.1093/nar/gkr1029. Epub 2011 Nov 21. Nucleic Acids Res. 2012. PMID: 22110037 Free PMC article.
Saccharomyces genome database provides new regulation data.
Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM. Costanzo MC, et al. Among authors: chan et. Nucleic Acids Res. 2014 Jan;42(Database issue):D717-25. doi: 10.1093/nar/gkt1158. Epub 2013 Nov 21. Nucleic Acids Res. 2014. PMID: 24265222 Free PMC article.
Ontology application and use at the ENCODE DCC.
Malladi VS, Erickson DT, Podduturi NR, Rowe LD, Chan ET, Davidson JM, Hitz BC, Ho M, Lee BT, Miyasato S, Roe GR, Simison M, Sloan CA, Strattan JS, Tanaka F, Kent WJ, Cherry JM, Hong EL. Malladi VS, et al. Among authors: chan et. Database (Oxford). 2015 Mar 16;2015:bav010. doi: 10.1093/database/bav010. Print 2015. Database (Oxford). 2015. PMID: 25776021 Free PMC article. Review.
Principles of metadata organization at the ENCODE data coordination center.
Hong EL, Sloan CA, Chan ET, Davidson JM, Malladi VS, Strattan JS, Hitz BC, Gabdank I, Narayanan AK, Ho M, Lee BT, Rowe LD, Dreszer TR, Roe GR, Podduturi NR, Tanaka F, Hilton JA, Cherry JM. Hong EL, et al. Among authors: chan et. Database (Oxford). 2016 Mar 15;2016:baw001. doi: 10.1093/database/baw001. Print 2016. Database (Oxford). 2016. PMID: 26980513 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: chan et. 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 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: chan et. Nucleic Acids Res. 2018 Jan 4;46(D1):D794-D801. doi: 10.1093/nar/gkx1081. Nucleic Acids Res. 2018. PMID: 29126249 Free PMC article.
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: chan et. Database (Oxford). 2018 Jan 1;2018:bay008. doi: 10.1093/database/bay008. Database (Oxford). 2018. PMID: 29688363 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.
53 results