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Page 1
The UCSC Genome Browser database: update 2011.
Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine BM, Harte RA, Hillman-Jackson J, Hsu F, Kirkup V, Kuhn RM, Learned K, Li CH, Meyer LR, Pohl A, Raney BJ, Rosenbloom KR, Smith KE, Haussler D, Kent WJ. Fujita PA, et al. Among authors: hillman jackson j. Nucleic Acids Res. 2011 Jan;39(Database issue):D876-82. doi: 10.1093/nar/gkq963. Epub 2010 Oct 18. Nucleic Acids Res. 2011. PMID: 20959295 Free PMC article.
The ENCODE Project at UC Santa Cruz.
Thomas DJ, Rosenbloom KR, Clawson H, Hinrichs AS, Trumbower H, Raney BJ, Karolchik D, Barber GP, Harte RA, Hillman-Jackson J, Kuhn RM, Rhead BL, Smith KE, Thakkapallayil A, Zweig AS; ENCODE Project Consortium; Haussler D, Kent WJ. Thomas DJ, et al. Nucleic Acids Res. 2007 Jan;35(Database issue):D663-7. doi: 10.1093/nar/gkl1017. Epub 2006 Dec 13. Nucleic Acids Res. 2007. PMID: 17166863 Free PMC article.
The UCSC Genome Browser database: update 2010.
Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ, Pohl A, Pheasant M, Meyer LR, Learned K, Hsu F, Hillman-Jackson J, Harte RA, Giardine B, Dreszer TR, Clawson H, Barber GP, Haussler D, Kent WJ. Rhead B, et al. Among authors: hillman jackson j. Nucleic Acids Res. 2010 Jan;38(Database issue):D613-9. doi: 10.1093/nar/gkp939. Epub 2009 Nov 11. Nucleic Acids Res. 2010. PMID: 19906737 Free PMC article.
The UCSC Genome Browser Database: update 2006.
Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte RA, Hsu F, Hillman-Jackson J, Kuhn RM, Pedersen JS, Pohl A, Raney BJ, Rosenbloom KR, Siepel A, Smith KE, Sugnet CW, Sultan-Qurraie A, Thomas DJ, Trumbower H, Weber RJ, Weirauch M, Zweig AS, Haussler D, Kent WJ. Hinrichs AS, et al. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D590-8. doi: 10.1093/nar/gkj144. Nucleic Acids Res. 2006. PMID: 16381938 Free PMC article.
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
ENCODE Project Consortium; Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foiss… See abstract for full author list ➔ ENCODE Project Consortium, et al. Nature. 2007 Jun 14;447(7146):799-816. doi: 10.1038/nature05874. Nature. 2007. PMID: 17571346 Free PMC article.
Using Galaxy to perform large-scale interactive data analyses.
Hillman-Jackson J, Clements D, Blankenberg D, Taylor J, Nekrutenko A, Team G. Hillman-Jackson J, et al. Curr Protoc Bioinformatics. 2012 Jun;Chapter 10:10.5.1-10.5.47. doi: 10.1002/0471250953.bi1005s38. Curr Protoc Bioinformatics. 2012. PMID: 22700312 Free PMC article.
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update.
Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Eberhard C, Grüning B, Guerler A, Hillman-Jackson J, Von Kuster G, Rasche E, Soranzo N, Turaga N, Taylor J, Nekrutenko A, Goecks J. Afgan E, et al. Among authors: hillman jackson j. Nucleic Acids Res. 2016 Jul 8;44(W1):W3-W10. doi: 10.1093/nar/gkw343. Epub 2016 May 2. Nucleic Acids Res. 2016. PMID: 27137889 Free PMC article.
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update.
Afgan E, Baker D, Batut B, van den Beek M, Bouvier D, Cech M, Chilton J, Clements D, Coraor N, Grüning BA, Guerler A, Hillman-Jackson J, Hiltemann S, Jalili V, Rasche H, Soranzo N, Goecks J, Taylor J, Nekrutenko A, Blankenberg D. Afgan E, et al. Among authors: hillman jackson j. Nucleic Acids Res. 2018 Jul 2;46(W1):W537-W544. doi: 10.1093/nar/gky379. Nucleic Acids Res. 2018. PMID: 29790989 Free PMC article.
Analysis of next-generation sequencing data using Galaxy.
Blankenberg D, Hillman-Jackson J. Blankenberg D, et al. Among authors: hillman jackson j. Methods Mol Biol. 2014;1150:21-43. doi: 10.1007/978-1-4939-0512-6_2. Methods Mol Biol. 2014. PMID: 24743989
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