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Items: 1 to 20 of 44

1.

The UCSC Genome Browser database: 2018 update.

Casper J, Zweig AS, Villarreal C, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Karolchik D, Hinrichs AS, Haeussler M, Guruvadoo L, Navarro Gonzalez J, Gibson D, Fiddes IT, Eisenhart C, Diekhans M, Clawson H, Barber GP, Armstrong J, Haussler D, Kuhn RM, Kent WJ.

Nucleic Acids Res. 2018 Jan 4;46(D1):D762-D769. doi: 10.1093/nar/gkx1020.

2.

The UCSC Genome Browser database: 2017 update.

Tyner C, Barber GP, Casper J, Clawson H, Diekhans M, Eisenhart C, Fischer CM, Gibson D, Gonzalez JN, Guruvadoo L, Haeussler M, Heitner S, Hinrichs AS, Karolchik D, Lee BT, Lee CM, Nejad P, Raney BJ, Rosenbloom KR, Speir ML, Villarreal C, Vivian J, Zweig AS, Haussler D, Kuhn RM, Kent WJ.

Nucleic Acids Res. 2017 Jan 4;45(D1):D626-D634. doi: 10.1093/nar/gkw1134. Epub 2016 Nov 29.

3.

UCSC Data Integrator and Variant Annotation Integrator.

Hinrichs AS, Raney BJ, Speir ML, Rhead B, Casper J, Karolchik D, Kuhn RM, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ.

Bioinformatics. 2016 May 1;32(9):1430-2. doi: 10.1093/bioinformatics/btv766. Epub 2016 Jan 6.

4.

The UCSC Genome Browser database: 2016 update.

Speir ML, Zweig AS, Rosenbloom KR, Raney BJ, Paten B, Nejad P, Lee BT, Learned K, Karolchik D, Hinrichs AS, Heitner S, Harte RA, Haeussler M, Guruvadoo L, Fujita PA, Eisenhart C, Diekhans M, Clawson H, Casper J, Barber GP, Haussler D, Kuhn RM, Kent WJ.

Nucleic Acids Res. 2016 Jan 4;44(D1):D717-25. doi: 10.1093/nar/gkv1275. Epub 2015 Nov 20.

5.

The UCSC Ebola Genome Portal.

Haeussler M, Karolchik D, Clawson H, Raney BJ, Rosenbloom KR, Fujita PA, Hinrichs AS, Speir ML, Eisenhart C, Zweig AS, Haussler D, Kent WJ.

PLoS Curr. 2014 Nov 7;6. pii: ecurrents.outbreaks.386ab0964ab4d6c8cb550bfb6071d822. doi: 10.1371/currents.outbreaks.386ab0964ab4d6c8cb550bfb6071d822.

6.

The UCSC Genome Browser database: 2015 update.

Rosenbloom KR, Armstrong J, Barber GP, Casper J, Clawson H, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hickey G, Hinrichs AS, Hubley R, Karolchik D, Learned K, Lee BT, Li CH, Miga KH, Nguyen N, Paten B, Raney BJ, Smit AF, Speir ML, Zweig AS, Haussler D, Kuhn RM, Kent WJ.

Nucleic Acids Res. 2015 Jan;43(Database issue):D670-81. doi: 10.1093/nar/gku1177. Epub 2014 Nov 26.

7.

Navigating protected genomics data with UCSC Genome Browser in a Box.

Haeussler M, Raney BJ, Hinrichs AS, Clawson H, Zweig AS, Karolchik D, Casper J, Speir ML, Haussler D, Kent WJ.

Bioinformatics. 2015 Mar 1;31(5):764-6. doi: 10.1093/bioinformatics/btu712. Epub 2014 Oct 27.

8.

Comparative assembly hubs: web-accessible browsers for comparative genomics.

Nguyen N, Hickey G, Raney BJ, Armstrong J, Clawson H, Zweig A, Karolchik D, Kent WJ, Haussler D, Paten B.

Bioinformatics. 2014 Dec 1;30(23):3293-301. doi: 10.1093/bioinformatics/btu534. Epub 2014 Aug 18.

9.

The UCSC Genome Browser database: 2014 update.

Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hinrichs AS, Learned K, Lee BT, Li CH, Raney BJ, Rhead B, Rosenbloom KR, Sloan CA, Speir ML, Zweig AS, Haussler D, Kuhn RM, Kent WJ.

Nucleic Acids Res. 2014 Jan;42(Database issue):D764-70. doi: 10.1093/nar/gkt1168. Epub 2013 Nov 21.

10.

Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser.

Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, Nguyen N, Paten B, Zweig AS, Karolchik D, Kent WJ.

Bioinformatics. 2014 Apr 1;30(7):1003-5. doi: 10.1093/bioinformatics/btt637. Epub 2013 Nov 13.

11.

The UCSC Genome Browser.

Karolchik D, Hinrichs AS, Kent WJ.

Curr Protoc Bioinformatics. 2012 Dec;Chapter 1:Unit1.4. doi: 10.1002/0471250953.bi0104s40.

PMID:
23255150
12.

ENCODE data in the UCSC Genome Browser: year 5 update.

Rosenbloom KR, Sloan CA, Malladi VS, Dreszer TR, Learned K, Kirkup VM, Wong MC, Maddren M, Fang R, Heitner SG, Lee BT, Barber GP, Harte RA, Diekhans M, Long JC, Wilder SP, Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ.

Nucleic Acids Res. 2013 Jan;41(Database issue):D56-63. doi: 10.1093/nar/gks1172. Epub 2012 Nov 27.

13.

The UCSC Genome Browser database: extensions and updates 2013.

Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Raney BJ, Pohl A, Malladi VS, Li CH, Lee BT, Learned K, Kirkup V, Hsu F, Heitner S, Harte RA, Haeussler M, Guruvadoo L, Goldman M, Giardine BM, Fujita PA, Dreszer TR, Diekhans M, Cline MS, Clawson H, Barber GP, Haussler D, Kent WJ.

Nucleic Acids Res. 2013 Jan;41(Database issue):D64-9. doi: 10.1093/nar/gks1048. Epub 2012 Nov 15.

14.

The UCSC Genome Browser database: extensions and updates 2011.

Dreszer TR, Karolchik D, Zweig AS, Hinrichs AS, Raney BJ, Kuhn RM, Meyer LR, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Pohl A, Malladi VS, Li CH, Learned K, Kirkup V, Hsu F, Harte RA, Guruvadoo L, Goldman M, Giardine BM, Fujita PA, Diekhans M, Cline MS, Clawson H, Barber GP, Haussler D, James Kent W.

Nucleic Acids Res. 2012 Jan;40(Database issue):D918-23. doi: 10.1093/nar/gkr1055. Epub 2011 Nov 15.

15.

ENCODE whole-genome data in the UCSC Genome Browser: update 2012.

Rosenbloom KR, Dreszer TR, Long JC, Malladi VS, Sloan CA, Raney BJ, Cline MS, Karolchik D, Barber GP, Clawson H, Diekhans M, Fujita PA, Goldman M, Gravell RC, Harte RA, Hinrichs AS, Kirkup VM, Kuhn RM, Learned K, Maddren M, Meyer LR, Pohl A, Rhead B, Wong MC, Zweig AS, Haussler D, Kent WJ.

Nucleic Acids Res. 2012 Jan;40(Database issue):D912-7. doi: 10.1093/nar/gkr1012. Epub 2011 Nov 9.

16.

The UCSC Genome Browser.

Karolchik D, Hinrichs AS, Kent WJ.

Curr Protoc Hum Genet. 2011 Oct;Chapter 18:Unit18.6. doi: 10.1002/0471142905.hg1806s71.

17.

The UCSC Cancer Genomics Browser: update 2011.

Sanborn JZ, Benz SC, Craft B, Szeto C, Kober KM, Meyer L, Vaske CJ, Goldman M, Smith KE, Kuhn RM, Karolchik D, Kent WJ, Stuart JM, Haussler D, Zhu J.

Nucleic Acids Res. 2011 Jan;39(Database issue):D951-9. doi: 10.1093/nar/gkq1113. Epub 2010 Nov 8.

18.

ENCODE whole-genome data in the UCSC genome browser (2011 update).

Raney BJ, Cline MS, Rosenbloom KR, Dreszer TR, Learned K, Barber GP, Meyer LR, Sloan CA, Malladi VS, Roskin KM, Suh BB, Hinrichs AS, Clawson H, Zweig AS, Kirkup V, Fujita PA, Rhead B, Smith KE, Pohl A, Kuhn RM, Karolchik D, Haussler D, Kent WJ.

Nucleic Acids Res. 2011 Jan;39(Database issue):D871-5. doi: 10.1093/nar/gkq1017. Epub 2010 Oct 30.

19.

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.

Nucleic Acids Res. 2011 Jan;39(Database issue):D876-82. doi: 10.1093/nar/gkq963. Epub 2010 Oct 18.

20.

BigWig and BigBed: enabling browsing of large distributed datasets.

Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D.

Bioinformatics. 2010 Sep 1;26(17):2204-7. doi: 10.1093/bioinformatics/btq351. Epub 2010 Jul 17.

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