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Items: 1 to 20 of 190

1.

Phylogenomic resources at the UCSC Genome Browser.

Rosenbloom K, Taylor J, Schaeffer S, Kent J, Haussler D, Miller W.

Methods Mol Biol. 2008;422:133-44. doi: 10.1007/978-1-59745-581-7_9.

PMID:
18629665
2.

Comparative genomic analysis using the UCSC genome browser.

Karolchik D, Bejerano G, Hinrichs AS, Kuhn RM, Miller W, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ.

Methods Mol Biol. 2007;395:17-34.

PMID:
17993665
3.

ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes.

Ovcharenko I, Nobrega MA, Loots GG, Stubbs L.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W280-6.

4.

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.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D590-8.

5.

The UCSC Archaeal Genome Browser.

Schneider KL, Pollard KS, Baertsch R, Pohl A, Lowe TM.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D407-10.

6.

The UCSC Genome Browser.

Karolchik D, Hinrichs AS, Kent WJ.

Curr Protoc Bioinformatics. 2007 Mar;Chapter 1:Unit 1.4. doi: 10.1002/0471250953.bi0104s17.

PMID:
18428780
7.

VISTA: computational tools for comparative genomics.

Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W273-9.

8.
9.

Analysis of genomic DNA with the UCSC genome browser.

Pevsner J.

Methods Mol Biol. 2009;537:277-301. doi: 10.1007/978-1-59745-251-9_14.

PMID:
19378150
10.

UCSC genome browser tutorial.

Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ.

Genomics. 2008 Aug;92(2):75-84. doi: 10.1016/j.ygeno.2008.02.003. Epub 2008 Jun 2. Review.

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.

FlyPhy: a phylogenomic analysis platform for Drosophila genes and gene families.

Wu J, Xu X, Xiao J, Xu L, Yi H, Gao S, Liu J, Bao Q, Zhao F, Li X.

BMC Bioinformatics. 2009 Apr 25;10:123. doi: 10.1186/1471-2105-10-123.

13.

GeneTrees: a phylogenomics resource for prokaryotes.

Tian Y, Dickerman AW.

Nucleic Acids Res. 2007 Jan;35(Database issue):D328-31. Epub 2006 Dec 6.

14.

Using native and syntenically mapped cDNA alignments to improve de novo gene finding.

Stanke M, Diekhans M, Baertsch R, Haussler D.

Bioinformatics. 2008 Mar 1;24(5):637-44. doi: 10.1093/bioinformatics/btn013. Epub 2008 Jan 24.

15.

Obtaining comparative genomic data with the VISTA family of computational tools.

Ratnere I, Dubchak I.

Curr Protoc Bioinformatics. 2009 Jun;Chapter 10:Unit 10.6. doi: 10.1002/0471250953.bi1006s26.

PMID:
19496056
16.

The UCSC genome browser database: update 2007.

Kuhn RM, Karolchik D, Zweig AS, Trumbower H, Thomas DJ, Thakkapallayil A, Sugnet CW, Stanke M, Smith KE, Siepel A, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pedersen JS, Hsu F, Hinrichs AS, Harte RA, Diekhans M, Clawson H, Bejerano G, Barber GP, Baertsch R, Haussler D, Kent WJ.

Nucleic Acids Res. 2007 Jan;35(Database issue):D668-73. Epub 2006 Nov 16.

17.

Comparative and evolutionary genomics of globin genes in fish.

Negrisolo E, Bargelloni L, Patarnello T, Ozouf-Costaz C, Pisano E, di Prisco G, Verde C.

Methods Enzymol. 2008;436:511-38. doi: 10.1016/S0076-6879(08)36029-7. Review.

PMID:
18237652
18.

The UCSC Proteome Browser.

Hsu F, Pringle TH, Kuhn RM, Karolchik D, Diekhans M, Haussler D, Kent WJ.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D454-8.

19.

PhyLAT: a phylogenetic local alignment tool.

Sun H, Buhler JD.

Bioinformatics. 2012 May 15;28(10):1336-44. doi: 10.1093/bioinformatics/bts158. Epub 2012 Apr 6.

20.

The UCSC Genome Browser Database: 2008 update.

Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, Diekhans M, Giardine B, Harte RA, Hinrichs AS, Hsu F, Kober KM, Miller W, Pedersen JS, Pohl A, Raney BJ, Rhead B, Rosenbloom KR, Smith KE, Stanke M, Thakkapallayil A, Trumbower H, Wang T, Zweig AS, Haussler D, Kent WJ.

Nucleic Acids Res. 2008 Jan;36(Database issue):D773-9. Epub 2007 Dec 17.

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