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Results: 1 to 20 of 113

1.

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 Aug 18. pii: btu534. [Epub ahead of print]

PMID:
25138168
[PubMed - as supplied by publisher]
2.

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.

PMID:
24227676
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
24270787
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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
[PubMed - indexed for MEDLINE]
5.

HAL: a hierarchical format for storing and analyzing multiple genome alignments.

Hickey G, Paten B, Earl D, Zerbino D, Haussler D.

Bioinformatics. 2013 May 15;29(10):1341-2. doi: 10.1093/bioinformatics/btt128. Epub 2013 Mar 16.

PMID:
23505295
[PubMed - indexed for MEDLINE]
Free PMC Article
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
[PubMed - indexed for MEDLINE]
7.

GenColors: annotation and comparative genomics of prokaryotes made easy.

Romualdi A, Felder M, Rose D, Gausmann U, Schilhabel M, Glöckner G, Platzer M, Sühnel J.

Methods Mol Biol. 2007;395:75-96.

PMID:
17993668
[PubMed - indexed for MEDLINE]
8.

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.

PMID:
21975940
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

PyBamView: a browser based application for viewing short read alignments.

Gymrek M.

Bioinformatics. 2014 Aug 21. pii: btu565. [Epub ahead of print]

PMID:
25147359
[PubMed - as supplied by publisher]
10.

The UCSC genome browser and associated tools.

Kuhn RM, Haussler D, Kent WJ.

Brief Bioinform. 2013 Mar;14(2):144-61. doi: 10.1093/bib/bbs038. Epub 2012 Aug 20.

PMID:
22908213
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web.

Miller CA, Anthony J, Meyer MM, Marth G.

Bioinformatics. 2013 Feb 1;29(3):381-3. doi: 10.1093/bioinformatics/bts677. Epub 2012 Nov 19.

PMID:
23172864
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

GenPlay Multi-Genome, a tool to compare and analyze multiple human genomes in a graphical interface.

Lajugie J, Fourel N, Bouhassira EE.

Bioinformatics. 2014 Aug 31. pii: btu588. [Epub ahead of print]

PMID:
25178461
[PubMed - as supplied by publisher]
13.

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
[PubMed - indexed for MEDLINE]
14.

coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics.

Chaudhuri RR, Khan AM, Pallen MJ.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D296-9.

PMID:
14681417
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

A brief introduction to web-based genome browsers.

Wang J, Kong L, Gao G, Luo J.

Brief Bioinform. 2013 Mar;14(2):131-43. doi: 10.1093/bib/bbs029. Epub 2012 Jul 3. Review.

PMID:
22764121
[PubMed - indexed for MEDLINE]
16.

SynTView - an interactive multi-view genome browser for next-generation comparative microorganism genomics.

Lechat P, Souche E, Moszer I.

BMC Bioinformatics. 2013 Sep 22;14:277. doi: 10.1186/1471-2105-14-277.

PMID:
24053737
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Genome Maps, a new generation genome browser.

Medina I, Salavert F, Sanchez R, de Maria A, Alonso R, Escobar P, Bleda M, Dopazo J.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W41-6. doi: 10.1093/nar/gkt530. Epub 2013 Jun 8.

PMID:
23748955
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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.

PMID:
21059681
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Editorial: protein systems biology: method, regulation, and network.

Chen Q, Chen M.

Curr Protein Pept Sci. 2014;15(6):519-21.

PMID:
25135673
[PubMed - in process]
20.

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.

PMID:
22086951
[PubMed - indexed for MEDLINE]
Free PMC Article

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