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Results: 1 to 20 of 52

1.

Comparative analysis of pseudogenes across three phyla.

Sisu C, Pei B, Leng J, Frankish A, Zhang Y, Balasubramanian S, Harte R, Wang D, Rutenberg-Schoenberg M, Clark W, Diekhans M, Rozowsky J, Hubbard T, Harrow J, Gerstein MB.

Proc Natl Acad Sci U S A. 2014 Aug 25. pii: 201407293. [Epub ahead of print]

PMID:
25157146
[PubMed - as supplied by publisher]
Free Article
2.

Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes.

Ezkurdia I, Juan D, Rodriguez JM, Frankish A, Diekhans M, Harrow J, Vazquez J, Valencia A, Tress ML.

Hum Mol Genet. 2014 Jun 16. pii: ddu309. [Epub ahead of print]

PMID:
24939910
[PubMed - as supplied by publisher]
Free 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.

Current status and new features of the Consensus Coding Sequence database.

Farrell CM, O'Leary NA, Harte RA, Loveland JE, Wilming LG, Wallin C, Diekhans M, Barrell D, Searle SM, Aken B, Hiatt SM, Frankish A, Suner MM, Rajput B, Steward CA, Brown GR, Bennett R, Murphy M, Wu W, Kay MP, Hart J, Rajan J, Weber J, Snow C, Riddick LD, Hunt T, Webb D, Thomas M, Tamez P, Rangwala SH, McGarvey KM, Pujar S, Shkeda A, Mudge JM, Gonzalez JM, Gilbert JG, Trevanion SJ, Baertsch R, Harrow JL, Hubbard T, Ostell JM, Haussler D, Pruitt KD.

Nucleic Acids Res. 2014 Jan;42(Database issue):D865-72. doi: 10.1093/nar/gkt1059. Epub 2013 Nov 11.

PMID:
24217909
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures.

Niknafs N, Kim D, Kim R, Diekhans M, Ryan M, Stenson PD, Cooper DN, Karchin R.

Hum Genet. 2013 Nov;132(11):1235-43. doi: 10.1007/s00439-013-1325-0. Epub 2013 Jun 23.

PMID:
23793516
[PubMed - indexed for MEDLINE]
6.

CRAVAT: cancer-related analysis of variants toolkit.

Douville C, Carter H, Kim R, Niknafs N, Diekhans M, Stenson PD, Cooper DN, Ryan M, Karchin R.

Bioinformatics. 2013 Mar 1;29(5):647-8. doi: 10.1093/bioinformatics/btt017. Epub 2013 Jan 16.

PMID:
23325621
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
23193274
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
23155063
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

The UCSC Cancer Genomics Browser: update 2013.

Goldman M, Craft B, Swatloski T, Ellrott K, Cline M, Diekhans M, Ma S, Wilks C, Stuart J, Haussler D, Zhu J.

Nucleic Acids Res. 2013 Jan;41(Database issue):D949-54. doi: 10.1093/nar/gks1008. Epub 2012 Oct 29.

PMID:
23109555
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

GENCODE: the reference human genome annotation for The ENCODE Project.

Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, Rodriguez JM, Ezkurdia I, van Baren J, Brent M, Haussler D, Kellis M, Valencia A, Reymond A, Gerstein M, Guig├│ R, Hubbard TJ.

Genome Res. 2012 Sep;22(9):1760-74. doi: 10.1101/gr.135350.111.

PMID:
22955987
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

An integrated encyclopedia of DNA elements in the human genome.

ENCODE Project Consortium.

Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247.

PMID:
22955616
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

The GENCODE pseudogene resource.

Pei B, Sisu C, Frankish A, Howald C, Habegger L, Mu XJ, Harte R, Balasubramanian S, Tanzer A, Diekhans M, Reymond A, Hubbard TJ, Harrow J, Gerstein MB.

Genome Biol. 2012 Sep 26;13(9):R51. doi: 10.1186/gb-2012-13-9-r51.

PMID:
22951037
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Tracking and coordinating an international curation effort for the CCDS Project.

Harte RA, Farrell CM, Loveland JE, Suner MM, Wilming L, Aken B, Barrell D, Frankish A, Wallin C, Searle S, Diekhans M, Harrow J, Pruitt KD.

Database (Oxford). 2012 Mar 20;2012:bas008. doi: 10.1093/database/bas008. Print 2012.

PMID:
22434842
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

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

PMID:
22075998
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Assemblathon 1: a competitive assessment of de novo short read assembly methods.

Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol ─░, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B.

Genome Res. 2011 Dec;21(12):2224-41. doi: 10.1101/gr.126599.111. Epub 2011 Sep 16.

PMID:
21926179
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer.

Wong WC, Kim D, Carter H, Diekhans M, Ryan MC, Karchin R.

Bioinformatics. 2011 Aug 1;27(15):2147-8. doi: 10.1093/bioinformatics/btr357. Epub 2011 Jun 17.

PMID:
21685053
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Cactus: Algorithms for genome multiple sequence alignment.

Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, Haussler D.

Genome Res. 2011 Sep;21(9):1512-28. doi: 10.1101/gr.123356.111. Epub 2011 Jun 10.

PMID:
21665927
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

A user's guide to the encyclopedia of DNA elements (ENCODE).

ENCODE Project Consortium.

PLoS Biol. 2011 Apr;9(4):e1001046. doi: 10.1371/journal.pbio.1001046. Epub 2011 Apr 19.

PMID:
21526222
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Cactus graphs for genome comparisons.

Paten B, Diekhans M, Earl D, John JS, Ma J, Suh B, Haussler D.

J Comput Biol. 2011 Mar;18(3):469-81. doi: 10.1089/cmb.2010.0252.

PMID:
21385048
[PubMed - indexed for MEDLINE]

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