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Results: 1 to 20 of 172

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 J, Haussler D, Paten B.

Bioinformatics. 2014 Aug 18. pii: btu534. [Epub ahead of print]

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

A cell-permeable inhibitor to trap gαq proteins in the empty pocket conformation.

Schmitz AL, Schrage R, Gaffal E, Charpentier TH, Wiest J, Hiltensperger G, Morschel J, Hennen S, Häußler D, Horn V, Wenzel D, Grundmann M, Büllesbach KM, Schröder R, Brewitz HH, Schmidt J, Gomeza J, Galés C, Fleischmann BK, Tüting T, Imhof D, Tietze D, Gütschow M, Holzgrabe U, Sondek J, Harden TK, Mohr K, Kostenis E.

Chem Biol. 2014 Jul 17;21(7):890-902. doi: 10.1016/j.chembiol.2014.06.003.

PMID:
25036778
[PubMed - in process]
3.

A unifying model of genome evolution under parsimony.

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

BMC Bioinformatics. 2014 Jun 19;15:206. doi: 10.1186/1471-2105-15-206.

PMID:
24946830
[PubMed - in process]
Free PMC Article
4.

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
5.

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
6.

The somatic genomic landscape of glioblastoma.

Brennan CW, Verhaak RG, McKenna A, Campos B, Noushmehr H, Salama SR, Zheng S, Chakravarty D, Sanborn JZ, Berman SH, Beroukhim R, Bernard B, Wu CJ, Genovese G, Shmulevich I, Barnholtz-Sloan J, Zou L, Vegesna R, Shukla SA, Ciriello G, Yung WK, Zhang W, Sougnez C, Mikkelsen T, Aldape K, Bigner DD, Van Meir EG, Prados M, Sloan A, Black KL, Eschbacher J, Finocchiaro G, Friedman W, Andrews DW, Guha A, Iacocca M, O'Neill BP, Foltz G, Myers J, Weisenberger DJ, Penny R, Kucherlapati R, Perou CM, Hayes DN, Gibbs R, Marra M, Mills GB, Lander E, Spellman P, Wilson R, Sander C, Weinstein J, Meyerson M, Gabriel S, Laird PW, Haussler D, Getz G, Chin L; TCGA Research Network.

Cell. 2013 Oct 10;155(2):462-77. doi: 10.1016/j.cell.2013.09.034. Erratum in: Cell. 2014 Apr 24;157(3):753.

PMID:
24120142
[PubMed - indexed for MEDLINE]
7.

Exploring TCGA Pan-Cancer data at the UCSC Cancer Genomics Browser.

Cline MS, Craft B, Swatloski T, Goldman M, Ma S, Haussler D, Zhu J.

Sci Rep. 2013 Oct 2;3:2652. doi: 10.1038/srep02652.

PMID:
24084870
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE).

Paull EO, Carlin DE, Niepel M, Sorger PK, Haussler D, Stuart JM.

Bioinformatics. 2013 Nov 1;29(21):2757-64. doi: 10.1093/bioinformatics/btt471. Epub 2013 Aug 27.

PMID:
23986566
[PubMed - indexed for MEDLINE]
9.

Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons.

Sanborn JZ, Salama SR, Grifford M, Brennan CW, Mikkelsen T, Jhanwar S, Katzman S, Chin L, Haussler D.

Cancer Res. 2013 Oct 1;73(19):6036-45. doi: 10.1158/0008-5472.CAN-13-0186. Epub 2013 Aug 12.

PMID:
23940299
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF.

Gigascience. 2013 Jul 22;2(1):10. doi: 10.1186/2047-217X-2-10.

PMID:
23870653
[PubMed]
Free PMC Article
11.

The UCSC Interaction Browser: multidimensional data views in pathway context.

Wong CK, Vaske CJ, Ng S, Sanborn JZ, Benz SC, Haussler D, Stuart JM.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W218-24. doi: 10.1093/nar/gkt473. Epub 2013 Jun 8.

PMID:
23748957
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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
13.

Retrotransposition of gene transcripts leads to structural variation in mammalian genomes.

Ewing AD, Ballinger TJ, Earl D; Broad Institute Genome Sequencing and Analysis Program and Platform, Harris CC, Ding L, Wilson RK, Haussler D.

Genome Biol. 2013 Mar 13;14(3):R22.

PMID:
23497673
[PubMed - as supplied by publisher]
Free PMC Article
14.

Life, the universe, and everything: an interview with David Haussler. Interviewed by Jane Gitschier.

Haussler D.

PLoS Genet. 2013;9(1):e1003282. doi: 10.1371/journal.pgen.1003282. Epub 2013 Jan 31. No abstract available.

PMID:
23382705
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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
16.

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
17.

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
18.

Active site mapping of trypsin, thrombin and matriptase-2 by sulfamoyl benzamidines.

Dosa S, Stirnberg M, Lülsdorff V, Häußler D, Maurer E, Gütschow M.

Bioorg Med Chem. 2012 Nov 1;20(21):6489-505. doi: 10.1016/j.bmc.2012.08.042. Epub 2012 Sep 5.

PMID:
23026080
[PubMed - indexed for MEDLINE]
19.

PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis.

Ng S, Collisson EA, Sokolov A, Goldstein T, Gonzalez-Perez A, Lopez-Bigas N, Benz C, Haussler D, Stuart JM.

Bioinformatics. 2012 Sep 15;28(18):i640-i646. doi: 10.1093/bioinformatics/bts402.

PMID:
22962493
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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, Guigó 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

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