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Results: 1 to 20 of 50

1.

An SF1 affinity model to identify branch point sequences in human introns.

Pastuszak AW, Joachimiak MP, Blanchette M, Rio DC, Brenner SE, Frankel AD.

Nucleic Acids Res. 2011 Mar;39(6):2344-56. doi: 10.1093/nar/gkq1046. Epub 2010 Nov 10.

PMID:
21071404
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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.

PMID:
20959295
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Conservation of an RNA regulatory map between Drosophila and mammals.

Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR.

Genome Res. 2011 Feb;21(2):193-202. doi: 10.1101/gr.108662.110. Epub 2010 Oct 4.

PMID:
20921232
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB.

Llorian M, Schwartz S, Clark TA, Hollander D, Tan LY, Spellman R, Gordon A, Schweitzer AC, de la Grange P, Ast G, Smith CW.

Nat Struct Mol Biol. 2010 Sep;17(9):1114-23. doi: 10.1038/nsmb.1881. Epub 2010 Aug 15.

PMID:
20711188
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Drosophila polypyrimidine tract-binding protein is necessary for spermatid individualization.

Robida M, Sridharan V, Morgan S, Rao T, Singh R.

Proc Natl Acad Sci U S A. 2010 Jul 13;107(28):12570-5. doi: 10.1073/pnas.1007935107. Epub 2010 Jun 28.

PMID:
20616016
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Chromatin density and splicing destiny: on the cross-talk between chromatin structure and splicing.

Schwartz S, Ast G.

EMBO J. 2010 May 19;29(10):1629-36. doi: 10.1038/emboj.2010.71. Epub 2010 Apr 20.

PMID:
20407423
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Competing upstream 5' splice sites enhance the rate of proximal splicing.

Hicks MJ, Mueller WF, Shepard PJ, Hertel KJ.

Mol Cell Biol. 2010 Apr;30(8):1878-86. doi: 10.1128/MCB.01071-09. Epub 2010 Feb 1.

PMID:
20123971
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Computational prediction of splicing regulatory elements shared by Tetrapoda organisms.

Churbanov A, Vorechovsk√Ĺ I, Hicks C.

BMC Genomics. 2009 Nov 4;10:508. doi: 10.1186/1471-2164-10-508.

PMID:
19889216
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches.

Chen M, Manley JL.

Nat Rev Mol Cell Biol. 2009 Nov;10(11):741-54. doi: 10.1038/nrm2777. Epub 2009 Sep 23. Review.

PMID:
19773805
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

HRP-2, the Caenorhabditis elegans homolog of mammalian heterogeneous nuclear ribonucleoproteins Q and R, is an alternative splicing factor that binds to UCUAUC splicing regulatory elements.

Kabat JL, Barberan-Soler S, Zahler AM.

J Biol Chem. 2009 Oct 16;284(42):28490-7. doi: 10.1074/jbc.M109.023101. Epub 2009 Aug 24.

PMID:
19706616
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of the Drosophila hnRNP A/B family members.

Blanchette M, Green RE, MacArthur S, Brooks AN, Brenner SE, Eisen MB, Rio DC.

Mol Cell. 2009 Feb 27;33(4):438-49. doi: 10.1016/j.molcel.2009.01.022.

PMID:
19250905
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Splicing of designer exons reveals unexpected complexity in pre-mRNA splicing.

Zhang XH, Arias MA, Ke S, Chasin LA.

RNA. 2009 Mar;15(3):367-76. doi: 10.1261/rna.1498509. Epub 2009 Jan 20.

PMID:
19155327
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts.

Sanford JR, Wang X, Mort M, Vanduyn N, Cooper DN, Mooney SD, Edenberg HJ, Liu Y.

Genome Res. 2009 Mar;19(3):381-94. doi: 10.1101/gr.082503.108. Epub 2008 Dec 30.

PMID:
19116412
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

FlyBase: enhancing Drosophila Gene Ontology annotations.

Tweedie S, Ashburner M, Falls K, Leyland P, McQuilton P, Marygold S, Millburn G, Osumi-Sutherland D, Schroeder A, Seal R, Zhang H; FlyBase Consortium.

Nucleic Acids Res. 2009 Jan;37(Database issue):D555-9. doi: 10.1093/nar/gkn788. Epub 2008 Oct 23.

PMID:
18948289
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Identification of nuclear and cytoplasmic mRNA targets for the shuttling protein SF2/ASF.

Sanford JR, Coutinho P, Hackett JA, Wang X, Ranahan W, Caceres JF.

PLoS One. 2008 Oct 8;3(10):e3369. doi: 10.1371/journal.pone.0003369.

PMID:
18841201
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Human branch point consensus sequence is yUnAy.

Gao K, Masuda A, Matsuura T, Ohno K.

Nucleic Acids Res. 2008 Apr;36(7):2257-67. doi: 10.1093/nar/gkn073. Epub 2008 Feb 19.

PMID:
18285363
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes.

Schwartz SH, Silva J, Burstein D, Pupko T, Eyras E, Ast G.

Genome Res. 2008 Jan;18(1):88-103. Epub 2007 Nov 21.

PMID:
18032728
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Coevolutionary networks of splicing cis-regulatory elements.

Xiao X, Wang Z, Jang M, Burge CB.

Proc Natl Acad Sci U S A. 2007 Nov 20;104(47):18583-8. Epub 2007 Nov 12.

PMID:
17998536
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Clustal W and Clustal X version 2.0.

Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG.

Bioinformatics. 2007 Nov 1;23(21):2947-8. Epub 2007 Sep 10.

PMID:
17846036
[PubMed - indexed for MEDLINE]
Free Article
20.

Discovery and analysis of evolutionarily conserved intronic splicing regulatory elements.

Yeo GW, Van Nostrand EL, Liang TY.

PLoS Genet. 2007 May 25;3(5):e85. Epub 2007 Apr 13. Erratum in: PLoS Genet. 2007 Jul;3(7):e122. Nostrand, Eric L Van [corrected to Van Nostrand, Eric L].

PMID:
17530930
[PubMed - indexed for MEDLINE]
Free PMC Article

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