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Items: 1 to 20 of 69

1.

Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context.

Xiong HY, Barash Y, Frey BJ.

Bioinformatics. 2011 Sep 15;27(18):2554-62. doi: 10.1093/bioinformatics/btr444. Epub 2011 Jul 29.

PMID:
21803804
2.

Inferring global levels of alternative splicing isoforms using a generative model of microarray data.

Shai O, Morris QD, Blencowe BJ, Frey BJ.

Bioinformatics. 2006 Mar 1;22(5):606-13. Epub 2006 Jan 10.

PMID:
16403798
3.

RASE: recognition of alternatively spliced exons in C.elegans.

Rätsch G, Sonnenburg S, Schölkopf B.

Bioinformatics. 2005 Jun;21 Suppl 1:i369-77.

PMID:
15961480
4.

TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference.

Nariai N, Hirose O, Kojima K, Nagasaki M.

Bioinformatics. 2013 Sep 15;29(18):2292-9. doi: 10.1093/bioinformatics/btt381. Epub 2013 Jul 2.

PMID:
23821651
6.

Splicing regulation as a potential genetic modifier.

Nissim-Rafinia M, Kerem B.

Trends Genet. 2002 Mar;18(3):123-7. Review.

PMID:
11858835
7.

An exon-centric perspective.

Blencowe BJ.

Biochem Cell Biol. 2012 Oct;90(5):603-12. doi: 10.1139/o2012-019. Epub 2012 Jul 11.

PMID:
22779775
8.

Identification of novel first exons in Ad4BP/SF-1 (NR5A1) gene and their tissue- and species-specific usage.

Kimura R, Yoshii H, Nomura M, Kotomura N, Mukai T, Ishihara S, Ohba K, Yanase T, Gotoh O, Nawata H, Morohashi K.

Biochem Biophys Res Commun. 2000 Nov 11;278(1):63-71.

PMID:
11071856
9.

Deep learning of the tissue-regulated splicing code.

Leung MK, Xiong HY, Lee LJ, Frey BJ.

Bioinformatics. 2014 Jun 15;30(12):i121-9. doi: 10.1093/bioinformatics/btu277.

10.

Human brain derived neurotrophic factor (BDNF) genes, splicing patterns, and assessments of associations with substance abuse and Parkinson's Disease.

Liu QR, Walther D, Drgon T, Polesskaya O, Lesnick TG, Strain KJ, de Andrade M, Bower JH, Maraganore DM, Uhl GR.

Am J Med Genet B Neuropsychiatr Genet. 2005 Apr 5;134B(1):93-103.

PMID:
15666411
11.

Comparative analysis of sequence features involved in the recognition of tandem splice sites.

Bortfeldt R, Schindler S, Szafranski K, Schuster S, Holste D.

BMC Genomics. 2008 Apr 30;9:202. doi: 10.1186/1471-2164-9-202.

12.

Developmental and muscle-specific regulation of avian fast skeletal troponin T isoform expression by mRNA splicing.

Bucher EA, de la Brousse FC, Emerson CP Jr.

J Biol Chem. 1989 Jul 25;264(21):12482-91.

13.

Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls.

Zhang C, Frias MA, Mele A, Ruggiu M, Eom T, Marney CB, Wang H, Licatalosi DD, Fak JJ, Darnell RB.

Science. 2010 Jul 23;329(5990):439-43. doi: 10.1126/science.1191150. Epub 2010 Jun 17.

15.

Deciphering the splicing code.

Barash Y, Calarco JA, Gao W, Pan Q, Wang X, Shai O, Blencowe BJ, Frey BJ.

Nature. 2010 May 6;465(7294):53-9. doi: 10.1038/nature09000.

PMID:
20445623
16.

SpliceTrap: a method to quantify alternative splicing under single cellular conditions.

Wu J, Akerman M, Sun S, McCombie WR, Krainer AR, Zhang MQ.

Bioinformatics. 2011 Nov 1;27(21):3010-6. doi: 10.1093/bioinformatics/btr508. Epub 2011 Sep 6.

17.

Alternative splicing regulatory network reconstruction from exon array data.

Qu K, Yesnik AM, Ortoleva PJ.

J Theor Biol. 2010 Apr 21;263(4):471-80. doi: 10.1016/j.jtbi.2009.12.025. Epub 2010 Jan 5.

PMID:
20043923
18.

A bioinformatics analysis of alternative exon usage in human genes coding for extracellular matrix proteins.

Sakabe NJ, Vibranovski MD, de Souza SJ.

Genet Mol Res. 2004 Dec 30;3(4):532-44.

19.

Improved identification of conserved cassette exons using Bayesian networks.

Sinha R, Hiller M, Pudimat R, Gausmann U, Platzer M, Backofen R.

BMC Bioinformatics. 2008 Nov 12;9:477. doi: 10.1186/1471-2105-9-477.

20.

The mammalian HSF4 gene generates both an activator and a repressor of heat shock genes by alternative splicing.

Tanabe M, Sasai N, Nagata K, Liu XD, Liu PC, Thiele DJ, Nakai A.

J Biol Chem. 1999 Sep 24;274(39):27845-56.

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