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Results: 1 to 20 of 111

1.

SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data.

Rogers MF, Thomas J, Reddy AS, Ben-Hur A.

Genome Biol. 2012 Jan 31;13(1):R4. doi: 10.1186/gb-2012-13-1-r4.

PMID:
22293517
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Detection and prediction of alternative splicing in Arabidopsis thaliana.

Park M, Falcone DL, Daniels KM.

Int J Comput Biol Drug Des. 2008;1(1):39-58.

PMID:
20055000
[PubMed - indexed for MEDLINE]
3.

Mining Arabidopsis thaliana RNA-seq data with Integrated Genome Browser reveals stress-induced alternative splicing of the putative splicing regulator SR45a.

Gulledge AA, Roberts AD, Vora H, Patel K, Loraine AE.

Am J Bot. 2012 Feb;99(2):219-31. doi: 10.3732/ajb.1100355. Epub 2012 Jan 30.

PMID:
22291167
[PubMed - indexed for MEDLINE]
Free Article
4.

Gene structure prediction and alternative splicing analysis using genomically aligned ESTs.

Kan Z, Rouchka EC, Gish WR, States DJ.

Genome Res. 2001 May;11(5):889-900.

PMID:
11337482
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Integrating alternative splicing detection into gene prediction.

Foissac S, Schiex T.

BMC Bioinformatics. 2005 Feb 10;6:25.

PMID:
15705189
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

EASED: Extended Alternatively Spliced EST Database.

Pospisil H, Herrmann A, Bortfeldt RH, Reich JG.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D70-4.

PMID:
14681361
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Towards reliable isoform quantification using RNA-SEQ data.

Howard BE, Heber S.

BMC Bioinformatics. 2010 Apr 29;11 Suppl 3:S6. doi: 10.1186/1471-2105-11-S3-S6.

PMID:
20438653
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

ASD: the Alternative Splicing Database.

Thanaraj TA, Stamm S, Clark F, Riethoven JJ, Le Texier V, Muilu J.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D64-9.

PMID:
14681360
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Transcriptome and genome conservation of alternative splicing events in humans and mice.

Sugnet CW, Kent WJ, Ares M Jr, Haussler D.

Pac Symp Biocomput. 2004:66-77.

PMID:
14992493
[PubMed - indexed for MEDLINE]
10.

Detecting alternative gene structures from spliced ESTs: a computational approach.

Bonizzoni P, Mauri G, Pesole G, Picardi E, Pirola Y, Rizzi R.

J Comput Biol. 2009 Jan;16(1):43-66. doi: 10.1089/cmb.2008.0028.

PMID:
19119993
[PubMed - indexed for MEDLINE]
11.

Detection of splice junctions from paired-end RNA-seq data by SpliceMap.

Au KF, Jiang H, Lin L, Xing Y, Wong WH.

Nucleic Acids Res. 2010 Aug;38(14):4570-8. doi: 10.1093/nar/gkq211. Epub 2010 Apr 5.

PMID:
20371516
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Protein encoding genes in an ancient plant: analysis of codon usage, retained genes and splice sites in a moss, Physcomitrella patens.

Rensing SA, Fritzowsky D, Lang D, Reski R.

BMC Genomics. 2005 Mar 22;6:43.

PMID:
15784153
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

GeneSplicer: a new computational method for splice site prediction.

Pertea M, Lin X, Salzberg SL.

Nucleic Acids Res. 2001 Mar 1;29(5):1185-90.

PMID:
11222768
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki).

Sturgill D, Malone JH, Sun X, Smith HE, Rabinow L, Samson ML, Oliver B.

BMC Bioinformatics. 2013 Nov 9;14:320. doi: 10.1186/1471-2105-14-320.

PMID:
24209455
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Detection of novel splice forms in human and mouse using cross-species approach.

Kan Z, Castle J, Johnson JM, Tsinoremas NF.

Pac Symp Biocomput. 2004:42-53.

PMID:
14992491
[PubMed - indexed for MEDLINE]
16.

A non-EST-based method for exon-skipping prediction.

Sorek R, Shemesh R, Cohen Y, Basechess O, Ast G, Shamir R.

Genome Res. 2004 Aug;14(8):1617-23.

PMID:
15289480
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Detection, annotation and visualization of alternative splicing from RNA-Seq data with SplicingViewer.

Liu Q, Chen C, Shen E, Zhao F, Sun Z, Wu J.

Genomics. 2012 Mar;99(3):178-82. doi: 10.1016/j.ygeno.2011.12.003. Epub 2011 Dec 28.

PMID:
22226708
[PubMed - indexed for MEDLINE]
Free Article
18.

Computational analysis and experimental validation of tumor-associated alternative RNA splicing in human cancer.

Wang Z, Lo HS, Yang H, Gere S, Hu Y, Buetow KH, Lee MP.

Cancer Res. 2003 Feb 1;63(3):655-7.

PMID:
12566310
[PubMed - indexed for MEDLINE]
Free Article
19.

H-DBAS: human-transcriptome database for alternative splicing: update 2010.

Takeda J, Suzuki Y, Sakate R, Sato Y, Gojobori T, Imanishi T, Sugano S.

Nucleic Acids Res. 2010 Jan;38(Database issue):D86-90. doi: 10.1093/nar/gkp984. Epub 2009 Dec 7.

PMID:
19969536
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

HMMSplicer: a tool for efficient and sensitive discovery of known and novel splice junctions in RNA-Seq data.

Dimon MT, Sorber K, DeRisi JL.

PLoS One. 2010 Nov 8;5(11):e13875. doi: 10.1371/journal.pone.0013875.

PMID:
21079731
[PubMed - indexed for MEDLINE]
Free PMC Article

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