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Items: 1 to 20 of 74

1.

An automated method for detecting alternatively spliced protein domains.

Coelho V, Sammeth M.

Bioinformatics. 2018 Nov 15;34(22):3809-3816. doi: 10.1093/bioinformatics/bty425.

PMID:
29868795
2.

Read-Split-Run: an improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data.

Bai Y, Kinne J, Donham B, Jiang F, Ding L, Hassler JR, Kaufman RJ.

BMC Genomics. 2016 Aug 22;17 Suppl 7:503. doi: 10.1186/s12864-016-2896-7.

3.

Comparative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome.

Severing EI, van Dijk AD, Stiekema WJ, van Ham RC.

BMC Genomics. 2009 Apr 9;10:154. doi: 10.1186/1471-2164-10-154.

5.

Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.

Milanesi L, Petrillo M, Sepe L, Boccia A, D'Agostino N, Passamano M, Di Nardo S, Tasco G, Casadio R, Paolella G.

BMC Bioinformatics. 2005 Dec 1;6 Suppl 4:S20.

6.

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
7.

Integrating alternative splicing detection into gene prediction.

Foissac S, Schiex T.

BMC Bioinformatics. 2005 Feb 10;6:25.

8.

Alternative splicing in human transcriptome: functional and structural influence on proteins.

Yura K, Shionyu M, Hagino K, Hijikata A, Hirashima Y, Nakahara T, Eguchi T, Shinoda K, Yamaguchi A, Takahashi K, Itoh T, Imanishi T, Gojobori T, Go M.

Gene. 2006 Oct 1;380(2):63-71. Epub 2006 Jun 2.

PMID:
16872759
9.

Schizophyllum commune has an extensive and functional alternative splicing repertoire.

Gehrmann T, Pelkmans JF, Lugones LG, Wösten HA, Abeel T, Reinders MJ.

Sci Rep. 2016 Sep 23;6:33640. doi: 10.1038/srep33640.

10.

Detecting alternatively spliced transcript isoforms from single-molecule long-read sequences without a reference genome.

Liu X, Mei W, Soltis PS, Soltis DE, Barbazuk WB.

Mol Ecol Resour. 2017 Nov;17(6):1243-1256. doi: 10.1111/1755-0998.12670. Epub 2017 Jun 5.

PMID:
28316149
12.

A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing.

Zhang R, Calixto CPG, Marquez Y, Venhuizen P, Tzioutziou NA, Guo W, Spensley M, Entizne JC, Lewandowska D, Ten Have S, Frei Dit Frey N, Hirt H, James AB, Nimmo HG, Barta A, Kalyna M, Brown JWS.

Nucleic Acids Res. 2017 May 19;45(9):5061-5073. doi: 10.1093/nar/gkx267.

13.

Characterization of kinase gene expression and splicing profile in prostate cancer with RNA-Seq data.

Feng H, Li T, Zhang X.

BMC Genomics. 2018 Aug 13;19(Suppl 6):564. doi: 10.1186/s12864-018-4925-1.

15.

Spliced leader trapping reveals widespread alternative splicing patterns in the highly dynamic transcriptome of Trypanosoma brucei.

Nilsson D, Gunasekera K, Mani J, Osteras M, Farinelli L, Baerlocher L, Roditi I, Ochsenreiter T.

PLoS Pathog. 2010 Aug 5;6(8):e1001037. doi: 10.1371/journal.ppat.1001037.

16.

Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes.

Gascoigne DK, Cheetham SW, Cattenoz PB, Clark MB, Amaral PP, Taft RJ, Wilhelm D, Dinger ME, Mattick JS.

Bioinformatics. 2012 Dec 1;28(23):3042-50. doi: 10.1093/bioinformatics/bts582. Epub 2012 Oct 7.

PMID:
23044541
17.
18.

A generic Deep Convolutional Neural Network framework for prediction of Receptor-ligand Interactions. NetPhosPan; Application to Kinase Phosphorylation prediction.

Fenoy E, Izarzugaza JMG, Jurtz V, Brunak S, Nielsen M.

Bioinformatics. 2018 Aug 31. doi: 10.1093/bioinformatics/bty715. [Epub ahead of print]

PMID:
30169744
19.

Using mRNAs lengths to accurately predict the alternatively spliced gene products in Caenorhabditis elegans.

Agrawal R, Stormo GD.

Bioinformatics. 2006 May 15;22(10):1239-44. Epub 2006 Apr 4.

PMID:
16595562
20.

Alternative splicing: increasing diversity in the proteomic world.

Graveley BR.

Trends Genet. 2001 Feb;17(2):100-7. Review.

PMID:
11173120

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