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Items: 1 to 20 of 142

1.

Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq.

Sheynkman GM, Shortreed MR, Frey BL, Smith LM.

Mol Cell Proteomics. 2013 Aug;12(8):2341-53. doi: 10.1074/mcp.O113.028142. Epub 2013 Apr 29.

2.
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Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations.

Sheynkman GM, Johnson JE, Jagtap PD, Shortreed MR, Onsongo G, Frey BL, Griffin TJ, Smith LM.

BMC Genomics. 2014 Aug 22;15:703. doi: 10.1186/1471-2164-15-703.

4.

Proteomic Validation of Transcript Isoforms, Including Those Assembled from RNA-Seq Data.

Tay AP, Pang CN, Twine NA, Hart-Smith G, Harkness L, Kassem M, Wilkins MR.

J Proteome Res. 2015 Sep 4;14(9):3541-54. doi: 10.1021/pr5011394. Epub 2015 May 20.

PMID:
25961807
5.

Discovery of novel genes and gene isoforms by integrating transcriptomic and proteomic profiling from mouse liver.

Wu P, Zhang H, Lin W, Hao Y, Ren L, Zhang C, Li N, Wei H, Jiang Y, He F.

J Proteome Res. 2014 May 2;13(5):2409-19. doi: 10.1021/pr4012206. Epub 2014 Apr 18.

PMID:
24717071
6.

Chromosome-Based Proteomic Study for Identifying Novel Protein Variants from Human Hippocampal Tissue Using Customized neXtProt and GENCODE Databases.

Hwang H, Park GW, Kim KH, Lee JY, Lee HK, Ji ES, Park SK, Xu T, Yates JR 3rd, Kwon KH, Park YM, Lee HJ, Paik YK, Kim JY, Yoo JS.

J Proteome Res. 2015 Dec 4;14(12):5028-37. doi: 10.1021/acs.jproteome.5b00472. Epub 2015 Nov 16.

PMID:
26549206
7.

SpliceVista, a tool for splice variant identification and visualization in shotgun proteomics data.

Zhu Y, Hultin-Rosenberg L, Forshed J, Branca RM, Orre LM, Lehtiö J.

Mol Cell Proteomics. 2014 Jun;13(6):1552-62. doi: 10.1074/mcp.M113.031203. Epub 2014 Apr 1.

8.

PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq.

Wen B, Xu S, Zhou R, Zhang B, Wang X, Liu X, Xu X, Liu S.

BMC Bioinformatics. 2016 Jun 17;17(1):244. doi: 10.1186/s12859-016-1133-3.

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10.

PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data.

Zhang Y, Lameijer EW, 't Hoen PA, Ning Z, Slagboom PE, Ye K.

Bioinformatics. 2012 Feb 15;28(4):479-86. doi: 10.1093/bioinformatics/btr712. Epub 2012 Jan 4.

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.

12.

Deep proteome coverage based on ribosome profiling aids mass spectrometry-based protein and peptide discovery and provides evidence of alternative translation products and near-cognate translation initiation events.

Menschaert G, Van Criekinge W, Notelaers T, Koch A, Crappé J, Gevaert K, Van Damme P.

Mol Cell Proteomics. 2013 Jul;12(7):1780-90. doi: 10.1074/mcp.M113.027540. Epub 2013 Feb 21.

13.

PASTA: splice junction identification from RNA-sequencing data.

Tang S, Riva A.

BMC Bioinformatics. 2013 Apr 4;14:116. doi: 10.1186/1471-2105-14-116.

14.

Discover hidden splicing variations by mapping personal transcriptomes to personal genomes.

Stein S, Lu ZX, Bahrami-Samani E, Park JW, Xing Y.

Nucleic Acids Res. 2015 Dec 15;43(22):10612-22. doi: 10.1093/nar/gkv1099. Epub 2015 Nov 17.

15.

Differentially expressed alternatively spliced genes in malignant pleural mesothelioma identified using massively parallel transcriptome sequencing.

Dong L, Jensen RV, De Rienzo A, Gordon GJ, Xu Y, Sugarbaker DJ, Bueno R.

BMC Med Genet. 2009 Dec 31;10:149. doi: 10.1186/1471-2350-10-149.

16.

PEPPI: a peptidomic database of human protein isoforms for proteomics experiments.

Zhou A, Zhang F, Chen JY.

BMC Bioinformatics. 2010 Oct 7;11 Suppl 6:S7. doi: 10.1186/1471-2105-11-S6-S7.

17.

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.

18.

SpliceProt: a protein sequence repository of predicted human splice variants.

Tavares R, de Miranda Scherer N, Pauletti BA, Araújo E, Folador EL, Espindola G, Ferreira CG, Paes Leme AF, de Oliveira PS, Passetti F.

Proteomics. 2014 Feb;14(2-3):181-5. doi: 10.1002/pmic.201300078.

PMID:
24273012
19.

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.

20.

TrueSight: a new algorithm for splice junction detection using RNA-seq.

Li Y, Li-Byarlay H, Burns P, Borodovsky M, Robinson GE, Ma J.

Nucleic Acids Res. 2013 Feb 1;41(4):e51. doi: 10.1093/nar/gks1311. Epub 2012 Dec 18.

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