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Items: 1 to 20 of 91

1.

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients.

Kahles A, Lehmann KV, Toussaint NC, Hüser M, Stark SG, Sachsenberg T, Stegle O, Kohlbacher O, Sander C; Cancer Genome Atlas Research Network, Rätsch G.

Cancer Cell. 2018 Aug 13;34(2):211-224.e6. doi: 10.1016/j.ccell.2018.07.001. Epub 2018 Aug 2.

2.

Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types.

Seiler M, Peng S, Agrawal AA, Palacino J, Teng T, Zhu P, Smith PG; Cancer Genome Atlas Research Network, Buonamici S, Yu L.

Cell Rep. 2018 Apr 3;23(1):282-296.e4. doi: 10.1016/j.celrep.2018.01.088.

3.

A pan-cancer analysis of alternative splicing events reveals novel tumor-associated splice variants of matriptase.

Dargahi D, Swayze RD, Yee L, Bergqvist PJ, Hedberg BJ, Heravi-Moussavi A, Dullaghan EM, Dercho R, An J, Babcook JS, Jones SJ.

Cancer Inform. 2014 Dec 4;13:167-77. doi: 10.4137/CIN.S19435. eCollection 2014.

4.

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.

5.

A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events.

Brooks AN, Choi PS, de Waal L, Sharifnia T, Imielinski M, Saksena G, Pedamallu CS, Sivachenko A, Rosenberg M, Chmielecki J, Lawrence MS, DeLuca DS, Getz G, Meyerson M.

PLoS One. 2014 Jan 31;9(1):e87361. doi: 10.1371/journal.pone.0087361. eCollection 2014.

6.

Integrative genome-wide analysis of the determinants of RNA splicing in kidney renal clear cell carcinoma.

Lehmann KV, Kahles A, Kandoth C, Lee W, Schultz N, Stegle O, Rätsch G.

Pac Symp Biocomput. 2015:44-55.

7.

TSVdb: a web-tool for TCGA splicing variants analysis.

Sun W, Duan T, Ye P, Chen K, Zhang G, Lai M, Zhang H.

BMC Genomics. 2018 May 29;19(1):405. doi: 10.1186/s12864-018-4775-x.

8.

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.

9.

VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing.

Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK.

Genome Res. 2012 Mar;22(3):568-76. doi: 10.1101/gr.129684.111. Epub 2012 Feb 2.

11.

Splicing mutation analysis reveals previously unrecognized pathways in lymph node-invasive breast cancer.

Dorman SN, Viner C, Rogan PK.

Sci Rep. 2014 Nov 14;4:7063. doi: 10.1038/srep07063.

12.

Genome-wide Profiling of RNA splicing in prostate tumor from RNA-seq data using virtual microarrays.

Srinivasan S, Patil AH, Verma M, Bingham JL, Srivatsan R.

J Clin Bioinforma. 2012 Nov 26;2(1):21. doi: 10.1186/2043-9113-2-21.

13.

SF3B1 mutations constitute a novel therapeutic target in breast cancer.

Maguire SL, Leonidou A, Wai P, Marchiò C, Ng CK, Sapino A, Salomon AV, Reis-Filho JS, Weigelt B, Natrajan RC.

J Pathol. 2015 Mar;235(4):571-80. doi: 10.1002/path.4483. Epub 2014 Dec 22.

14.

Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing.

Helman E, Lawrence MS, Stewart C, Sougnez C, Getz G, Meyerson M.

Genome Res. 2014 Jul;24(7):1053-63. doi: 10.1101/gr.163659.113. Epub 2014 May 13.

15.

Advanced Proteogenomic Analysis Reveals Multiple Peptide Mutations and Complex Immunoglobulin Peptides in Colon Cancer.

Woo S, Cha SW, Bonissone S, Na S, Tabb DL, Pevzner PA, Bafna V.

J Proteome Res. 2015 Sep 4;14(9):3555-67. doi: 10.1021/acs.jproteome.5b00264. Epub 2015 Jul 21.

16.

Alternative RNA splicing and gastric cancer.

Li Y, Yuan Y.

Mutat Res. 2017 Jul;773:263-273. doi: 10.1016/j.mrrev.2016.07.011. Epub 2016 Jul 29. Review.

PMID:
28927534
17.

An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer.

Ruggles KV, Tang Z, Wang X, Grover H, Askenazi M, Teubl J, Cao S, McLellan MD, Clauser KR, Tabb DL, Mertins P, Slebos R, Erdmann-Gilmore P, Li S, Gunawardena HP, Xie L, Liu T, Zhou JY, Sun S, Hoadley KA, Perou CM, Chen X, Davies SR, Maher CA, Kinsinger CR, Rodland KD, Zhang H, Zhang Z, Ding L, Townsend RR, Rodriguez H, Chan D, Smith RD, Liebler DC, Carr SA, Payne S, Ellis MJ, Fenyő D.

Mol Cell Proteomics. 2016 Mar;15(3):1060-71. doi: 10.1074/mcp.M115.056226. Epub 2015 Dec 2.

18.

Sequence variants of KHDRBS1 as high penetrance susceptibility risks for primary ovarian insufficiency by mis-regulating mRNA alternative splicing.

Wang B, Li L, Zhu Y, Zhang W, Wang X, Chen B, Li T, Pan H, Wang J, Kee K, Cao Y.

Hum Reprod. 2017 Oct 1;32(10):2138-2146. doi: 10.1093/humrep/dex263.

PMID:
28938739
19.

Alternative splicing in colon, bladder, and prostate cancer identified by exon array analysis.

Thorsen K, Sørensen KD, Brems-Eskildsen AS, Modin C, Gaustadnes M, Hein AM, Kruhøffer M, Laurberg S, Borre M, Wang K, Brunak S, Krainer AR, Tørring N, Dyrskjøt L, Andersen CL, Orntoft TF.

Mol Cell Proteomics. 2008 Jul;7(7):1214-24. doi: 10.1074/mcp.M700590-MCP200. Epub 2008 Mar 18.

20.

A Description of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) Common Data Analysis Pipeline.

Rudnick PA, Markey SP, Roth J, Mirokhin Y, Yan X, Tchekhovskoi DV, Edwards NJ, Thangudu RR, Ketchum KA, Kinsinger CR, Mesri M, Rodriguez H, Stein SE.

J Proteome Res. 2016 Mar 4;15(3):1023-32. doi: 10.1021/acs.jproteome.5b01091. Epub 2016 Feb 25.

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