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Items: 1 to 20 of 96

1.

ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data.

Frenkel-Morgenstern M, Gorohovski A, Lacroix V, Rogers M, Ibanez K, Boullosa C, Andres Leon E, Ben-Hur A, Valencia A.

Nucleic Acids Res. 2013 Jan;41(Database issue):D142-51. doi: 10.1093/nar/gks1041. Epub 2012 Nov 9.

2.

ChiTaRS 2.1--an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts.

Frenkel-Morgenstern M, Gorohovski A, Vucenovic D, Maestre L, Valencia A.

Nucleic Acids Res. 2015 Jan;43(Database issue):D68-75. doi: 10.1093/nar/gku1199. Epub 2014 Nov 20.

3.

Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts.

Frenkel-Morgenstern M, Lacroix V, Ezkurdia I, Levin Y, Gabashvili A, Prilusky J, Del Pozo A, Tress M, Johnson R, Guigo R, Valencia A.

Genome Res. 2012 Jul;22(7):1231-42. doi: 10.1101/gr.130062.111. Epub 2012 May 15.

4.

Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data.

McPherson A, Wu C, Hajirasouliha I, Hormozdiari F, Hach F, Lapuk A, Volik S, Shah S, Collins C, Sahinalp SC.

Bioinformatics. 2011 Jun 1;27(11):1481-8. doi: 10.1093/bioinformatics/btr184. Epub 2011 Apr 9.

5.

Novel domain combinations in proteins encoded by chimeric transcripts.

Frenkel-Morgenstern M, Valencia A.

Bioinformatics. 2012 Jun 15;28(12):i67-74. doi: 10.1093/bioinformatics/bts216.

6.

ChimerDB--a knowledgebase for fusion sequences.

Kim N, Kim P, Nam S, Shin S, Lee S.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D21-4.

7.

Recurrent chimeric RNAs enriched in human prostate cancer identified by deep sequencing.

Kannan K, Wang L, Wang J, Ittmann MM, Li W, Yen L.

Proc Natl Acad Sci U S A. 2011 May 31;108(22):9172-7. doi: 10.1073/pnas.1100489108. Epub 2011 May 12.

8.

Short homologous sequences are strongly associated with the generation of chimeric RNAs in eukaryotes.

Li X, Zhao L, Jiang H, Wang W.

J Mol Evol. 2009 Jan;68(1):56-65. doi: 10.1007/s00239-008-9187-0. Epub 2008 Dec 17.

PMID:
19089307
9.

Identification of gene fusion transcripts by transcriptome sequencing in BRCA1-mutated breast cancers and cell lines.

Ha KC, Lalonde E, Li L, Cavallone L, Natrajan R, Lambros MB, Mitsopoulos C, Hakas J, Kozarewa I, Fenwick K, Lord CJ, Ashworth A, Vincent-Salomon A, Basik M, Reis-Filho JS, Majewski J, Foulkes WD.

BMC Med Genomics. 2011 Oct 27;4:75. doi: 10.1186/1755-8794-4-75.

10.

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.

11.

FUSIM: a software tool for simulating fusion transcripts.

Bruno AE, Miecznikowski JC, Qin M, Wang J, Liu S.

BMC Bioinformatics. 2013 Jan 16;14:13. doi: 10.1186/1471-2105-14-13.

12.
13.

A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines.

Asmann YW, Hossain A, Necela BM, Middha S, Kalari KR, Sun Z, Chai HS, Williamson DW, Radisky D, Schroth GP, Kocher JP, Perez EA, Thompson EA.

Nucleic Acids Res. 2011 Aug;39(15):e100. doi: 10.1093/nar/gkr362. Epub 2011 May 27.

14.

Bellerophontes: an RNA-Seq data analysis framework for chimeric transcripts discovery based on accurate fusion model.

Abate F, Acquaviva A, Paciello G, Foti C, Ficarra E, Ferrarini A, Delledonne M, Iacobucci I, Soverini S, Martinelli G, Macii E.

Bioinformatics. 2012 Aug 15;28(16):2114-21. doi: 10.1093/bioinformatics/bts334. Epub 2012 Jun 17.

15.

Long-range transcriptome sequencing reveals cancer cell growth regulatory chimeric mRNA.

Plebani R, Oliver GR, Trerotola M, Guerra E, Cantanelli P, Apicella L, Emerson A, Albiero A, Harkin PD, Kennedy RD, Alberti S.

Neoplasia. 2012 Nov;14(11):1087-96.

16.

starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data.

Yang JH, Li JH, Shao P, Zhou H, Chen YQ, Qu LH.

Nucleic Acids Res. 2011 Jan;39(Database issue):D202-9. doi: 10.1093/nar/gkq1056. Epub 2010 Oct 30.

17.

Identification and analysis of pig chimeric mRNAs using RNA sequencing data.

Ma L, Yang S, Zhao W, Tang Z, Zhang T, Li K.

BMC Genomics. 2012 Aug 28;13:429. doi: 10.1186/1471-2164-13-429.

18.

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.

19.

ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data.

Yang JH, Li JH, Jiang S, Zhou H, Qu LH.

Nucleic Acids Res. 2013 Jan;41(Database issue):D177-87. doi: 10.1093/nar/gks1060. Epub 2012 Nov 17.

20.

RNA-Seq mapping and detection of gene fusions with a suffix array algorithm.

Sakarya O, Breu H, Radovich M, Chen Y, Wang YN, Barbacioru C, Utiramerur S, Whitley PP, Brockman JP, Vatta P, Zhang Z, Popescu L, Muller MW, Kudlingar V, Garg N, Li CY, Kong BS, Bodeau JP, Nutter RC, Gu J, Bramlett KS, Ichikawa JK, Hyland FC, Siddiqui AS.

PLoS Comput Biol. 2012;8(4):e1002464. doi: 10.1371/journal.pcbi.1002464. Epub 2012 Apr 5.

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