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Discovering and understanding oncogenic gene fusions through data intensive computational approaches.

Latysheva NS, Babu MM.

Nucleic Acids Res. 2016 Jun 2;44(10):4487-503. doi: 10.1093/nar/gkw282. Epub 2016 Apr 21.


Fusion transcript loci share many genomic features with non-fusion loci.

Lai J, An J, Seim I, Walpole C, Hoffman A, Moya L, Srinivasan S, Perry-Keene JL; Australian Prostate Cancer Bioresource, Wang C, Lehman ML, Nelson CC, Clements JA, Batra J.

BMC Genomics. 2015 Dec 1;16:1021. doi: 10.1186/s12864-015-2235-4. Erratum in: BMC Genomics. 2016;17:424.


Novel RNA variants in colorectal cancers.

Hoff AM, Johannessen B, Alagaratnam S, Zhao S, Nome T, Løvf M, Bakken AC, Hektoen M, Sveen A, Lothe RA, Skotheim RI.

Oncotarget. 2015 Nov 3;6(34):36587-602. doi: 10.18632/oncotarget.5500.


Hypothesis: Artifacts, Including Spurious Chimeric RNAs with a Short Homologous Sequence, Caused by Consecutive Reverse Transcriptions and Endogenous Random Primers.

Peng Z, Yuan C, Zellmer L, Liu S, Xu N, Liao DJ.

J Cancer. 2015 May 1;6(6):555-67. doi: 10.7150/jca.11997. eCollection 2015. Review.


The Landscape of long noncoding RNA classification.

St Laurent G, Wahlestedt C, Kapranov P.

Trends Genet. 2015 May;31(5):239-51. doi: 10.1016/j.tig.2015.03.007. Epub 2015 Apr 10. Review.


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.


Assessing the hodgepodge of non-mapped reads in bacterial transcriptomes: real or artifactual RNA chimeras?

Lloréns-Rico V, Serrano L, Lluch-Senar M.

BMC Genomics. 2014 Jul 29;15:633. doi: 10.1186/1471-2164-15-633.


Is an observed non-co-linear RNA product spliced in trans, in cis or just in vitro?

Yu CY, Liu HJ, Hung LY, Kuo HC, Chuang TJ.

Nucleic Acids Res. 2014 Aug;42(14):9410-23. doi: 10.1093/nar/gku643. Epub 2014 Jul 22.


The dynamic architectural and epigenetic nuclear landscape: developing the genomic almanac of biology and disease.

Tai PW, Zaidi SK, Wu H, Grandy RA, Montecino M, van Wijnen AJ, Lian JB, Stein GS, Stein JL.

J Cell Physiol. 2014 Jun;229(6):711-27. doi: 10.1002/jcp.24508. Review.


Functional transcriptomics in the post-ENCODE era.

Mudge JM, Frankish A, Harrow J.

Genome Res. 2013 Dec;23(12):1961-73. doi: 10.1101/gr.161315.113. Epub 2013 Oct 30.


Common fusion transcripts identified in colorectal cancer cell lines by high-throughput RNA sequencing.

Nome T, Thomassen GO, Bruun J, Ahlquist T, Bakken AC, Hoff AM, Rognum T, Nesbakken A, Lorenz S, Sun J, Barros-Silva JD, Lind GE, Myklebost O, Teixeira MR, Meza-Zepeda LA, Lothe RA, Skotheim RI.

Transl Oncol. 2013 Oct 1;6(5):546-53. eCollection 2013.


Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency.

Wu CS, Yu CY, Chuang CY, Hsiao M, Kao CF, Kuo HC, Chuang TJ.

Genome Res. 2014 Jan;24(1):25-36. doi: 10.1101/gr.159483.113. Epub 2013 Oct 16.


Subcellular RNA sequencing reveals broad presence of cytoplasmic intron-sequence retaining transcripts in mouse and rat neurons.

Khaladkar M, Buckley PT, Lee MT, Francis C, Eghbal MM, Chuong T, Suresh S, Kuhn B, Eberwine J, Kim J.

PLoS One. 2013 Oct 3;8(10):e76194. doi: 10.1371/journal.pone.0076194. eCollection 2013.


Unravelling the hidden DNA structural/physical code provides novel insights on promoter location.

Durán E, Djebali S, González S, Flores O, Mercader JM, Guigó R, Torrents D, Soler-López M, Orozco M.

Nucleic Acids Res. 2013 Aug;41(15):7220-30. doi: 10.1093/nar/gkt511. Epub 2013 Jun 12.


Colocalization of coregulated genes: a steered molecular dynamics study of human chromosome 19.

Di Stefano M, Rosa A, Belcastro V, di Bernardo D, Micheletti C.

PLoS Comput Biol. 2013;9(3):e1003019. doi: 10.1371/journal.pcbi.1003019. Epub 2013 Mar 28.


Non-Coding RNAs: Functional Aspects and Diagnostic Utility in Oncology.

Kim T, Reitmair A.

Int J Mol Sci. 2013 Mar 1;14(3):4934-68. doi: 10.3390/ijms14034934.


RNA-mediated genome rearrangement: hypotheses and evidence.

Fang W, Landweber LF.

Bioessays. 2013 Feb;35(2):84-7. doi: 10.1002/bies.201200140. Epub 2012 Dec 20. No abstract available.


Detection of a common chimeric transcript between human chromosomes 7 and 16.

Fang W, Wei Y, Kang Y, Landweber LF.

Biol Direct. 2012 Dec 29;7:49. doi: 10.1186/1745-6150-7-49.


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.

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