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Items: 1 to 20 of 41


ChiTaRS-3.1-the enhanced chimeric transcripts and RNA-seq database matched with protein-protein interactions.

Gorohovski A, Tagore S, Palande V, Malka A, Raviv-Shay D, Frenkel-Morgenstern M.

Nucleic Acids Res. 2017 Jan 4;45(D1):D790-D795. doi: 10.1093/nar/gkw1127. Epub 2016 Nov 29.


Lessons from non-canonical splicing.

Sibley CR, Blazquez L, Ule J.

Nat Rev Genet. 2016 Jul;17(7):407-21. doi: 10.1038/nrg.2016.46. Epub 2016 May 31. Review.


Altered expression pattern of circular RNAs in primary and metastatic sites of epithelial ovarian carcinoma.

Ahmed I, Karedath T, Andrews SS, Al-Azwani IK, Mohamoud YA, Querleu D, Rafii A, Malek JA.

Oncotarget. 2016 Jun 14;7(24):36366-36381. doi: 10.18632/oncotarget.8917.


Evolutionary Insights into RNA trans-Splicing in Vertebrates.

Lei Q, Li C, Zuo Z, Huang C, Cheng H, Zhou R.

Genome Biol Evol. 2016 Mar 10;8(3):562-77. doi: 10.1093/gbe/evw025. Review.


Recurrent chimeric fusion RNAs in non-cancer tissues and cells.

Babiceanu M, Qin F, Xie Z, Jia Y, Lopez K, Janus N, Facemire L, Kumar S, Pang Y, Qi Y, Lazar IM, Li H.

Nucleic Acids Res. 2016 Apr 7;44(6):2859-72. doi: 10.1093/nar/gkw032. Epub 2016 Feb 2.


The evolutionary landscape of intergenic trans-splicing events in insects.

Kong Y, Zhou H, Yu Y, Chen L, Hao P, Li X.

Nat Commun. 2015 Nov 2;6:8734. doi: 10.1038/ncomms9734.


NCLscan: accurate identification of non-co-linear transcripts (fusion, trans-splicing and circular RNA) with a good balance between sensitivity and precision.

Chuang TJ, Wu CS, Chen CY, Hung LY, Chiang TW, Yang MY.

Nucleic Acids Res. 2016 Feb 18;44(3):e29. doi: 10.1093/nar/gkv1013. Epub 2015 Oct 5.


Determining exon connectivity in complex mRNAs by nanopore sequencing.

Bolisetty MT, Rajadinakaran G, Graveley BR.

Genome Biol. 2015 Sep 30;16:204. doi: 10.1186/s13059-015-0777-z.


Biogenesis, identification, and function of exonic circular RNAs.

Chen I, Chen CY, Chuang TJ.

Wiley Interdiscip Rev RNA. 2015 Sep-Oct;6(5):563-79. doi: 10.1002/wrna.1294. Epub 2015 Jul 31. Review.


Gene Model Annotations for Drosophila melanogaster: The Rule-Benders.

Crosby MA, Gramates LS, Dos Santos G, Matthews BB, St Pierre SE, Zhou P, Schroeder AJ, Falls K, Emmert DB, Russo SM, Gelbart WM; FlyBase Consortium.

G3 (Bethesda). 2015 Jun 24;5(8):1737-49. doi: 10.1534/g3.115.018937.


Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level.

Abascal F, Ezkurdia I, Rodriguez-Rivas J, Rodriguez JM, del Pozo A, Vázquez J, Valencia A, Tress ML.

PLoS Comput Biol. 2015 Jun 10;11(6):e1004325. doi: 10.1371/journal.pcbi.1004325. eCollection 2015 Jun.


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.


A conserved intronic U1 snRNP-binding sequence promotes trans-splicing in Drosophila.

Gao JL, Fan YJ, Wang XY, Zhang Y, Pu J, Li L, Shao W, Zhan S, Hao J, Xu YZ.

Genes Dev. 2015 Apr 1;29(7):760-71. doi: 10.1101/gad.258863.115.


Genome-wide analysis of drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation.

Westholm JO, Miura P, Olson S, Shenker S, Joseph B, Sanfilippo P, Celniker SE, Graveley BR, Lai EC.

Cell Rep. 2014 Dec 11;9(5):1966-80. doi: 10.1016/j.celrep.2014.10.062. Epub 2014 Nov 26.


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.


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.


Genome-wide identification of transcript start and end sites by transcript isoform sequencing.

Pelechano V, Wei W, Jakob P, Steinmetz LM.

Nat Protoc. 2014 Jul;9(7):1740-59. doi: 10.1038/nprot.2014.121. Epub 2014 Jun 26.


Detecting and characterizing circular RNAs.

Jeck WR, Sharpless NE.

Nat Biotechnol. 2014 May;32(5):453-61. doi: 10.1038/nbt.2890.


Brahma regulates a specific trans-splicing event at the mod(mdg4) locus of Drosophila melanogaster.

Yu S, Waldholm J, Böhm S, Visa N.

RNA Biol. 2014;11(2):134-45. doi: 10.4161/rna.27866. Epub 2014 Feb 6.


Evolution of splicing regulatory networks in Drosophila.

McManus CJ, Coolon JD, Eipper-Mains J, Wittkopp PJ, Graveley BR.

Genome Res. 2014 May;24(5):786-96. doi: 10.1101/gr.161521.113. Epub 2014 Feb 10.

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