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Polycomb repressive complex 1 provides a molecular explanation for repeat copy number dependency in FSHD muscular dystrophy.

Casa V, Runfola V, Micheloni S, Aziz A, Dilworth FJ, Gabellini D.

Hum Mol Genet. 2017 Feb 15;26(4):753-767. doi: 10.1093/hmg/ddw426.


Novel Role of 3'UTR-Embedded Alu Elements as Facilitators of Processed Pseudogene Genesis and Host Gene Capture by Viral Genomes.

Farré D, Engel P, Angulo A.

PLoS One. 2016 Dec 29;11(12):e0169196. doi: 10.1371/journal.pone.0169196. eCollection 2016.


Alu-miRNA interactions modulate transcript isoform diversity in stress response and reveal signatures of positive selection.

Pandey R, Bhattacharya A, Bhardwaj V, Jha V, Mandal AK, Mukerji M.

Sci Rep. 2016 Sep 2;6:32348. doi: 10.1038/srep32348.


Restricting retrotransposons: a review.

Goodier JL.

Mob DNA. 2016 Aug 11;7:16. doi: 10.1186/s13100-016-0070-z. eCollection 2016. Review.


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.


Retrotransposons as regulators of gene expression.

Elbarbary RA, Lucas BA, Maquat LE.

Science. 2016 Feb 12;351(6274):aac7247. doi: 10.1126/science.aac7247. Epub 2016 Feb 11. Review.


Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome.

Gu Z, Jin K, Crabbe MJ, Zhang Y, Liu X, Huang Y, Hua M, Nan P, Zhang Z, Zhong Y.

Protein Cell. 2016 Apr;7(4):250-66. doi: 10.1007/s13238-015-0240-7. Epub 2016 Feb 10.


The contribution of Alu exons to the human proteome.

Lin L, Jiang P, Park JW, Wang J, Lu ZX, Lam MP, Ping P, Xing Y.

Genome Biol. 2016 Jan 28;17:15. doi: 10.1186/s13059-016-0876-5.


Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development.

Szabo L, Morey R, Palpant NJ, Wang PL, Afari N, Jiang C, Parast MM, Murry CE, Laurent LC, Salzman J.

Genome Biol. 2015 Jun 16;16:126. doi: 10.1186/s13059-015-0690-5. Erratum in: Genome Biol. 2016 Dec 19;17 (1):263.


Alternative splicing and co-option of transposable elements: the case of TMPO/LAP2α and ZNF451 in mammals.

Abascal F, Tress ML, Valencia A.

Bioinformatics. 2015 Jul 15;31(14):2257-61. doi: 10.1093/bioinformatics/btv132. Epub 2015 Mar 2.


Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions.

Kelley DR, Hendrickson DG, Tenen D, Rinn JL.

Genome Biol. 2014 Dec 3;15(12):537. doi: 10.1186/s13059-014-0537-5.


Species-specific exon loss in human transcriptomes.

Wang J, Lu ZX, Tokheim CJ, Miller SE, Xing Y.

Mol Biol Evol. 2015 Feb;32(2):481-94. doi: 10.1093/molbev/msu317. Epub 2014 Nov 14.


The persistent contributions of RNA to eukaryotic gen(om)e architecture and cellular function.

Brosius J.

Cold Spring Harb Perspect Biol. 2014 Jul 31;6(12):a016089. doi: 10.1101/cshperspect.a016089. Review.


Excision efficiency is not strongly coupled to transgenic rate: cell type-dependent transposition efficiency of sleeping beauty and piggyBac DNA transposons.

Kolacsek O, Erdei Z, Apáti A, Sándor S, Izsvák Z, Ivics Z, Sarkadi B, Orbán TI.

Hum Gene Ther Methods. 2014 Aug;25(4):241-52. doi: 10.1089/hgtb.2013.149.


An expanding universe of the non-coding genome in cancer biology.

Xue B, He L.

Carcinogenesis. 2014 Jun;35(6):1209-16. doi: 10.1093/carcin/bgu099. Epub 2014 Apr 18. Review.


PrimerSeq: Design and visualization of RT-PCR primers for alternative splicing using RNA-seq data.

Tokheim C, Park JW, Xing Y.

Genomics Proteomics Bioinformatics. 2014 Apr;12(2):105-9. doi: 10.1016/j.gpb.2014.04.001. Epub 2014 Apr 18.


Validation of predicted mRNA splicing mutations using high-throughput transcriptome data.

Viner C, Dorman SN, Shirley BC, Rogan PK.

Version 2. F1000Res. 2014 Jan 13 [revised 2014 Apr 7];3:8. doi: 10.12688/f1000research.3-8.v2. eCollection 2014.


Alu elements shape the primate transcriptome by cis-regulation of RNA editing.

Daniel C, Silberberg G, Behm M, Öhman M.

Genome Biol. 2014 Feb 3;15(2):R28. doi: 10.1186/gb-2014-15-2-r28.


ADAR regulates RNA editing, transcript stability, and gene expression.

Wang IX, So E, Devlin JL, Zhao Y, Wu M, Cheung VG.

Cell Rep. 2013 Nov 14;5(3):849-60. doi: 10.1016/j.celrep.2013.10.002. Epub 2013 Oct 31.


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.

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