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Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends.

Tajnik M, Vigilante A, Braun S, Hänel H, Luscombe NM, Ule J, Zarnack K, König J.

Nucleic Acids Res. 2015 Sep 22. pii: gkv956. [Epub ahead of print]


Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome.

Schoenfelder S, Sugar R, Dimond A, Javierre BM, Armstrong H, Mifsud B, Dimitrova E, Matheson L, Tavares-Cadete F, Furlan-Magaril M, Segonds-Pichon A, Jurkowski W, Wingett SW, Tabbada K, Andrews S, Herman B, LeProust E, Osborne CS, Koseki H, Fraser P, Luscombe NM, Elderkin S.

Nat Genet. 2015 Oct;47(10):1179-86. doi: 10.1038/ng.3393. Epub 2015 Aug 31.


Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C.

Mifsud B, Tavares-Cadete F, Young AN, Sugar R, Schoenfelder S, Ferreira L, Wingett SW, Andrews S, Grey W, Ewels PA, Herman B, Happe S, Higgs A, LeProust E, Follows GA, Fraser P, Luscombe NM, Osborne CS.

Nat Genet. 2015 Jun;47(6):598-606. doi: 10.1038/ng.3286. Epub 2015 May 4.


hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1.

Sugimoto Y, Vigilante A, Darbo E, Zirra A, Militti C, D'Ambrogio A, Luscombe NM, Ule J.

Nature. 2015 Mar 26;519(7544):491-4. doi: 10.1038/nature14280. Epub 2015 Mar 18.


The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements.

Schoenfelder S, Furlan-Magaril M, Mifsud B, Tavares-Cadete F, Sugar R, Javierre BM, Nagano T, Katsman Y, Sakthidevi M, Wingett SW, Dimitrova E, Dimond A, Edelman LB, Elderkin S, Tabbada K, Darbo E, Andrews S, Herman B, Higgs A, LeProust E, Osborne CS, Mitchell JA, Luscombe NM, Fraser P.

Genome Res. 2015 Apr;25(4):582-97. doi: 10.1101/gr.185272.114. Epub 2015 Mar 9.


Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt.

Murn J, Zarnack K, Yang YJ, Durak O, Murphy EA, Cheloufi S, Gonzalez DM, Teplova M, Curk T, Zuber J, Patel DJ, Ule J, Luscombe NM, Tsai LH, Walsh CA, Shi Y.

Genes Dev. 2015 Mar 1;29(5):501-12. doi: 10.1101/gad.258483.115.


Role of histone modifications and early termination in pervasive transcription and antisense-mediated gene silencing in yeast.

Castelnuovo M, Zaugg JB, Guffanti E, Maffioletti A, Camblong J, Xu Z, Clauder-Münster S, Steinmetz LM, Luscombe NM, Stutz F.

Nucleic Acids Res. 2014 Apr;42(7):4348-62. doi: 10.1093/nar/gku100. Epub 2014 Feb 4.


Small RNA profiling of Xenopus embryos reveals novel miRNAs and a new class of small RNAs derived from intronic transposable elements.

Harding JL, Horswell S, Heliot C, Armisen J, Zimmerman LB, Luscombe NM, Miska EA, Hill CS.

Genome Res. 2014 Jan;24(1):96-106. doi: 10.1101/gr.144469.112. Epub 2013 Sep 24.


Cellular resolution models for even skipped regulation in the entire Drosophila embryo.

Ilsley GR, Fisher J, Apweiler R, De Pace AH, Luscombe NM.

Elife. 2013 Aug 6;2:e00522. doi: 10.7554/eLife.00522.


Response to Comments on "Drosophila Dosage Compensation Involves Enhanced Pol II Recruitment to Male X-Linked Promoters".

Vaquerizas JM, Cavalli FM, Conrad T, Akhtar A, Luscombe NM.

Science. 2013 Apr 19;340(6130):273. doi: 10.1126/science.1232874.


Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements.

Zarnack K, König J, Tajnik M, Martincorena I, Eustermann S, Stévant I, Reyes A, Anders S, Luscombe NM, Ule J.

Cell. 2013 Jan 31;152(3):453-66. doi: 10.1016/j.cell.2012.12.023.


DNA-binding specificities of human transcription factors.

Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P, Morgunova E, Enge M, Taipale M, Wei G, Palin K, Vaquerizas JM, Vincentelli R, Luscombe NM, Hughes TR, Lemaire P, Ukkonen E, Kivioja T, Taipale J.

Cell. 2013 Jan 17;152(1-2):327-39. doi: 10.1016/j.cell.2012.12.009.


Non-random mutation: the evolution of targeted hypermutation and hypomutation.

Martincorena I, Luscombe NM.

Bioessays. 2013 Feb;35(2):123-30. doi: 10.1002/bies.201200150. Epub 2012 Dec 20. Review.


Gene loops enhance transcriptional directionality.

Tan-Wong SM, Zaugg JB, Camblong J, Xu Z, Zhang DW, Mischo HE, Ansari AZ, Luscombe NM, Steinmetz LM, Proudfoot NJ.

Science. 2012 Nov 2;338(6107):671-5. doi: 10.1126/science.1224350. Epub 2012 Sep 27.


Drosophila dosage compensation involves enhanced Pol II recruitment to male X-linked promoters.

Conrad T, Cavalli FM, Vaquerizas JM, Luscombe NM, Akhtar A.

Science. 2012 Aug 10;337(6095):742-6. doi: 10.1126/science.1221428. Epub 2012 Jul 19.


The NSL complex regulates housekeeping genes in Drosophila.

Lam KC, Mühlpfordt F, Vaquerizas JM, Raja SJ, Holz H, Luscombe NM, Manke T, Akhtar A.

PLoS Genet. 2012;8(6):e1002736. doi: 10.1371/journal.pgen.1002736. Epub 2012 Jun 14.


m:Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence.

Reimand J, Aun A, Vilo J, Vaquerizas JM, Sedman J, Luscombe NM.

Genome Biol. 2012 Jun 21;13(6):R55. doi: 10.1186/gb-2012-13-6-r55.


Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription.

Kahramanoglou C, Prieto AI, Khedkar S, Haase B, Gupta A, Benes V, Fraser GM, Luscombe NM, Seshasayee AS.

Nat Commun. 2012 Jun 6;3:886. doi: 10.1038/ncomms1878.


Evidence of non-random mutation rates suggests an evolutionary risk management strategy.

Martincorena I, Seshasayee AS, Luscombe NM.

Nature. 2012 May 3;485(7396):95-8. doi: 10.1038/nature10995.


The MOF chromobarrel domain controls genome-wide H4K16 acetylation and spreading of the MSL complex.

Conrad T, Cavalli FM, Holz H, Hallacli E, Kind J, Ilik I, Vaquerizas JM, Luscombe NM, Akhtar A.

Dev Cell. 2012 Mar 13;22(3):610-24. doi: 10.1016/j.devcel.2011.12.016.

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