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Items: 1 to 20 of 44

1.

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 Dec 2;43(21):10492-505. doi: 10.1093/nar/gkv956. Epub 2015 Sep 22.

2.

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.

3.

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.

4.

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.

5.

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.

6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12.

Prieto AI, Kahramanoglou C, Ali RM, Fraser GM, Seshasayee AS, Luscombe NM.

Nucleic Acids Res. 2012 Apr;40(8):3524-37. doi: 10.1093/nar/gkr1236. Epub 2011 Dec 17.

13.

SpeCond: a method to detect condition-specific gene expression.

Cavalli FM, Bourgon R, Vaquerizas JM, Luscombe NM.

Genome Biol. 2011 Oct 18;12(10):R101. doi: 10.1186/gb-2011-12-10-r101. Erratum in: Genome Biol. 2011;12(12):413. Huber, Wolfgang [removed].

14.

A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast.

Zaugg JB, Luscombe NM.

Genome Res. 2012 Jan;22(1):84-94. doi: 10.1101/gr.124099.111. Epub 2011 Sep 19.

15.

The RNA-binding protein Rrm4 is essential for efficient secretion of endochitinase Cts1.

Koepke J, Kaffarnik F, Haag C, Zarnack K, Luscombe NM, König J, Ule J, Kellner R, Begerow D, Feldbrügge M.

Mol Cell Proteomics. 2011 Dec;10(12):M111.011213. doi: 10.1074/mcp.M111.011213. Epub 2011 Aug 1.

16.

iCLIP--transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution.

Konig J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J.

J Vis Exp. 2011 Apr 30;(50). pii: 2638. doi: 10.3791/2638.

17.

Sensitized phenotypic screening identifies gene dosage sensitive region on chromosome 11 that predisposes to disease in mice.

Ermakova O, Piszczek L, Luciani L, Cavalli FM, Ferreira T, Farley D, Rizzo S, Paolicelli RC, Al-Banchaabouchi M, Nerlov C, Moriggl R, Luscombe NM, Gross C.

EMBO Mol Med. 2011 Jan;3(1):50-66. doi: 10.1002/emmm.201000112.

18.

Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli.

Kahramanoglou C, Seshasayee AS, Prieto AI, Ibberson D, Schmidt S, Zimmermann J, Benes V, Fraser GM, Luscombe NM.

Nucleic Acids Res. 2011 Mar;39(6):2073-91. doi: 10.1093/nar/gkq934. Epub 2010 Nov 21.

19.

iCLIP predicts the dual splicing effects of TIA-RNA interactions.

Wang Z, Kayikci M, Briese M, Zarnack K, Luscombe NM, Rot G, Zupan B, Curk T, Ule J.

PLoS Biol. 2010 Oct 26;8(10):e1000530. doi: 10.1371/journal.pbio.1000530.

20.

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution.

König J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J.

Nat Struct Mol Biol. 2010 Jul;17(7):909-15. doi: 10.1038/nsmb.1838. Epub 2010 Jul 4.

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