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Items: 1 to 50 of 117

1.

Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates.

Riba A, Di Nanni N, Mittal N, Arhné E, Schmidt A, Zavolan M.

Proc Natl Acad Sci U S A. 2019 Jul 10. pii: 201817299. doi: 10.1073/pnas.1817299116. [Epub ahead of print]

PMID:
31292258
Free Article
2.

Alternative cleavage and polyadenylation in health and disease.

Gruber AJ, Zavolan M.

Nat Rev Genet. 2019 Jul 2. doi: 10.1038/s41576-019-0145-z. [Epub ahead of print] Review.

PMID:
31267064
3.

MINA-1 and WAGO-4 are part of regulatory network coordinating germ cell death and RNAi in C. elegans.

Sendoel A, Subasic D, Ducoli L, Keller M, Michel E, Kohler I, Singh KD, Zheng X, Brümmer A, Imig J, Kishore S, Wu Y, Kanitz A, Kaech A, Mittal N, Matia-González AM, Gerber AP, Zavolan M, Aebersold R, Hall J, Allain FH, Hengartner MO.

Cell Death Differ. 2019 Feb 6. doi: 10.1038/s41418-019-0291-z. [Epub ahead of print]

PMID:
30728462
4.

Conserved regulation of RNA processing in somatic cell reprogramming.

Kanitz A, Syed AP, Kaji K, Zavolan M.

BMC Genomics. 2019 Jan 31;20(1):100. doi: 10.1186/s12864-019-5438-2.

5.

Roquin targets mRNAs in a 3'-UTR-specific manner by different modes of regulation.

Essig K, Kronbeck N, Guimaraes JC, Lohs C, Schlundt A, Hoffmann A, Behrens G, Brenner S, Kowalska J, Lopez-Rodriguez C, Jemielity J, Holtmann H, Reiche K, Hackermüller J, Sattler M, Zavolan M, Heissmeyer V.

Nat Commun. 2018 Sep 19;9(1):3810. doi: 10.1038/s41467-018-06184-3.

6.

Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms.

Gruber AJ, Gypas F, Riba A, Schmidt R, Zavolan M.

Nat Methods. 2018 Oct;15(10):832-836. doi: 10.1038/s41592-018-0114-z. Epub 2018 Sep 10.

PMID:
30202060
7.

Mirroring the multifaceted role of RNA and its partners in gene expression.

Zavolan M, Gerber AP.

FEBS Lett. 2018 Sep;592(17):2825-2827. doi: 10.1002/1873-3468.13230. No abstract available.

PMID:
30198187
8.

Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction.

Rzepiela AJ, Ghosh S, Breda J, Vina-Vilaseca A, Syed AP, Gruber AJ, Eschbach K, Beisel C, van Nimwegen E, Zavolan M.

Mol Syst Biol. 2018 Aug 27;14(8):e8266. doi: 10.15252/msb.20188266.

9.

Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC.

Gruber AJ, Schmidt R, Ghosh S, Martin G, Gruber AR, van Nimwegen E, Zavolan M.

Genome Biol. 2018 Mar 28;19(1):44. doi: 10.1186/s13059-018-1415-3.

10.

RNA splicing and its connection with other regulatory layers in somatic cell reprogramming.

Zavolan M, Kanitz A.

Curr Opin Cell Biol. 2018 Jun;52:8-13. doi: 10.1016/j.ceb.2017.12.002. Epub 2017 Dec 21. Review.

PMID:
29275148
11.

Roquin Suppresses the PI3K-mTOR Signaling Pathway to Inhibit T Helper Cell Differentiation and Conversion of Treg to Tfr Cells.

Essig K, Hu D, Guimaraes JC, Alterauge D, Edelmann S, Raj T, Kranich J, Behrens G, Heiseke A, Floess S, Klein J, Maiser A, Marschall S, Hrabĕ de Angelis M, Leonhardt H, Calkhoven CF, Noessner E, Brocker T, Huehn J, Krug AB, Zavolan M, Baumjohann D, Heissmeyer V.

Immunity. 2017 Dec 19;47(6):1067-1082.e12. doi: 10.1016/j.immuni.2017.11.008. Epub 2017 Dec 12.

12.

RNAs: dynamic and mutable.

Zavolan M, Graveley BR.

Genome Biol. 2017 Nov 29;18(1):226. doi: 10.1186/s13059-017-1361-5. No abstract available.

13.

3' End Sequencing Library Preparation with A-seq2.

Martin G, Schmidt R, Gruber AJ, Ghosh S, Keller W, Zavolan M.

J Vis Exp. 2017 Oct 10;(128). doi: 10.3791/56129.

14.

The Gcn4 transcription factor reduces protein synthesis capacity and extends yeast lifespan.

Mittal N, Guimaraes JC, Gross T, Schmidt A, Vina-Vilaseca A, Nedialkova DD, Aeschimann F, Leidel SA, Spang A, Zavolan M.

Nat Commun. 2017 Sep 6;8(1):457. doi: 10.1038/s41467-017-00539-y.

15.

Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors.

Omidi S, Zavolan M, Pachkov M, Breda J, Berger S, van Nimwegen E.

PLoS Comput Biol. 2017 Jul 28;13(7):e1005176. doi: 10.1371/journal.pcbi.1005176. eCollection 2017 Jul.

16.

TFAP2A is a component of the ZEB1/2 network that regulates TGFB1-induced epithelial to mesenchymal transition.

Dimitrova Y, Gruber AJ, Mittal N, Ghosh S, Dimitriades B, Mathow D, Grandy WA, Christofori G, Zavolan M.

Biol Direct. 2017 Apr 17;12(1):8. doi: 10.1186/s13062-017-0180-7.

17.

Explicit Modeling of siRNA-Dependent On- and Off-Target Repression Improves the Interpretation of Screening Results.

Riba A, Emmenlauer M, Chen A, Sigoillot F, Cong F, Dehio C, Jenkins J, Zavolan M.

Cell Syst. 2017 Feb 22;4(2):182-193.e4. doi: 10.1016/j.cels.2017.01.011. Epub 2017 Feb 15.

18.

High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq.

Gumienny R, Jedlinski DJ, Schmidt A, Gypas F, Martin G, Vina-Vilaseca A, Zavolan M.

Nucleic Acids Res. 2017 Mar 17;45(5):2341-2353. doi: 10.1093/nar/gkw1321.

19.
20.

TUT-DIS3L2 is a mammalian surveillance pathway for aberrant structured non-coding RNAs.

Ustianenko D, Pasulka J, Feketova Z, Bednarik L, Zigackova D, Fortova A, Zavolan M, Vanacova S.

EMBO J. 2016 Oct 17;35(20):2179-2191. Epub 2016 Sep 19.

21.

A comprehensive analysis of 3' end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation.

Gruber AJ, Schmidt R, Gruber AR, Martin G, Ghosh S, Belmadani M, Keller W, Zavolan M.

Genome Res. 2016 Aug;26(8):1145-59. doi: 10.1101/gr.202432.115. Epub 2016 Jul 5.

22.

Corrigendum to "Quantifying the strength of miRNA-target interactions" [Methods (2015) 90-99].

Breda J, Rzepiela AJ, Gumienny R, van Nimwegen E, Zavolan M.

Methods. 2016 Jul 15;104:204-205. doi: 10.1016/j.ymeth.2015.12.016. Epub 2016 Jan 13. No abstract available.

23.

Redesigning CLIP for efficiency, accuracy and speed.

Martin G, Zavolan M.

Nat Methods. 2016 May 31;13(6):482-3. doi: 10.1038/nmeth.3870. No abstract available.

PMID:
27243472
24.

An updated human snoRNAome.

Jorjani H, Kehr S, Jedlinski DJ, Gumienny R, Hertel J, Stadler PF, Zavolan M, Gruber AR.

Nucleic Acids Res. 2016 Jun 20;44(11):5068-82. doi: 10.1093/nar/gkw386. Epub 2016 May 12.

25.

Roquin recognizes a non-canonical hexaloop structure in the 3'-UTR of Ox40.

Janowski R, Heinz GA, Schlundt A, Wommelsdorf N, Brenner S, Gruber AR, Blank M, Buch T, Buhmann R, Zavolan M, Niessing D, Heissmeyer V, Sattler M.

Nat Commun. 2016 Mar 24;7:11032. doi: 10.1038/ncomms11032.

26.

Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G.

Gumienny R, Zavolan M.

Nucleic Acids Res. 2015 Oct 15;43(18):9095. doi: 10.1093/nar/gkv924. Epub 2015 Sep 13. No abstract available.

27.

Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans.

Subasic D, Brümmer A, Wu Y, Pinto SM, Imig J, Keller M, Jovanovic M, Lightfoot HL, Nasso S, Goetze S, Brunner E, Hall J, Aebersold R, Zavolan M, Hengartner MO.

Genome Res. 2015 Nov;25(11):1680-91. doi: 10.1101/gr.183160.114. Epub 2015 Jul 31.

28.

Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data.

Kanitz A, Gypas F, Gruber AJ, Gruber AR, Martin G, Zavolan M.

Genome Biol. 2015 Jul 23;16:150. doi: 10.1186/s13059-015-0702-5.

29.

Inferring gene expression regulatory networks from high-throughput measurements.

Zavolan M.

Methods. 2015 Sep 1;85:1-2. doi: 10.1016/j.ymeth.2015.07.006. Epub 2015 Jul 15. No abstract available.

PMID:
26188125
30.

miR-184 Regulates Pancreatic β-Cell Function According to Glucose Metabolism.

Tattikota SG, Rathjen T, Hausser J, Khedkar A, Kabra UD, Pandey V, Sury M, Wessels HH, Mollet IG, Eliasson L, Selbach M, Zinzen RP, Zavolan M, Kadener S, Tschöp MH, Jastroch M, Friedländer MR, Poy MN.

J Biol Chem. 2015 Aug 14;290(33):20284-94. doi: 10.1074/jbc.M115.658625. Epub 2015 Jul 7.

31.

Quantifying the strength of miRNA-target interactions.

Breda J, Rzepiela AJ, Gumienny R, van Nimwegen E, Zavolan M.

Methods. 2015 Sep 1;85:90-99. doi: 10.1016/j.ymeth.2015.04.012. Epub 2015 Apr 16.

32.

Reflections on the RNA world.

Zavolan M, Keller W.

RNA. 2015 Apr;21(4):531-3. doi: 10.1261/rna.049999.115. No abstract available.

33.

Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G.

Gumienny R, Zavolan M.

Nucleic Acids Res. 2015 Feb 18;43(3):1380-91. doi: 10.1093/nar/gkv050. Epub 2015 Jan 27. Erratum in: Nucleic Acids Res. 2015 Oct 15;43(18):9095.

34.

miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction.

Imig J, Brunschweiger A, Brümmer A, Guennewig B, Mittal N, Kishore S, Tsikrika P, Gerber AP, Zavolan M, Hall J.

Nat Chem Biol. 2015 Feb;11(2):107-14. doi: 10.1038/nchembio.1713. Epub 2014 Dec 22.

PMID:
25531890
35.

Global 3' UTR shortening has a limited effect on protein abundance in proliferating T cells.

Gruber AR, Martin G, Müller P, Schmidt A, Gruber AJ, Gumienny R, Mittal N, Jayachandran R, Pieters J, Keller W, van Nimwegen E, Zavolan M.

Nat Commun. 2014 Nov 21;5:5465. doi: 10.1038/ncomms6465.

PMID:
25413384
36.

Reconstitution of CPSF active in polyadenylation: recognition of the polyadenylation signal by WDR33.

Schönemann L, Kühn U, Martin G, Schäfer P, Gruber AR, Keller W, Zavolan M, Wahle E.

Genes Dev. 2014 Nov 1;28(21):2381-93. doi: 10.1101/gad.250985.114. Epub 2014 Oct 9.

37.

Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways.

Gruber AJ, Grandy WA, Balwierz PJ, Dimitrova YA, Pachkov M, Ciaudo C, Nimwegen Ev, Zavolan M.

Nucleic Acids Res. 2014 Aug;42(14):9313-26. doi: 10.1093/nar/gku544. Epub 2014 Jul 16.

38.

Identification and consequences of miRNA-target interactions--beyond repression of gene expression.

Hausser J, Zavolan M.

Nat Rev Genet. 2014 Sep;15(9):599-612. doi: 10.1038/nrg3765. Epub 2014 Jul 15. Review. Erratum in: Nat Rev Genet. 2014 Oct;15(10):702.

PMID:
25022902
39.

Structural and functional implications of the QUA2 domain on RNA recognition by GLD-1.

Daubner GM, Brümmer A, Tocchini C, Gerhardy S, Ciosk R, Zavolan M, Allain FH.

Nucleic Acids Res. 2014 Jul;42(12):8092-105. doi: 10.1093/nar/gku445. Epub 2014 May 16.

40.

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support.

Stockinger H, Altenhoff AM, Arnold K, Bairoch A, Bastian F, Bergmann S, Bougueleret L, Bucher P, Delorenzi M, Lane L, Le Mercier P, Lisacek F, Michielin O, Palagi PM, Rougemont J, Schwede T, von Mering C, van Nimwegen E, Walther D, Xenarios I, Zavolan M, Zdobnov EM, Zoete V, Appel RD.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W436-41. doi: 10.1093/nar/gku380. Epub 2014 May 3.

41.

MicroRNA-7a regulates pancreatic β cell function.

Latreille M, Hausser J, Stützer I, Zhang Q, Hastoy B, Gargani S, Kerr-Conte J, Pattou F, Zavolan M, Esguerra JL, Eliasson L, Rülicke T, Rorsman P, Stoffel M.

J Clin Invest. 2014 Jun;124(6):2722-35. doi: 10.1172/JCI73066. Epub 2014 May 1.

42.

Widespread context dependency of microRNA-mediated regulation.

Erhard F, Haas J, Lieber D, Malterer G, Jaskiewicz L, Zavolan M, Dölken L, Zimmer R.

Genome Res. 2014 Jun;24(6):906-19. doi: 10.1101/gr.166702.113. Epub 2014 Mar 25.

43.

PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation): a step-by-step protocol to the transcriptome-wide identification of binding sites of RNA-binding proteins.

Spitzer J, Hafner M, Landthaler M, Ascano M, Farazi T, Wardle G, Nusbaum J, Khorshid M, Burger L, Zavolan M, Tuschl T.

Methods Enzymol. 2014;539:113-61. doi: 10.1016/B978-0-12-420120-0.00008-6.

44.

ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs.

Balwierz PJ, Pachkov M, Arnold P, Gruber AJ, Zavolan M, van Nimwegen E.

Genome Res. 2014 May;24(5):869-84. doi: 10.1101/gr.169508.113. Epub 2014 Feb 10.

45.

Seq and CLIP through the miRNA world.

Mittal N, Zavolan M.

Genome Biol. 2014 Jan 25;15(1):202. doi: 10.1186/gb4151. Review.

46.

TSSer: an automated method to identify transcription start sites in prokaryotic genomes from differential RNA sequencing data.

Jorjani H, Zavolan M.

Bioinformatics. 2014 Apr 1;30(7):971-4. doi: 10.1093/bioinformatics/btt752. Epub 2013 Dec 25.

PMID:
24371151
47.

Argonaute2 mediates compensatory expansion of the pancreatic β cell.

Tattikota SG, Rathjen T, McAnulty SJ, Wessels HH, Akerman I, van de Bunt M, Hausser J, Esguerra JL, Musahl A, Pandey AK, You X, Chen W, Herrera PL, Johnson PR, O'Carroll D, Eliasson L, Zavolan M, Gloyn AL, Ferrer J, Shalom-Feuerstein R, Aberdam D, Poy MN.

Cell Metab. 2014 Jan 7;19(1):122-34. doi: 10.1016/j.cmet.2013.11.015. Epub 2013 Dec 19.

48.

Timescales and bottlenecks in miRNA-dependent gene regulation.

Hausser J, Syed AP, Selevsek N, van Nimwegen E, Jaskiewicz L, Aebersold R, Zavolan M.

Mol Syst Biol. 2013 Dec 3;9:711. doi: 10.1038/msb.2013.68.

49.

Modulation of epigenetic regulators and cell fate decisions by miRNAs.

Gruber AJ, Zavolan M.

Epigenomics. 2013 Dec;5(6):671-83. doi: 10.2217/epi.13.65. Review.

50.

Means to an end: mechanisms of alternative polyadenylation of messenger RNA precursors.

Gruber AR, Martin G, Keller W, Zavolan M.

Wiley Interdiscip Rev RNA. 2014 Mar-Apr;5(2):183-96. doi: 10.1002/wrna.1206. Epub 2013 Nov 14. Review.

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