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Items: 28

1.

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.

2.

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.

3.

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.

4.

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.

5.

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.

6.

The ViennaRNA web services.

Gruber AR, Bernhart SH, Lorenz R.

Methods Mol Biol. 2015;1269:307-26. doi: 10.1007/978-1-4939-2291-8_19.

PMID:
25577387
7.

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
8.

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.

9.

RNA Polymerase III promoter screen uncovers a novel noncoding RNA family conserved in Caenorhabditis and other clade V nematodes.

Gruber AR.

Gene. 2014 Jul 10;544(2):236-40. doi: 10.1016/j.gene.2014.04.068. Epub 2014 Apr 30.

PMID:
24792899
10.

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.

11.

Translation-dependent displacement of UPF1 from coding sequences causes its enrichment in 3' UTRs.

Zünd D, Gruber AR, Zavolan M, Mühlemann O.

Nat Struct Mol Biol. 2013 Aug;20(8):936-43. doi: 10.1038/nsmb.2635. Epub 2013 Jul 7.

PMID:
23832275
12.

Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing.

Kishore S, Gruber AR, Jedlinski DJ, Syed AP, Jorjani H, Zavolan M.

Genome Biol. 2013 May 26;14(5):R45. doi: 10.1186/gb-2013-14-5-r45.

13.

Cleavage factor Im is a key regulator of 3' UTR length.

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

RNA Biol. 2012 Dec;9(12):1405-12. doi: 10.4161/rna.22570. Epub 2012 Nov 27.

PMID:
23187700
14.

Genome-wide analysis of pre-mRNA 3' end processing reveals a decisive role of human cleavage factor I in the regulation of 3' UTR length.

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

Cell Rep. 2012 Jun 28;1(6):753-63. doi: 10.1016/j.celrep.2012.05.003. Epub 2012 Jun 7.

15.

Tristetraprolin-driven regulatory circuit controls quality and timing of mRNA decay in inflammation.

Kratochvill F, Machacek C, Vogl C, Ebner F, Sedlyarov V, Gruber AR, Hartweger H, Vielnascher R, Karaghiosoff M, Rülicke T, Müller M, Hofacker I, Lang R, Kovarik P.

Mol Syst Biol. 2011 Dec 20;7:560. doi: 10.1038/msb.2011.93.

16.

Animal snoRNAs and scaRNAs with exceptional structures.

Marz M, Gruber AR, Höner Zu Siederdissen C, Amman F, Badelt S, Bartschat S, Bernhart SH, Beyer W, Kehr S, Lorenz R, Tanzer A, Yusuf D, Tafer H, Hofacker IL, Stadler PF.

RNA Biol. 2011 Nov-Dec;8(6):938-46. doi: 10.4161/rna.8.6.16603. Epub 2011 Nov 1.

17.

AREsite: a database for the comprehensive investigation of AU-rich elements.

Gruber AR, Fallmann J, Kratochvill F, Kovarik P, Hofacker IL.

Nucleic Acids Res. 2011 Jan;39(Database issue):D66-9. doi: 10.1093/nar/gkq990. Epub 2010 Nov 11.

18.

Nematode sbRNAs: homologs of vertebrate Y RNAs.

Boria I, Gruber AR, Tanzer A, Bernhart SH, Lorenz R, Mueller MM, Hofacker IL, Stadler PF.

J Mol Evol. 2010 Apr;70(4):346-58. doi: 10.1007/s00239-010-9332-4. Epub 2010 Mar 27.

PMID:
20349053
19.

RNAz 2.0: improved noncoding RNA detection.

Gruber AR, Findeiß S, Washietl S, Hofacker IL, Stadler PF.

Pac Symp Biocomput. 2010:69-79.

20.

RNAalifold: improved consensus structure prediction for RNA alignments.

Bernhart SH, Hofacker IL, Will S, Gruber AR, Stadler PF.

BMC Bioinformatics. 2008 Nov 11;9:474. doi: 10.1186/1471-2105-9-474.

21.

Arthropod 7SK RNA.

Gruber AR, Kilgus C, Mosig A, Hofacker IL, Hennig W, Stadler PF.

Mol Biol Evol. 2008 Sep;25(9):1923-30. doi: 10.1093/molbev/msn140. Epub 2008 Jun 19.

PMID:
18566019
22.

The Vienna RNA websuite.

Gruber AR, Lorenz R, Bernhart SH, Neuböck R, Hofacker IL.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W70-4. doi: 10.1093/nar/gkn188. Epub 2008 Apr 19.

23.

Strategies for measuring evolutionary conservation of RNA secondary structures.

Gruber AR, Bernhart SH, Hofacker IL, Washietl S.

BMC Bioinformatics. 2008 Feb 26;9:122. doi: 10.1186/1471-2105-9-122.

24.

Invertebrate 7SK snRNAs.

Gruber AR, Koper-Emde D, Marz M, Tafer H, Bernhart S, Obernosterer G, Mosig A, Hofacker IL, Stadler PF, Benecke BJ.

J Mol Evol. 2008 Feb;66(2):107-15. doi: 10.1007/s00239-007-9052-6. Epub 2008 Jan 12.

25.

Structured RNAs in the ENCODE selected regions of the human genome.

Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A, Ucla C, Wyss C, Antonarakis SE, Denoeud F, Lagarde J, Drenkow J, Kapranov P, Gingeras TR, Guigó R, Snyder M, Gerstein MB, Reymond A, Hofacker IL, Stadler PF.

Genome Res. 2007 Jun;17(6):852-64.

26.

The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures.

Gruber AR, Neuböck R, Hofacker IL, Washietl S.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W335-8. Epub 2007 Apr 22.

27.

Capture, care, and captive breeding of 13-lined ground squirrels, Spermophilus tridecemlineatus.

Vaughan DK, Gruber AR, Michalski ML, Seidling J, Schlink S.

Lab Anim (NY). 2006 Apr;35(4):33-40.

PMID:
16582898
28.

Children who set fires: some background and behavioral characteristics.

Gruber AR, Heck ET, Mintzer E.

Am J Orthopsychiatry. 1981 Jul;51(3):484-488. doi: 10.1111/j.1939-0025.1981.tb01396.x.

PMID:
7258313

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