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Items: 1 to 20 of 103


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.


Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high-resolution tiling arrays.

Sellam A, Hogues H, Askew C, Tebbji F, van Het Hoog M, Lavoie H, Kumamoto CA, Whiteway M, Nantel A.

Genome Biol. 2010;11(7):R71. doi: 10.1186/gb-2010-11-7-r71. Epub 2010 Jul 9.


Structured RNAs and synteny regions in the pig genome.

Anthon C, Tafer H, Havgaard JH, Thomsen B, Hedegaard J, Seemann SE, Pundhir S, Kehr S, Bartschat S, Nielsen M, Nielsen RO, Fredholm M, Stadler PF, Gorodkin J.

BMC Genomics. 2014 Jun 10;15:459. doi: 10.1186/1471-2164-15-459.


Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome.

Washietl S, Hofacker IL, Lukasser M, Hüttenhofer A, Stadler PF.

Nat Biotechnol. 2005 Nov;23(11):1383-90.


Detection of RNA structures in porcine EST data and related mammals.

Seemann SE, Gilchrist MJ, Hofacker IL, Stadler PF, Gorodkin J.

BMC Genomics. 2007 Sep 10;8:316.


Identifying structural noncoding RNAs using RNAz.

Washietl S, Hofacker IL.

Curr Protoc Bioinformatics. 2007 Sep;Chapter 12:Unit 12.7. doi: 10.1002/0471250953.bi1207s19.


Identification of expressed and conserved human noncoding RNAs.

Nielsen MM, Tehler D, Vang S, Sudzina F, Hedegaard J, Nordentoft I, Orntoft TF, Lund AH, Pedersen JS.

RNA. 2014 Feb;20(2):236-51. doi: 10.1261/rna.038927.113. Epub 2013 Dec 16.


Structure-based whole-genome realignment reveals many novel noncoding RNAs.

Will S, Yu M, Berger B.

Genome Res. 2013 Jun;23(6):1018-27. doi: 10.1101/gr.137091.111. Epub 2013 Jan 7.


Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.

Howald C, Tanzer A, Chrast J, Kokocinski F, Derrien T, Walters N, Gonzalez JM, Frankish A, Aken BL, Hourlier T, Vogel JH, White S, Searle S, Harrow J, Hubbard TJ, Guigó R, Reymond A.

Genome Res. 2012 Sep;22(9):1698-710. doi: 10.1101/gr.134478.111.


New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes.

Parker BJ, Moltke I, Roth A, Washietl S, Wen J, Kellis M, Breaker R, Pedersen JS.

Genome Res. 2011 Nov;21(11):1929-43. doi: 10.1101/gr.112516.110. Epub 2011 Oct 12.


Computational analysis of functional long noncoding RNAs reveals lack of peptide-coding capacity and parallels with 3' UTRs.

Niazi F, Valadkhan S.

RNA. 2012 Apr;18(4):825-43. doi: 10.1261/rna.029520.111. Epub 2012 Feb 23.


Computational RNomics of drosophilids.

Rose D, Hackermüller J, Washietl S, Reiche K, Hertel J, Findeiss S, Stadler PF, Prohaska SJ.

BMC Genomics. 2007 Nov 8;8:406.


Conserved introns reveal novel transcripts in Drosophila melanogaster.

Hiller M, Findeiss S, Lein S, Marz M, Nickel C, Rose D, Schulz C, Backofen R, Prohaska SJ, Reuter G, Stadler PF.

Genome Res. 2009 Jul;19(7):1289-300. doi: 10.1101/gr.090050.108. Epub 2009 May 20.


Long noncoding intronic RNAs are differentially expressed in primary and metastatic pancreatic cancer.

Tahira AC, Kubrusly MS, Faria MF, Dazzani B, Fonseca RS, Maracaja-Coutinho V, Verjovski-Almeida S, Machado MC, Reis EM.

Mol Cancer. 2011 Nov 13;10:141. doi: 10.1186/1476-4598-10-141.


Mapping of small RNAs in the human ENCODE regions.

Borel C, Gagnebin M, Gehrig C, Kriventseva EV, Zdobnov EM, Antonarakis SE.

Am J Hum Genet. 2008 Apr;82(4):971-81. doi: 10.1016/j.ajhg.2008.02.016.


RNAz 2.0: improved noncoding RNA detection.

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

Pac Symp Biocomput. 2010:69-79.


Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum.

Mourier T, Carret C, Kyes S, Christodoulou Z, Gardner PP, Jeffares DC, Pinches R, Barrell B, Berriman M, Griffiths-Jones S, Ivens A, Newbold C, Pain A.

Genome Res. 2008 Feb;18(2):281-92. Epub 2007 Dec 20.

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