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Items: 1 to 20 of 33

1.

Energy-based RNA consensus secondary structure prediction in multiple sequence alignments.

Washietl S, Bernhart SH, Kellis M.

Methods Mol Biol. 2014;1097:125-41. doi: 10.1007/978-1-62703-709-9_7. Review.

PMID:
24639158
2.

Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals.

Washietl S, Kellis M, Garber M.

Genome Res. 2014 Apr;24(4):616-28. doi: 10.1101/gr.165035.113. Epub 2014 Jan 15.

3.

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo.

Rouskin S, Zubradt M, Washietl S, Kellis M, Weissman JS.

Nature. 2014 Jan 30;505(7485):701-5. doi: 10.1038/nature12894. Epub 2013 Dec 15.

4.

Computational analysis of noncoding RNAs.

Washietl S, Will S, Hendrix DA, Goff LA, Rinn JL, Berger B, Kellis M.

Wiley Interdiscip Rev RNA. 2012 Nov-Dec;3(6):759-78. doi: 10.1002/wrna.1134. Epub 2012 Sep 18. Review.

5.

RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction.

Washietl S, Hofacker IL, Stadler PF, Kellis M.

Nucleic Acids Res. 2012 May;40(10):4261-72. doi: 10.1093/nar/gks009. Epub 2012 Jan 28.

6.

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.

7.

Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes.

Lin MF, Kheradpour P, Washietl S, Parker BJ, Pedersen JS, Kellis M.

Genome Res. 2011 Nov;21(11):1916-28. doi: 10.1101/gr.108753.110. Epub 2011 Oct 12.

8.

A high-resolution map of human evolutionary constraint using 29 mammals.

Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC; Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA; Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK; Genome Institute at Washington University, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M.

Nature. 2011 Oct 12;478(7370):476-82. doi: 10.1038/nature10530.

9.

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.

Washietl S, Findeiss S, Müller SA, Kalkhof S, von Bergen M, Hofacker IL, Stadler PF, Goldman N.

RNA. 2011 Apr;17(4):578-94. doi: 10.1261/rna.2536111. Epub 2011 Feb 28.

10.

Identification of functional elements and regulatory circuits by Drosophila modENCODE.

modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M.

Science. 2010 Dec 24;330(6012):1787-97. doi: 10.1126/science.1198374. Epub 2010 Dec 22.

11.

Optimization of parameters for coverage of low molecular weight proteins.

Müller SA, Kohajda T, Findeiss S, Stadler PF, Washietl S, Kellis M, von Bergen M, Kalkhof S.

Anal Bioanal Chem. 2010 Dec;398(7-8):2867-81. doi: 10.1007/s00216-010-4093-x. Epub 2010 Aug 28.

12.

Sequence and structure analysis of noncoding RNAs.

Washietl S.

Methods Mol Biol. 2010;609:285-306. doi: 10.1007/978-1-60327-241-4_17. Review.

PMID:
20221926
13.

Nucleic acid sequence and structure databases.

Washietl S, Hofacker IL.

Methods Mol Biol. 2010;609:3-15. doi: 10.1007/978-1-60327-241-4_1. Review.

PMID:
20221910
14.

RNAz 2.0: improved noncoding RNA detection.

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

Pac Symp Biocomput. 2010:69-79.

15.

Evolutionary footprints of nucleosome positions in yeast.

Washietl S, Machné R, Goldman N.

Trends Genet. 2008 Dec;24(12):583-7. doi: 10.1016/j.tig.2008.09.003. Epub 2008 Oct 24.

PMID:
18951646
16.

Dinucleotide controlled null models for comparative RNA gene prediction.

Gesell T, Washietl S.

BMC Bioinformatics. 2008 May 27;9:248. doi: 10.1186/1471-2105-9-248.

17.

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.

PMID:
18428784
18.

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.

19.

Evolutionary patterns of non-coding RNAs.

Bompfünewerer AF, Flamm C, Fried C, Fritzsch G, Hofacker IL, Lehmann J, Missal K, Mosig A, Müller B, Prohaska SJ, Stadler BM, Stadler PF, Tanzer A, Washietl S, Witwer C.

Theory Biosci. 2005 Apr;123(4):301-69. doi: 10.1016/j.thbio.2005.01.002.

PMID:
18202870
20.

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.

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