Year |
Citation |
Score |
2014 |
Washietl S, Bernhart SH, Kellis M. Energy-based RNA consensus secondary structure prediction in multiple sequence alignments. Methods in Molecular Biology (Clifton, N.J.). 1097: 125-41. PMID 24639158 DOI: 10.1007/978-1-62703-709-9_7 |
0.627 |
|
2014 |
Washietl S, Kellis M, Garber M. Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals. Genome Research. 24: 616-28. PMID 24429298 DOI: 10.1101/Gr.165035.113 |
0.638 |
|
2014 |
Rouskin S, Zubradt M, Washietl S, Kellis M, Weissman JS. Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Nature. 505: 701-5. PMID 24336214 DOI: 10.1038/Nature12894 |
0.638 |
|
2012 |
Washietl S, Will S, Hendrix DA, Goff LA, Rinn JL, Berger B, Kellis M. Computational analysis of noncoding RNAs. Wiley Interdisciplinary Reviews. Rna. 3: 759-78. PMID 22991327 DOI: 10.1002/Wrna.1134 |
0.76 |
|
2012 |
Washietl S, Hofacker IL, Stadler PF, Kellis M. RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction. Nucleic Acids Research. 40: 4261-72. PMID 22287623 DOI: 10.1093/Nar/Gks009 |
0.508 |
|
2011 |
Parker BJ, Moltke I, Roth A, Washietl S, Wen J, Kellis M, Breaker R, Pedersen JS. New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes. Genome Research. 21: 1929-43. PMID 21994249 DOI: 10.1101/Gr.112516.110 |
0.69 |
|
2011 |
Lin MF, Kheradpour P, Washietl S, Parker BJ, Pedersen JS, Kellis M. Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes. Genome Research. 21: 1916-28. PMID 21994248 DOI: 10.1101/Gr.108753.110 |
0.802 |
|
2011 |
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, et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 478: 476-82. PMID 21993624 DOI: 10.1038/Nature10530 |
0.693 |
|
2011 |
Washietl S, Findeiss S, Müller SA, Kalkhof S, von Bergen M, Hofacker IL, Stadler PF, Goldman N. RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. Rna (New York, N.Y.). 17: 578-94. PMID 21357752 DOI: 10.1261/Rna.2536111 |
0.533 |
|
2010 |
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, et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (New York, N.Y.). 330: 1787-97. PMID 21177974 DOI: 10.1126/Science.1198374 |
0.564 |
|
2010 |
Müller SA, Kohajda T, Findeiss S, Stadler PF, Washietl S, Kellis M, von Bergen M, Kalkhof S. Optimization of parameters for coverage of low molecular weight proteins. Analytical and Bioanalytical Chemistry. 398: 2867-81. PMID 20803007 DOI: 10.1007/S00216-010-4093-X |
0.475 |
|
2010 |
Washietl S. Sequence and structure analysis of noncoding RNAs. Methods in Molecular Biology (Clifton, N.J.). 609: 285-306. PMID 20221926 DOI: 10.1007/978-1-60327-241-4_17 |
0.516 |
|
2010 |
Washietl S, Hofacker IL. Nucleic acid sequence and structure databases. Methods in Molecular Biology (Clifton, N.J.). 609: 3-15. PMID 20221910 DOI: 10.1007/978-1-60327-241-4_1 |
0.468 |
|
2010 |
Gruber AR, Findeiß S, Washietl S, Hofacker IL, Stadler PF. RNAz 2.0: improved noncoding RNA detection. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 69-79. PMID 19908359 |
0.395 |
|
2008 |
Washietl S, Machné R, Goldman N. Evolutionary footprints of nucleosome positions in yeast. Trends in Genetics : Tig. 24: 583-7. PMID 18951646 DOI: 10.1016/J.Tig.2008.09.003 |
0.457 |
|
2008 |
Gesell T, Washietl S. Dinucleotide controlled null models for comparative RNA gene prediction. Bmc Bioinformatics. 9: 248. PMID 18505553 DOI: 10.1186/1471-2105-9-248 |
0.533 |
|
2008 |
Gruber AR, Bernhart SH, Hofacker IL, Washietl S. Strategies for measuring evolutionary conservation of RNA secondary structures. Bmc Bioinformatics. 9: 122. PMID 18302738 DOI: 10.1186/1471-2105-9-122 |
0.504 |
|
2007 |
Washietl S, Hofacker IL. Identifying structural noncoding RNAs using RNAz. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 12.7. PMID 18428784 DOI: 10.1002/0471250953.Bi1207S19 |
0.564 |
|
2007 |
Rose D, Hackermüller J, Washietl S, Reiche K, Hertel J, Findeiss S, Stadler PF, Prohaska SJ. Computational RNomics of drosophilids. Bmc Genomics. 8: 406. PMID 17996037 DOI: 10.1186/1471-2164-8-406 |
0.641 |
|
2007 |
Washietl S. Prediction of structural noncoding RNAs with RNAz. Methods in Molecular Biology (Clifton, N.J.). 395: 503-26. PMID 17993695 DOI: 10.1007/978-1-59745-514-5_32 |
0.531 |
|
2007 |
Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Washietl S, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874 |
0.707 |
|
2007 |
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, et al. Structured RNAs in the ENCODE selected regions of the human genome. Genome Research. 17: 852-64. PMID 17568003 DOI: 10.1101/Gr.5650707 |
0.623 |
|
2007 |
Gruber AR, Neuböck R, Hofacker IL, Washietl S. The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures. Nucleic Acids Research. 35: W335-8. PMID 17452347 DOI: 10.1093/Nar/Gkm222 |
0.569 |
|
2007 |
Backofen R, Bernhart SH, Flamm C, Fried C, Fritzsch G, Hackermüller J, Hertel J, Hofacker IL, Missal K, Mosig A, Prohaska SJ, Rose D, Stadler PF, Tanzer A, ... Washietl S, et al. RNAs everywhere: genome-wide annotation of structured RNAs. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 308: 1-25. PMID 17171697 DOI: 10.1002/Jez.B.21130 |
0.59 |
|
2006 |
Hsu PW, Huang HD, Hsu SD, Lin LZ, Tsou AP, Tseng CP, Stadler PF, Washietl S, Hofacker IL. miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. Nucleic Acids Research. 34: D135-9. PMID 16381831 DOI: 10.1093/Nar/Gkj135 |
0.347 |
|
2005 |
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. Evolutionary patterns of non-coding RNAs. Theory in Biosciences = Theorie in Den Biowissenschaften. 123: 301-69. PMID 18202870 DOI: 10.1016/J.Thbio.2005.01.002 |
0.492 |
|
2005 |
Washietl S, Hofacker IL, Lukasser M, Hüttenhofer A, Stadler PF. Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nature Biotechnology. 23: 1383-90. PMID 16273071 DOI: 10.1038/Nbt1144 |
0.681 |
|
2005 |
Gardner PP, Wilm A, Washietl S. A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Research. 33: 2433-9. PMID 15860779 DOI: 10.1093/Nar/Gki541 |
0.407 |
|
2005 |
Washietl S, Hofacker IL, Stadler PF. Fast and reliable prediction of noncoding RNAs. Proceedings of the National Academy of Sciences of the United States of America. 102: 2454-9. PMID 15665081 DOI: 10.1073/Pnas.0409169102 |
0.588 |
|
2004 |
Washietl S, Hofacker IL. Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. Journal of Molecular Biology. 342: 19-30. PMID 15313604 DOI: 10.1016/J.Jmb.2004.07.018 |
0.594 |
|
2003 |
Washietl S, Eisenhaber F. Reannotation of the CELO genome characterizes a set of previously unassigned open reading frames and points to novel modes of host interaction in avian adenoviruses. Bmc Bioinformatics. 4: 55. PMID 14604445 DOI: 10.1186/1471-2105-4-55 |
0.469 |
|
2003 |
Maurer-Stroh S, Washietl S, Eisenhaber F. Protein prenyltransferases: anchor size, pseudogenes and parasites. Biological Chemistry. 384: 977-89. PMID 12956414 DOI: 10.1515/Bc.2003.110 |
0.35 |
|
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