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Stefan Washietl - Publications

Affiliations: 
Massachusetts Institute of Technology, Cambridge, MA, United States 
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32 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

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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