Stefan Washietl - Publications

Affiliations: 
Massachusetts Institute of Technology, Cambridge, MA, United States 

20 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, 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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
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  0.32
2003 Maurer-Stroh S, Washietl S, Eisenhaber F. Protein prenyltransferases. Genome Biology. 4: 212. PMID 12702202 DOI: 10.1186/gb-2003-4-4-212  0.32
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