Research Topics
Species | Stefan WashietlSummaryAffiliation: University of Vienna Country: Austria Publications
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Detail Information
Publications
Computational RNomics of drosophilidsDominic Rose
Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstrasse 16 18, Leipzig, Germany
BMC Genomics 8:406. 2007..This class of loci includes the majority of the known small ncRNAs as well as structured RNA motifs in mRNAs. We report here on a genome-wide survey using RNAz...- Structured RNAs in the ENCODE selected regions of the human genomeStefan Washietl
Institute for Theoretical Chemistry, University of Vienna, A 1090 Wien, Austria
Genome Res 17:852-64. 2007..One hundred seventy-five selected candidates were tested by RT-PCR in six tissues, and expression could be verified in 43 cases (24.6%)... - Reannotation of the CELO genome characterizes a set of previously unassigned open reading frames and points to novel modes of host interaction in avian adenovirusesStefan Washietl
Research Institute of Molecular Pathology, Dr, Bohrgasse 7, A 1030 Vienna, Austria
BMC Bioinformatics 4:55. 2003..We conducted a systematic reannotation and in-depth sequence analysis of the CELO genome... - The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structuresAndreas R Gruber
Institute for Theoretical Chemistry, University of Vienna, Wahringerstrasse 17, 1090 Vienna, Austria
Nucleic Acids Res 35:W335-8. 2007..Results are presented on a website that is illustrated by various structure representations and can be downloaded for local view. The web server is available at: rna.tbi.univie.ac.at/RNAz... 
Sequence and structure analysis of noncoding RNAsStefan Washietl
Department of Theoretical Chemistry, University of Vienna, Vienna, Wien, Austria
Methods Mol Biol 609:285-306. 2010....- Strategies for measuring evolutionary conservation of RNA secondary structuresAndreas R Gruber
Institute for Theoretical Chemistry, University of Vienna, Wahringerstrasse 17, 1090 Wien, Austria
BMC Bioinformatics 9:122. 2008..Since almost all of the available methods used for prediction and annotation of non-coding RNA genes rely on this evolutionary signature, accurate measures for structural conservation are essential... 
Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genomeStefan Washietl
Institute for Theoretical Chemistry, University of Vienna, , 1090 Vienna, Austria
Nat Biotechnol 23:1383-90. 2005..The widespread conservation of secondary structure points to a large number of functional ncRNAs and cis-acting mRNA structures in the human genome...- Identifying structural noncoding RNAs using RNAzStefan Washietl
University of Vienna, Vienna, Austria
Curr Protoc Bioinformatics . 2007..It can be used to efficiently filter multiple alignments for noncoding RNA candidates in genomic screens... - Dinucleotide controlled null models for comparative RNA gene predictionTanja Gesell
Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, Dr Bohr Gasse 9, A 1030 Vienna, Austria
BMC Bioinformatics 9:248. 2008..While there have been randomization algorithms for single sequences for many years, the problem has remained challenging for multiple alignments and there is currently no algorithm available... - Nucleic acid sequence and structure databasesStefan Washietl
Department of Theoretical Chemistry, University of Vienna, Wien, Austria
Methods Mol Biol 609:3-15. 2010..We cover general sequence databases, databases for specific DNA features, noncoding RNA sequences, and RNA secondary and tertiary structures... - Protein prenyltransferases: anchor size, pseudogenes and parasitesSebastian Maurer-Stroh
Research Institute of Molecular Pathology, Dr Bohr Gasse 7, A 1030 Vienna, Austria
Biol Chem 384:977-89. 2003.... - Nematode sbRNAs: homologs of vertebrate Y RNAsIlenia Boria
Department of Medical Sciences and Interdisciplinary Research Centre for Autoimmune Diseases, Universita del Piemonte Orientale, Via Solaroli 17, 28100 Novara, Italy
J Mol Evol 70:346-58. 2010..The single Y RNA that was previously described in C. elegans, however, does not show this motif, and in general bears the hallmarks of a highly derived family member... - Evolution of microRNAsAndrea Tanzer
Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
Methods Mol Biol 342:335-50. 2006..Some miRNAs are transcribed from polycistronic primary transcripts. In these cases, we will study the evolution of entire clusters... - Fast and reliable prediction of noncoding RNAsStefan Washietl
Department of Theoretical Chemistry and Structural Biology, University of Vienna, , A-1090 Wien, Austria
Proc Natl Acad Sci U S A 102:2454-9. 2005..We recovered all of the known noncoding RNAs and cis-acting elements with high significance and found compelling evidence for many other conserved RNA secondary structures not described so far to our knowledge... - Protein prenyltransferasesSebastian Maurer-Stroh
Research Institute of Molecular Pathology, Dr Bohr Gasse 7, A 1030 Vienna, Austria
Genome Biol 4:212. 2003..The effects of these inhibitors are complicated, however, by the overlapping substrate specificities of geranylgeranyltransferase I and farnesyltransferase... - RNPomics: defining the ncRNA transcriptome by cDNA library generation from ribonucleo-protein particlesMathieu Rederstorff
Division of Genomics and RNomics, Innsbruck Biocentre, Innsbruck Medical University, Innsbruck and Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria
Nucleic Acids Res 38:e113. 2010..Additionally, a number of ncRNAs mapped to repetitive sequences. Thus, our RNP approach provides an efficient way to identify new functional small ncRNA candidates, involved in RNP formation... - Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot projectEwan Birney
Nature 447:799-816. 2007..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function... - Paired-end mapping reveals extensive structural variation in the human genomeJan O Korbel
Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA
Science 318:420-6. 2007..The breakpoint junction sequences of more than 200 SVs were determined with a novel pooling strategy and computational analysis. Our analysis provided insights into the mechanisms of SV formation in humans... - Folding kinetics of large RNAsMichael Geis
Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16 18, 04107 Leipzig, Germany
J Mol Biol 379:160-73. 2008..The software is available as part of the ViennaRNA Package... - Comparative promoter region analysis powered by CORGChristoph Dieterich
Computational Molecular Biology Department, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
BMC Genomics 6:24. 2005..To support promoter analysis, we present CORG http://corg.molgen.mpg.de, a framework for studying upstream regions including untranslated exons (5' UTR)... - Evolution of microRNAs located within Hox gene clustersAndrea Tanzer
Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Kreuzstrasse 7b, D 04103 Leipzig, Germany
J Exp Zool B Mol Dev Evol 304:75-85. 2005..Here we describe their evolution in detail. We show that the micro RNAs closely follow the patterns of protein evolution in the Hox clusters, which is characterized by cluster duplications followed by differential gene loss...