Stefan Washietl

Summary

Affiliation: University of Vienna
Country: Austria

Publications

  1. pmc The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures
    Andreas R Gruber
    Institute for Theoretical Chemistry, University of Vienna, Wahringerstrasse 17, 1090 Vienna, Austria
    Nucleic Acids Res 35:W335-8. 2007
  2. pmc Computational RNomics of drosophilids
    Dominic Rose
    Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstrasse 16 18, Leipzig, Germany
    BMC Genomics 8:406. 2007
  3. pmc 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
    Stefan Washietl
    Research Institute of Molecular Pathology, Dr, Bohrgasse 7, A 1030 Vienna, Austria
    BMC Bioinformatics 4:55. 2003
  4. pmc Structured RNAs in the ENCODE selected regions of the human genome
    Stefan Washietl
    Institute for Theoretical Chemistry, University of Vienna, A 1090 Wien, Austria
    Genome Res 17:852-64. 2007
  5. ncbi request reprint Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome
    Stefan Washietl
    Institute for Theoretical Chemistry, University of Vienna, Wahringerstrasse 17, 1090 Vienna, Austria
    Nat Biotechnol 23:1383-90. 2005
  6. doi request reprint Sequence and structure analysis of noncoding RNAs
    Stefan Washietl
    Department of Theoretical Chemistry, University of Vienna, Vienna, Wien, Austria
    Methods Mol Biol 609:285-306. 2010
  7. ncbi request reprint Identifying structural noncoding RNAs using RNAz
    Stefan Washietl
    University of Vienna, Vienna, Austria
    Curr Protoc Bioinformatics . 2007
  8. pmc Strategies for measuring evolutionary conservation of RNA secondary structures
    Andreas R Gruber
    Institute for Theoretical Chemistry, University of Vienna, Wahringerstrasse 17, 1090 Wien, Austria
    BMC Bioinformatics 9:122. 2008
  9. pmc Fast and reliable prediction of noncoding RNAs
    Stefan Washietl
    Department of Theoretical Chemistry and Structural Biology, University of Vienna, Wahringerstrasse 17, A 1090 Wien, Austria
    Proc Natl Acad Sci U S A 102:2454-9. 2005
  10. pmc Dinucleotide controlled null models for comparative RNA gene prediction
    Tanja Gesell
    Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, Dr Bohr Gasse 9, A 1030 Vienna, Austria
    BMC Bioinformatics 9:248. 2008

Detail Information

Publications22

  1. pmc The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures
    Andreas 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...
  2. pmc Computational RNomics of drosophilids
    Dominic 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...
  3. pmc 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
    Stefan 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...
  4. pmc Structured RNAs in the ENCODE selected regions of the human genome
    Stefan 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%)...
  5. ncbi request reprint Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome
    Stefan Washietl
    Institute for Theoretical Chemistry, University of Vienna, Wahringerstrasse 17, 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...
  6. doi request reprint Sequence and structure analysis of noncoding RNAs
    Stefan Washietl
    Department of Theoretical Chemistry, University of Vienna, Vienna, Wien, Austria
    Methods Mol Biol 609:285-306. 2010
    ....
  7. ncbi request reprint Identifying structural noncoding RNAs using RNAz
    Stefan 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...
  8. pmc Strategies for measuring evolutionary conservation of RNA secondary structures
    Andreas 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...
  9. pmc Fast and reliable prediction of noncoding RNAs
    Stefan Washietl
    Department of Theoretical Chemistry and Structural Biology, University of Vienna, Wahringerstrasse 17, 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...
  10. pmc Dinucleotide controlled null models for comparative RNA gene prediction
    Tanja 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...
  11. ncbi request reprint Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics
    Stefan Washietl
    Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universitat Wien, Wahringerstrasse 17, A 1090, Austria
    J Mol Biol 342:19-30. 2004
    ..Most RNAs can be detected with high significance. We provide a Perl implementation that can be used readily to score single alignments and discuss how the methods described here can be extended to allow for efficient genome-wide screens...
  12. doi request reprint Nucleic acid sequence and structure databases
    Stefan 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...
  13. ncbi request reprint Protein prenyltransferases: anchor size, pseudogenes and parasites
    Sebastian Maurer-Stroh
    Research Institute of Molecular Pathology, Dr Bohr Gasse 7, A 1030 Vienna, Austria
    Biol Chem 384:977-89. 2003
    ....
  14. doi request reprint Nematode sbRNAs: homologs of vertebrate Y RNAs
    Ilenia 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...
  15. ncbi request reprint Evolution of microRNAs
    Andrea 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...
  16. pmc Protein prenyltransferases
    Sebastian 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...
  17. pmc RNPomics: defining the ncRNA transcriptome by cDNA library generation from ribonucleo-protein particles
    Mathieu 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...
  18. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
  19. pmc Paired-end mapping reveals extensive structural variation in the human genome
    Jan 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...
  20. doi request reprint Folding kinetics of large RNAs
    Michael 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...
  21. pmc Comparative promoter region analysis powered by CORG
    Christoph 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)...
  22. ncbi request reprint Evolution of microRNAs located within Hox gene clusters
    Andrea 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...