Ivo L Hofacker

Summary

Affiliation: University of Vienna
Country: Austria

Publications

  1. ncbi request reprint How microRNAs choose their targets
    Ivo L Hofacker
    Nat Genet 39:1191-2. 2007
  2. pmc Bcheck: a wrapper tool for detecting RNase P RNA genes
    Dilmurat Yusuf
    Institute for Theoretical Chemistry, University of Vienna, Wahringerstrasse 17, A 1090 Wien, Austria
    BMC Genomics 11:432. 2010
  3. pmc Detection of RNA structures in porcine EST data and related mammals
    Stefan E Seemann
    Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Grønnegårdsvej 3, DK 1870 Frederiksberg, Denmark
    BMC Genomics 8:316. 2007
  4. pmc The expansion of the metazoan microRNA repertoire
    Jana Hertel
    Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstrasse 16 18, D 04107 Leipzig, Germany
    BMC Genomics 7:25. 2006
  5. pmc Hybridization thermodynamics of NimbleGen microarrays
    Ulrike Mueckstein
    WWTF Chair of Bioinformatics, BOKU University Vienna, Muthgasse 18, 1190 Vienna, Austria
    BMC Bioinformatics 11:35. 2010
  6. pmc RNAalifold: improved consensus structure prediction for RNA alignments
    Stephan H Bernhart
    Department of Computer Science, University of Leipzig, Leipzig, Germany
    BMC Bioinformatics 9:474. 2008
  7. pmc Multiple sequence alignments of partially coding nucleic acid sequences
    Roman R Stocsits
    Interdisciplinary Centre for Bioinformatics, University of Leipzig, Haertelstrasse 16 18, D 04107 Leipzig, Germany
    BMC Bioinformatics 6:160. 2005
  8. pmc Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation
    Christian V Forst
    Bioscience Division, Los Alamos National Laboratory, Mailstop M888, PO Box 1663, Los Alamos, NM 87545, USA
    BMC Bioinformatics 7:67. 2006
  9. ncbi request reprint RNAs everywhere: genome-wide annotation of structured RNAs
    Ivo L Hofacker
    Institute for Theoretical Chemistry, University of Vienna, Austria
    Genome Inform 17:281-2. 2006
  10. pmc BarMap: RNA folding on dynamic energy landscapes
    Ivo L Hofacker
    Institute for Theoretical Chemistry, University of Vienna, 1090 Wien, Austria
    RNA 16:1308-16. 2010

Detail Information

Publications66

  1. ncbi request reprint How microRNAs choose their targets
    Ivo L Hofacker
    Nat Genet 39:1191-2. 2007
  2. pmc Bcheck: a wrapper tool for detecting RNase P RNA genes
    Dilmurat Yusuf
    Institute for Theoretical Chemistry, University of Vienna, Wahringerstrasse 17, A 1090 Wien, Austria
    BMC Genomics 11:432. 2010
    ..The core of Bcheck is a library of subfamily specific descriptor models and covariance models...
  3. pmc Detection of RNA structures in porcine EST data and related mammals
    Stefan E Seemann
    Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Grønnegårdsvej 3, DK 1870 Frederiksberg, Denmark
    BMC Genomics 8:316. 2007
    ..To investigate this further, we examined the large data set in the Sino-Danish PigEST resource http://pigest.ku.dk which also contains expression information distributed on 97 non-normalized cDNA libraries...
  4. pmc The expansion of the metazoan microRNA repertoire
    Jana Hertel
    Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstrasse 16 18, D 04107 Leipzig, Germany
    BMC Genomics 7:25. 2006
    ..This allows us to reliably identify microRNA clusters that are derived from a common transcript...
  5. pmc Hybridization thermodynamics of NimbleGen microarrays
    Ulrike Mueckstein
    WWTF Chair of Bioinformatics, BOKU University Vienna, Muthgasse 18, 1190 Vienna, Austria
    BMC Bioinformatics 11:35. 2010
    ..Probe signal is sequence dependent and affected by probe-target binding strength and the competing formation of probe-probe dimers and secondary structures in probes and targets...
  6. pmc RNAalifold: improved consensus structure prediction for RNA alignments
    Stephan H Bernhart
    Department of Computer Science, University of Leipzig, Leipzig, Germany
    BMC Bioinformatics 9:474. 2008
    ..In recent years, several alternative approaches have been advocated, pointing to several shortcomings of the original RNAalifold approach...
  7. pmc Multiple sequence alignments of partially coding nucleic acid sequences
    Roman R Stocsits
    Interdisciplinary Centre for Bioinformatics, University of Leipzig, Haertelstrasse 16 18, D 04107 Leipzig, Germany
    BMC Bioinformatics 6:160. 2005
    ..On the other hand, overlapping reading frames may encode multiple alternative proteins, possibly with intermittent non-coding parts. Examples are, in particular, RNA virus genomes...
  8. pmc Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation
    Christian V Forst
    Bioscience Division, Los Alamos National Laboratory, Mailstop M888, PO Box 1663, Los Alamos, NM 87545, USA
    BMC Bioinformatics 7:67. 2006
    ..This approach disregards functional replacements as well as orthologies that are misannotated. Direct comparison of the structure of metabolic networks can circumvent these problems...
  9. ncbi request reprint RNAs everywhere: genome-wide annotation of structured RNAs
    Ivo L Hofacker
    Institute for Theoretical Chemistry, University of Vienna, Austria
    Genome Inform 17:281-2. 2006
  10. pmc BarMap: RNA folding on dynamic energy landscapes
    Ivo L Hofacker
    Institute for Theoretical Chemistry, University of Vienna, 1090 Wien, Austria
    RNA 16:1308-16. 2010
    ....
  11. ncbi request reprint Prediction of locally stable RNA secondary structures for genome-wide surveys
    I L Hofacker
    Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universitat Wien, Wahringerstrasse 17, Vienna, A 1090, Austria
    Bioinformatics 20:186-90. 2004
    ..Only few techniques are known, however, to survey genomes for such RNA genes. When sufficiently similar sequences are not available for comparative approaches the only known remedy is to search directly for structural features...
  12. ncbi request reprint Conserved RNA secondary structures in viral genomes: a survey
    I L Hofacker
    Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universitat Wien, Wahringerstrasse 17, Vienna, A 1090, Austria
    Bioinformatics 20:1495-9. 2004
    ..Here we present results from pilot studies on a variety of viral families performed during bioinformatics computer lab courses in past years...
  13. pmc Vienna RNA secondary structure server
    Ivo L Hofacker
    Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universitat Wien, Wahringerstrasse 17, A 1090 Wien, Austria
    Nucleic Acids Res 31:3429-31. 2003
    ..All three services can be accessed via the Vienna RNA web server at http://rna.tbi.univie.ac.at/...
  14. ncbi request reprint Alignment of RNA base pairing probability matrices
    Ivo L Hofacker
    Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universitat Wien, Wahringerstrasse 17, Vienna, Austria
    Bioinformatics 20:2222-7. 2004
    ..Since multiple alignments are used as input for many subsequent methods of data analysis, structure-based alignments are an indispensable necessity in RNA bioinformatics...
  15. 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...
  16. 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...
  17. ncbi request reprint Local RNA base pairing probabilities in large sequences
    Stephan H Bernhart
    Institut fur Theoretische Chemie, Universitat Wien, Währingerstr 17, A 1090 Wien, Austria
    Bioinformatics 22:614-5. 2006
    ..Here we present a method for robustly computing the probabilities of local base pairs from long RNA sequences independent of the exact positions of the sequence window...
  18. doi request reprint RNAsnoop: efficient target prediction for H/ACA snoRNAs
    Hakim Tafer
    Institute for Theoretical Chemistry, University of Vienna, Wahringerstrasse 17, A 1090 Vienna, Austria
    Bioinformatics 26:610-6. 2010
    ....
  19. 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...
  20. 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...
  21. ncbi request reprint Thermodynamics of RNA-RNA binding
    Ulrike Mückstein
    Institute for Theoretical Chemistry, University of Vienna Währingerstrasse 17, A 1090 Vienna, Austria
    Bioinformatics 22:1177-82. 2006
    ..The thermodynamics of such RNA-RNA interactions can be understood as the sum of two energy contributions: (1) the energy necessary to 'open' the binding site and (2) the energy gained from hybridization...
  22. ncbi request reprint Prediction of consensus RNA secondary structures including pseudoknots
    Christina Witwer
    Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universitat Wien, Wahringerstrasse 17, A 1090 Wien, Austria
    IEEE/ACM Trans Comput Biol Bioinform 1:66-77. 2004
    ..We applied our algorithm to a number of different types of RNA known to contain pseudoknots. All pseudoknots were predicted correctly and more than 85 percent of the base pairs were identified...
  23. 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...
  24. pmc The Vienna RNA websuite
    Andreas R Gruber
    Institute for Theoretical Chemistry, University of Vienna, Wahringerstrasse 17, 1090 Wien, Austria
    Nucleic Acids Res 36:W70-4. 2008
    ..The web server together with software packages for download is freely accessible at http://rna.tbi.univie.ac.at/...
  25. doi request reprint The impact of target site accessibility on the design of effective siRNAs
    Hakim Tafer
    Institute of Theoretical Biochemistry TBI, University of Vienna, Austria
    Nat Biotechnol 26:578-83. 2008
    ..Overall, RNAxs proves to be a robust siRNA selection tool that substantially improves the prediction of highly efficient siRNAs...
  26. pmc A folding algorithm for extended RNA secondary structures
    Christian Höner zu Siederdissen
    Institute for Theoretical Chemistry, University of Vienna, A 1090 Vienna, Austria
    Bioinformatics 27:i129-36. 2011
    ..Successful prediction of these structural features leads to improved secondary structures with applications in tertiary structure prediction and simultaneous folding and alignment...
  27. pmc Invertebrate 7SK snRNAs
    Andreas R Gruber
    Institute for Theoretical Chemistry, University of Vienna, Wahringerstrasse 17, A 1090 Wien, Austria
    J Mol Evol 66:107-15. 2008
    ..The additional sequence data confirm the evolutionary conservation and hence functional importance of the previously described 3' and 5' stem-loop motifs, and provide evidence for a third, structurally well-conserved domain...
  28. doi request reprint Arthropod 7SK RNA
    Andreas R Gruber
    Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
    Mol Biol Evol 25:1923-30. 2008
    ..Our results demonstrate that a 7SK snRNA featuring 2 highly structured conserved domains was present already in the bilaterian ancestor...
  29. ncbi request reprint Memory efficient folding algorithms for circular RNA secondary structures
    Ivo L Hofacker
    Institute for Theoretical Chemistry, University of Vienna Währingerstr 17, A 1090 Vienna, Austria
    Bioinformatics 22:1172-6. 2006
    ..This is incompatible, however, with the memory-saving approach of the Vienna RNA Package which builds a linear RNA structure from shorter (internal) structures only...
  30. 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...
  31. ncbi request reprint Folding RNA/DNA hybrid duplexes
    Ronny Lorenz
    Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
    Bioinformatics 28:2530-1. 2012
    ..The lack of easy to use tools for predicting their structure may be in part responsible for the small number of reports of biologically relevant RNA/DNA hetero-dimers...
  32. doi request reprint RNA secondary structure analysis using the Vienna RNA package
    Ivo L Hofacker
    University of Vienna, Vienna, Austria
    Curr Protoc Bioinformatics . 2004
    ..Possible tasks include structure prediction for single sequences, prediction of consensus structures, and sequence design...
  33. ncbi request reprint Secondary structure prediction for aligned RNA sequences
    Ivo L Hofacker
    Institut fur Theoretische Chemie, Universitat Wien, Wahringerstrasse 17, Austria
    J Mol Biol 319:1059-66. 2002
    ..As an application we show that the Early Noduline mRNA contains significant secondary structure that is supported by sequence covariation...
  34. ncbi request reprint On the evolution of primitive genetic codes
    Günter Weberndorfer
    Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universitat Wien, Wien, Austria
    Orig Life Evol Biosph 33:491-514. 2003
    ..The driving force behind this effect is the possibility to produce fitter proteins when the repertoire of amino acids is enlarged...
  35. ncbi request reprint Conserved RNA secondary structures in Flaviviridae genomes
    Caroline Thurner
    Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universitat Wien, Wahringerstrasse 17, A 1090 Wien, Austria
    J Gen Virol 85:1113-24. 2004
    ..An electronic atlas organizes the information on the more than 150 conserved, and therefore putatively functional, RNA secondary structure elements...
  36. pmc ViennaRNA Package 2.0
    Ronny Lorenz
    Institute for Theoretical Chemistry and Structural Biology, University of Vienna, Währingerstraße 17 3, A 1090 Vienna, Austria
    Algorithms Mol Biol 6:26. 2011
    ..abstract:..
  37. 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...
  38. doi request reprint From consensus structure prediction to RNA gene finding
    Stephan H Bernhart
    Department of Theoretical Chemistry, University of Vienna, Wahringerstrasse 17, A 1090 Wien, Austria
    Brief Funct Genomic Proteomic 8:461-71. 2009
    ..Here, we review different strategies for the prediction of consensus secondary structures, and show how these approaches can be used to predict non-coding RNA genes...
  39. ncbi request reprint SnoReport: computational identification of snoRNAs with unknown targets
    Jana Hertel
    Institute for Theoretical Chemistry, University of Vienna, Wahringerstrasse 17, A 1090 Wien, Austria
    Bioinformatics 24:158-64. 2008
    ....
  40. pmc Discriminatory power of RNA family models
    Christian Höner zu Siederdissen
    Institute for Theoretical Chemistry, University of Vienna, Wien, Austria
    Bioinformatics 26:i453-9. 2010
    ..We explore the Rfam database to discover such problems...
  41. 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%)...
  42. doi request reprint RNA secondary structure analysis using the Vienna RNA package
    Ivo L Hofacker
    University of Vienna Institute of Theoretical Chemistry, Vienna, Austria
    Curr Protoc Bioinformatics . 2009
    ..Possible tasks include structure prediction for single sequences, prediction of consensus structures, prediction of RNA-RNA interactions, and sequence design...
  43. doi request reprint Designing optimal siRNA based on target site accessibility
    Ivo L Hofacker
    Institute for Theoretical Chemistry, University Vienna, Vienna, Austria
    Methods Mol Biol 623:137-54. 2010
    ..In this chapter, we present the algorithms behind these accessibility-aided tools and show how to design efficient siRNAs with their help...
  44. doi request reprint RNAplex: a fast tool for RNA-RNA interaction search
    Hakim Tafer
    Institute for Theoretical Chemistry, University of Vienna, Wahringerstrasse 17, A 1090 Vienna, Austria
    Bioinformatics 24:2657-63. 2008
    ..Tools like RNAhybrid that neglects intramolecular interactions have runtimes proportional to O(m x n), albeit with a large prefactor. Still in many cases the need for even faster methods exists...
  45. doi request reprint 2D Meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction
    Ronny Lorenz
    University of Vienna, Vienna
    IEEE/ACM Trans Comput Biol Bioinform 10:832-44. 2013
    ..Stable G-quadruplexes are strongly enriched, however, in the 5ʹUTR of protein coding mRNAs. ..
  46. 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...
  47. pmc CMCompare webserver: comparing RNA families via covariance models
    Florian Eggenhofer
    Institute for Theoretical Chemistry, University of Vienna, Wahringerstrasse 17, A 1090 Vienna, Austria
    Nucleic Acids Res 41:W499-503. 2013
    ..The CMCws is freely available, without any login requirements, at http://rna.tbi.univie.ac.at/cmcws, and the underlying software is available under the GPL-3 license. ..
  48. pmc AREsite: a database for the comprehensive investigation of AU-rich elements
    Andreas R Gruber
    Department of Microbiology and Immunobiology, Institute for Theoretical Chemistry, Max F Perutz Laboratories, University of Vienna, Vienna, Austria
    Nucleic Acids Res 39:D66-9. 2011
    ..The database is publicly available at: http://rna.tbi.univie.ac.at/AREsite...
  49. 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...
  50. doi request reprint Computational design of RNAs with complex energy landscapes
    Christian Höner zu Siederdissen
    Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A 1090 Wien, Austria
    Biopolymers 99:1124-36. 2013
    ..RNAdesign is freely available under the GPL-v3 license. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 1124-1136, 2013. ..
  51. pmc RNApredator: fast accessibility-based prediction of sRNA targets
    Florian Eggenhofer
    Institute of Theoretical Chemistry, University of Vienna, Wahringerstrasse 17, A 1090 Vienna, Austria
    Nucleic Acids Res 39:W149-54. 2011
    ..RNApredator is available at http://rna.tbi.univie.ac.at/RNApredator...
  52. doi request reprint Predicting RNA structure: advances and limitations
    Ivo L Hofacker
    Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
    Methods Mol Biol 1086:1-19. 2014
    ..Moreover, we present recent methods to assess the folding kinetics of an RNA via 2D projections of the energy landscape, identification of local minima and energy barriers, or simulation of RNA folding as a Markov process. ..
  53. doi request reprint Automated identification of RNA 3D modules with discriminative power in RNA structural alignments
    Corinna Theis
    Center for non coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Science, University of Copenhagen, Grønnegårdsvej 3, DK 1870 Frederiksberg, Denmark, Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A 1090 Vienna, Austria and Research Group Bioinformatics and Computational Biology, University of Vienna, Währingerstraße 17, A 1090 Vienna, Austria
    Nucleic Acids Res 41:9999-10009. 2013
    ..Indeed, mapping of the modules onto Rfam families results in 35 unique locations in 11 different families. The metaRNAmodules pipeline source for the internal loop modules is available at http://rth.dk/resources/mrm. ..
  54. pmc RNA Accessibility in cubic time
    Stephan H Bernhart
    Theoretical Biochemistry Group, Institute for Theoretical Chemistry, University of Vienna, Wahringerstrasse 17, Vienna, Austria
    Algorithms Mol Biol 6:3. 2011
    ..abstract:..
  55. ncbi request reprint RNA consensus structure prediction with RNAalifold
    Ivo L Hofacker
    Department of Theoretical Chemistry, University of Vienna
    Methods Mol Biol 395:527-44. 2007
    ..In this contribution, we provide a tutorial on how to install and use RNAalifold, as well as a guide on how to interpret the results...
  56. ncbi request reprint Variations on RNA folding and alignment: lessons from Benasque
    Athanasius F Bompfünewerer
    Zentralfriedhof Wien, 3 Tor Simmeringer Haupstrasse, Wien, Austria
    J Math Biol 56:129-44. 2008
    ..Furthermore, we demonstrate that a local structural alignment can be employed for ncRNA gene finding. In this context we discuss scanning variants for folding and alignment algorithms...
  57. 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...
  58. ncbi request reprint Structural and evolutionary analysis of the transcribed sequence of Boudicca, a Schistosoma mansoni retrotransposon
    Claudia S Copeland
    Department of Molecular Parasitology, Institute for Biology, Humboldt University Berlin, Berlin, Germany
    Gene 329:103-14. 2004
    ..In addition, phylogenetic analysis targeting discrete domains of Boudicca revealed a generalized radiation in sequences among the multiple copies of Boudicca resident in the schistosome genome...
  59. ncbi request reprint RNA maps reveal new RNA classes and a possible function for pervasive transcription
    Philipp Kapranov
    Affymetrix Laboratory, Affymetrix, Inc, 3420 Central Expressway, Santa Clara, CA, 95051, USA
    Science 316:1484-8. 2007
    ..These data support a highly interleaved organization of the human transcriptome...
  60. 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...
  61. pmc Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering
    Sebastian Will
    Bioinformatics Group, Institute of Computer Science, University of Freiburg, Freiburg, Germany
    PLoS Comput Biol 3:e65. 2007
    ....
  62. ncbi request reprint RNAs everywhere: genome-wide annotation of structured RNAs
    Rolf Backofen
    Bioinformatics Group, Department of Computer Science, University of Freiburg, D 79110 Freiburg, Germany
    J Exp Zool B Mol Dev Evol 308:1-25. 2007
    ..A series of exploratory studies are used to provide non-trivial examples for the discussion of some of the difficulties...
  63. ncbi request reprint Visualization of barrier tree sequences
    Christian Heine
    Image and Signal Processing Group, Department of Computer Science, University of Leipzig
    IEEE Trans Vis Comput Graph 12:781-8. 2006
    ..Since it is very general, we give a detailed description of each phase: constructing a supergraph for the trees, layout of that supergraph using a modified DoT algorithm, and presentation techniques for the final animation...
  64. pmc Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis
    Christoph Jöchl
    Innsbruck Biocenter, Division of Genomics and RNomics Innsbruck Medical University, Fritz Pregl Strasse 3, 6020 Innsbruck, Austria
    Nucleic Acids Res 36:2677-89. 2008
    ..Since conidia represent the resting state of A. fumigatus we propose that conidial tRNA depletion might be a novel mechanism to down-regulate protein synthesis in a filamentous fungus...
  65. pmc Unorthodox mRNA start site to extend the highly structured leader of retrotransposon Tto1 mRNA increases transposition rate
    Gudrun Böhmdorfer
    Max Planck Institute for Plant Breeding Research, Carlvon Linné Weg 10, D 50829 Cologne, Germany
    RNA 11:1181-91. 2005
    ....
  66. pmc miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes
    Paul W C Hsu
    Institute of Bioinformatics, National Chiao Tung University, Hsin Chu 300, Taiwan, ROC
    Nucleic Acids Res 34:D135-9. 2006
    ..Both textual and graphical web interface are provided to facilitate the retrieval of data from the miRNAMap. The database is freely available at http://mirnamap.mbc.nctu.edu.tw/...