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24 result(s) for 'author#Ivo L Hofacker' within BMC

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  1. The accessibility of RNA binding motifs controls the efficacy of many biological processes. Examples are the binding of miRNA, siRNA or bacterial sRNA to their respective targets. Similarly, the accessibility ...

    Authors: Stephan H Bernhart, Ullrike Mückstein and Ivo L Hofacker
    Citation: Algorithms for Molecular Biology 2011 6:3
  2. The prediction of a consensus structure for a set of related RNAs is an important first step for subsequent analyses. RNAalifold, which computes the minimum energy structure that is simultaneously formed by a ...

    Authors: Stephan H Bernhart, Ivo L Hofacker, Sebastian Will, Andreas R Gruber and Peter F Stadler
    Citation: BMC Bioinformatics 2008 9:474
  3. In the last few decades there has been a great deal of discussion concerning whether or not noncoding RNA sequences (ncRNAs) fold in a more well-defined manner than random sequences. In this paper, we investig...

    Authors: Eva Freyhult, Paul P Gardner and Vincent Moulton
    Citation: BMC Bioinformatics 2005 6:241
  4. RNA has been recognized as a key player in cellular regulation in recent years. In many cases, non-coding RNAs exert their function by binding to other nucleic acids, as in the case of microRNAs and snoRNAs. T...

    Authors: Stephan H Bernhart, Hakim Tafer, Ulrike Mückstein, Christoph Flamm, Peter F Stadler and Ivo L Hofacker
    Citation: Algorithms for Molecular Biology 2006 1:3
  5. Secondary structure forms an important intermediate level of description of nucleic acids that encapsulates the dominating part of the folding energy, is often well conserved in evolution, and is routinely use...

    Authors: Ronny Lorenz, Stephan H Bernhart, Christian Höner zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F Stadler and Ivo L Hofacker
    Citation: Algorithms for Molecular Biology 2011 6:26
  6. Evolutionary conservation of RNA secondary structure is a typical feature of many functional non-coding RNAs. Since almost all of the available methods used for prediction and annotation of non-coding RNA gene...

    Authors: Andreas R Gruber, Stephan H Bernhart, Ivo L Hofacker and Stefan Washietl
    Citation: BMC Bioinformatics 2008 9:122
  7. A large class of RNA secondary structure prediction programs uses an elaborate energy model grounded in extensive thermodynamic measurements and exact dynamic programming algorithms. External experimental evid...

    Authors: Ronny Lorenz, Ivo L. Hofacker and Peter F. Stadler
    Citation: Algorithms for Molecular Biology 2016 11:8
  8. MicroRNAs have been identified as crucial regulators in both animals and plants. Here we report on a comprehensive comparative study of all known miRNA families in animals. We expand the MicroRNA Registry 6.0 ...

    Authors: Jana Hertel, Manuela Lindemeyer, Kristin Missal, Claudia Fried, Andrea Tanzer, Christoph Flamm, Ivo L Hofacker and Peter F Stadler
    Citation: BMC Genomics 2006 7:25
  9. Differential RNA sequencing (dRNA-seq) is a high-throughput screening technique designed to examine the architecture of bacterial operons in general and the precise position of transcription start sites (TSS) ...

    Authors: Fabian Amman, Michael T Wolfinger, Ronny Lorenz, Ivo L Hofacker, Peter F Stadler and Sven Findeiß
    Citation: BMC Bioinformatics 2014 15:89
  10. Non-coding RNAs (ncRNAs) are involved in a wide spectrum of regulatory functions. Within recent years, there have been increasing reports of observed polyadenylated ncRNAs and mRNA like ncRNAs in eukaryotes. T...

    Authors: Stefan E Seemann, Michael J Gilchrist, Ivo L Hofacker, Peter F Stadler and Jan Gorodkin
    Citation: BMC Genomics 2007 8:316
  11. Effective bioinformatics solutions are needed to tackle challenges posed by industrial-scale genome annotation. We present Bcheck, a wrapper tool which predicts RNase P RNA genes by combining the speed of pattern...

    Authors: Dilmurat Yusuf, Manja Marz, Peter F Stadler and Ivo L Hofacker
    Citation: BMC Genomics 2010 11:432
  12. Comparison of metabolic networks is typically performed based on the organisms' enzyme contents. This approach disregards functional replacements as well as orthologies that are misannotated. Direct comparison...

    Authors: Christian V Forst, Christoph Flamm, Ivo L Hofacker and Peter F Stadler
    Citation: BMC Bioinformatics 2006 7:67
  13. The quality of progressive sequence alignments strongly depends on the accuracy of the individual pairwise alignment steps since gaps that are introduced at one step cannot be removed at later aggregation step...

    Authors: Matthias Kruspe and Peter F Stadler
    Citation: BMC Bioinformatics 2007 8:254
  14. Genomic studies have greatly expanded our knowledge of structural non-coding RNAs (ncRNAs). These RNAs fold into characteristic secondary structures and perform specific-structure dependent biological function...

    Authors: Avinash Achar and Pål Sætrom
    Citation: Biology Direct 2015 10:61