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Auflistung nach Autor:in "Backofen, Rolf"

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  • Zeitschriftenartikel
    Bioinformatik
    (Informatik-Spektrum: Vol. 22, No. 5, 1999) Backofen, Rolf; Bry, François; Clote, Peter; Kriegel, Hans-Peter; Seidl, Thomas; Schulz, Klaus
  • Konferenzbeitrag
    Blockclust: efficient clustering and classification of non-coding rnas from short Read RNA-seq profiles
    (German conference on bioinformatics 2014, 2014) Videm, Pavankumar; Rose, Dominic; Costa, Fabrizio; Backofen, Rolf
    Sequence and secondary structure analysis can be used to assign putative functions to non-coding RNAs. However sequence information is changed by post-transcriptional modifications and secondary structure is only a proxy for the true 3D conformation of the RNA polymer. In order to tackle these issues we can extract a different type of description using the pattern of processing that can be observed through the traces left in small RNA-seq reads data. To obtain an efficient and scalable procedure, we propose to encode expression profiles in discrete structures, and process them using fast graph-kernel techniques.
  • Konferenzbeitrag
    Feature based representation and detection of transcription factor binding sites
    (German Conference on Bioinformatics 2004, GCB 2004, 2004) Pudimat, Rainer; Schukat-Talamazzini, Ernst-Günter; Backofen, Rolf
    The prediction of transcription factor binding sites is an important problem, since it reveals information about the transcriptional regulation of genes. A commonly used representation of these sites are position specific weight matrices which show weak predictive power. We introduce a feature-based modelling approach, which is able to deal with various kind of biological properties of binding sites and models them via Bayesian belief networks. The presented results imply higher model accuracy in contrast to the PSSM approach.
  • Konferenzbeitrag
    Lightweight Comparison of RNAs Based on Exact Sequence-Structure Matches
    (German Conference on Bioinformatics, 2008) Heyne, Steffen; Will, Sebastian; Beckstette, Michael; Backofen, Rolf
    Specific functions of RNA molecules are often associated with different motifs in the RNA structure. The key feature that forms such an RNA motif is the combination of sequence and structure properties. In this paper we introduce a new RNA sequence-structure comparison method which maintains exact matching substructures. Existing common substructures are treated as whole unit while variability is allowed between such structural mo- tifs. Based on a fast detectable set of overlapping and crossing substructure matches for two nested RNA secondary structures, our method computes the longest colinear sequence of substructures common to two RNAs in O(n2m2) time and O(nm) space. Applied to different RNAs, our method correctly identifies sequence-structure similarities between two RNAs. The results of our experiments are in good agreement with existing alignment-based meth- ods, but can be obtained in a fraction of running time, in particular for larger RNAs. The proposed algorithm is implemented in the program expaRNA, which is available from our website (www.bioinf.uni-freiburg.de/Software).
  • Konferenzbeitrag
    Shape-based barrier estimation for RNAs
    (German Conference on Bioinformatics 2010, 2010) Bogomolov, Sergiy; Mann, Martin; Voß, Björn; Podelski, Andreas; Backofen, Rolf
    The ability of some RNA molecules to switch between different metastable conformations plays an important role in cellular processes. In order to identify such molecules and to predict their conformational changes one has to investigate the refolding pathways. As a qualitative measure of these transitions, the barrier height marks the energy peak along such refolding paths. We introduce a meta-heuristic to estimate such barriers, which is an NP-complete problem. To guide an arbitrary path heuristic, the method uses RNA shape representative structures as intermediate checkpoints for detours. This enables a broad but efficient search for refolding pathways. The resulting Shape Triples meta-heuristic enables a close to optimal estimation of the barrier height that outperforms the precision of the employed path heuristic.
  • Konferenzbeitrag
    Structure Local Multiple Alignment of RNA
    (German Conference on Bioinformatics, 2008) Otto, Wolfgang; Will, Sebastian; Backofen, Rolf
    Today, RNA is well known to perform important regulatory and catalytic function due to its distinguished structure. Consequently, state-of-the-art RNA multiple alignment algorithms consider structure as well as sequence information. However, existing tools neglect the important aspect of locality. Notably, locality in RNA occurs as similarity of subsequences as well as similarity of only substructures. We present a novel approach for multiple alignment of RNAs that deals with both kinds of locality. The approach extends LocARNA by structural locality for computing all- against-all pairwise, structural local alignments. The final construction of the multiple alignments from the pairwise ones is delegated to T-Coffee. The paper systematically investigates structural locality in known RNA families. Benchmarking multiple align- ment tools on structural local families shows the need for algorithmic support of this locality. The improvement in accuracy in special cases is achieved while staying competitive with state-of-the-art alignment tools across the whole Bralibase. LocARNA and its T-Coffee extended variant LocARNATE are freely available at http://www.bioinf.uni-freiburg.de/Software/LocARNA/.