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Auflistung nach Autor:in "Giegerich, Robert"

1 - 10 von 43
  • 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
    Characterizing metagenomic novelty with unexplained protein domain hits
    (German conference on bioinformatics 2014, 2014) Lingner, Thomas; Meinicke, Peter
    In metagenomics, the discovery of functional novelty has always been pursued in a gene-centered manner. In that way, sequence-based analysis has been restricted to particular features and to a sufficient length of the sequences. We propose a statistical approach that is independent from the identification of single sequences but rather yields an overall characterization of a metagenome. Our method is based on the analysis of significant differences between the functional profile of a metagenome and its reconstruction from a combination of genomic profiles using the Taxy-Pro mixture model. Here, protein families with a large proportion of domain hits that cannot be explained by the model are interesting candidates for the exploration of metagenomic novelty. The results of three case studies indicate that our method is able to characterize metagenomic novelty in terms of the protein families that significantly contribute to unexplained domain counts. We found a good correspondence between our predictions and the discoveries in the original studies as well as specific indicators of functional novelty that have not yet been described.
  • Konferenzbeitrag
    Combining secondary structure element alignment and profile-profile alignment for fold recognition
    (German Conference on Bioinformatics 2004, GCB 2004, 2004) Gewehr, Jan E.; Öhsen, Niklas von; Zimmer, Ralf
    One of the most intensely studied problems of bioinformatics is the prediction of a protein structure from an amino acid sequence. In fold recognition, one reduces this problem to assigning a protein of unknown structure to one of the known fold classes as defined in the SCOP or CATH classifications. Here, we combine two alignment methods, secondary structure element alignment and log average profile- profile alignment that have been proven to perform well on this task. Our results show that the combination yields remarkably better fold recognition accuracy on well- known benchmark sets obtained from the literature. Especially on a difficult set built by McGuffin and Jones this new approach significantly outperforms other recently proposed fold recognition methods.
  • Konferenzbeitrag
    Comparison of centralities for biological networks
    (German Conference on Bioinformatics 2004, GCB 2004, 2004) Koschützki, Dirk; Schreiber, Falk
    The analysis of biological networks involves the evaluation of the vertices within the connection structure of the network. To support this analysis we discuss five centrality measures and demonstrate their applicability on two example networks, a protein-protein-interaction network and a transcriptional regulation network. We show that all five centrality measures result in different valuations of the vertices and that for the analysis of biological networks all five measures are of interest.
  • Konferenzbeitrag
    Conserved RNA pseudoknots
    (German Conference on Bioinformatics 2004, GCB 2004, 2004) Thurner, Caroline; Hofacker, Ivo L.; Stadler, Peter F.
    Pseudoknots are essential for the functioning of many small RNA molecules. In addition, viral RNAs often exhibit pseudoknots that are required at various stages of the viral life-cycle. Techniques for detecting evolutionarily conserved, and hence most likely functional RNA pseudoknots, are therefore of interest. Here we present an extension of the alidot approach that extracts conserved secondary structures from a multiple sequence alignment and predicted secondary structures of the individual sequences. In contrast to purely phylogenetic methods, this approach yields good results already for small samples of 10 sequences or even less.
  • Konferenzbeitrag
    Explaining gene responses by linear modeling
    (German conference on bioinformatics 2014, 2014) Poeschl, Yvonne; Grosse, Ivo; Gogol-Döring, Andreas
    Increasing our knowledge about molecular processes in response to a certain treatment or infection in plants, insects, or other organisms requires the identification of the genes involved in this response. In this paper, we propose the Profile Interaction Finder (PIF) to identify such genes from gene expression data which is based on a convex linear model, and we investigate its efficacy for two applications related to stimulus response. First, we seek to identify sets of putative regulatory genes that explain the expression levels of a gene under different stimuli best. Second, we aim at identifying genes that show a specific response to a stimulus or a combination of stimuli. For both applications, we study the expression response of two Arabidopsis species to treatment with the plant hormone auxin and of Apis mellifera to pathogen infection. The proposed approach may be of general utility for analyzing expression data with a focus on genes and gene sets that explain specific stimulus response.
  • Konferenzbeitrag
    Fast track to disease-specific drugs? The impact of in-situ proteomics imaging (Toponomics)
    (German Conference on Bioinformatics 2004, GCB 2004, 2004) Schubert, Walter
  • 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
    Flexible database-assisted graphical representation of metabolic networks for model comparison and the display of experimental data
    (German conference on bioinformatics 2014, 2014) Tillack, Jana; Bende, Melanie; Rother, Michael; Scheer, Maurice; Ulas, Susanne; Schomburg, Dietmar
    Intracellular processes in living organisms are described by metabolic models. A visualization of metabolic models assists interpretation of data or analyzing results. We introduce the visualization tool DaViMM creating personalized graphical representations of metabolic networks for model comparison or the display of measurements or analyzing results. The tool is coupled to a relational database containing graphical network properties like coordinates, which ensure an intuitive network layout. A combination of DaViMM, the graphical database, and available biochemical databases enables an automated creation of metabolic network maps. The flexibility of this combination is demonstrated with some application examples.
  • Konferenzbeitrag
    From composite patters to pathways – Prediction of key regulators of gene expression
    (German Conference on Bioinformatics 2004, GCB 2004, 2004) Kel, Alexander; Voss, Nico; Konovalova, Tatyana; Tchekmenev, Dmitri; Wabnitz, Philipp; Kelmargoulis, Olga; Wingender, Edgar