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Auflistung nach Autor:in "Stoye, Jens"

1 - 10 von 32
  • Zeitschriftenartikel
    Approximative Gencluster und ihre Anwendung in der komparativen Genomik
    (Informatik-Spektrum: Vol. 32, No. 4, 2009) Jahn, Katharina; Stoye, Jens
    Durch die zunehmende Verfügbarkeit von komplett sequenzierten und assemblierten Genomen eröffnet sich die Möglichkeit, Spezies anhand der Gesamtstruktur ihrer Genome zu vergleichen. Zu diesem Zweck werden Genome häufig nicht mehr auf Ebene der Nukleotidsequenz dargestellt sondern als eine Folge von Genen, die deren Anordnung auf den Chromosomen widerspiegelt. Eine wichtige Aufgabe in diesem Bereich ist die Bestimmung von chromosomalen Bereichen, die über verschiedene Spezies hinweg komplett oder näherungsweise konserviert sind. In diesem Artikel werden informatische Methoden zur Bestimmung dieser Bereiche vorgestellt und Anwendungen im Bereich der Genclustervorhersage und der Phylogenie-Rekonstruktion beschrieben.
  • 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
    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
    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
  • Konferenzbeitrag
    Genlight: An interactive system for high-throughput sequence analysis and comparative genomics
    (German Conference on Bioinformatics 2004, GCB 2004, 2004) Beckstette, Michael; Sczyrba, Alexander; Selzer, Paul M.
  • Konferenzbeitrag
    Genome-wide analysis of functions regulated by sets of transcription factors
    (German Conference on Bioinformatics 2004, GCB 2004, 2004) Kielbasa, Szymon M.; Blüthgen, Nils; Herzel, Hanspeter
    We present a pipeline for inferring biological functions regulated by a combinatorial interaction of transcription factors. Using a robust statistical method the pipeline intersects the presence of transcription factor binding sites in gene upstream sequences with Gene Ontology terms associated with these genes. Positional frequency matrices for the transcription factors constitute the input of the pipeline and significantly enriched biological processes are reported as the output. We demonstrate the usage of the pipeline using two groups of transcription factors: a cell-cycle related family of E2F factors and a NFAT/AP-1 pair involved in immune response. In both cases the reported results match well the experimental knowledge. Furthermore, for the NFAT/AP-1 composite element novel functions are predicted.
  • Editiertes Buch