German Conference on Bioinformatics 2004

Transcription

1 Robert Giegerich, Jens Stoye (eds.) German Conference on Bioinformatics 2004 GCB 2004 October 4-6, 2004, Bielefeld, Germany Gesellschaft für Informatik 2004

2 Lecture Notes in Informatics (LNI) - Proceedings Series of the Gesellschaft für Informatik (GI) Volume P-53 ISBN ISSN Volume Editors Prof. Dr. Robert Giegerich AG Praktische Informatik Technische Fakultät Universität Bielefeld Bielefeld Prof. Dr. Jens Stoye AG Genominformatik Technische Fakultät Universität Bielefeld Bielefeld Series Editorial Board Heinrich C. Mayr, Universität Klagenfurt, Austria (Chairman, mayr@ifit.uni-klu.ac.at) Jörg Becker, Universität Münster, Germany Ulrich Furbach, Universität Koblenz, Germany Axel Lehmann, Universität der Bundeswehr München, Germany Peter Liggesmeyer, Universität Potsdam, Germany Ernst W. Mayr, Technische Universität München, Germany Heinrich Müller, Universität Dortmund, Germany Heinrich Reinermann, Hochschule für Verwaltungswissenschaften Speyer, Germany Karl-Heinz Rödiger, Universität Bremen, Germany Sigrid Schubert, Universität Siegen, Germany Dissertations Dorothea Wagner, Universität Karlsruhe, Germany Seminars Reinhard Wilhelm, Universität des Saarlandes, Germany Gesellschaft für Informatik, Bonn 2004 printed by Köllen Druck+Verlag GmbH, Bonn

3 Contents Dan Gusfield Invited Talk: Phylogenetic Networks with Constrained and Unconstrained Recombination O.D. Friedrichs, A.L. Halpern, R. Lippert, C. Rausch, S.C. Schuster, D.H. Huson Syntenic Layout of Two Assemblies of Related Genomes S. Böcker Weighted Sequencing from Compomers: DNA de-novo sequencing from mass spectrometry data in the presence of false negative peaks B. Morgenstern, S.J. Prohaska, N. Werner, J. Weyer-Menkhoff, I. Schneider, A.R. Subramanian, P.F. Stadler Multiple sequence alignment with user-defined constraints J. Slack, K. Hildebrand, T. Munzner, K. St. John SequenceJuxtaposer: Fluid Navigation For Large-Scale Sequence Comparison In Context R. Pudimat, E.-G. Schukat-Talamazzini, R. Backofen Feature Based Representation and Detection of Transcription Factor Binding Sites. 43 M. Beckstette, D. Strothmann, R. Homann, R. Giegerich, S. Kurtz PoSSuMsearch: Fast and Sensitive Matching of Position Specific Scoring Matrices using Enhanced Suffix Arrays H. Täubig, A. Buchner, J. Griebsch A Method for Fast Approximate Searching of Polypeptide Structures in the PDB. 65 N. Isermann, M. Weitzel, W. Wiechert Kleene s Theorem and the Solution of Metabolic Carbon Labeling Systems H. Strömbergsson, P. Prusis, H. Midelfart, J.E.S. Wikberg, J. Komorowski Proteochemometrics Modeling of Receptor-Ligand Interactions Using Rough Sets. 85 M. Scholz, Y. Gibon, M. Stitt, J. Selbig Independent components analysis of starch deficient pgm mutants S.M. Kielbasa, N. Blüthgen, H. Herzel Genome-wide Analysis of Functions Regulated by Sets of Transcription Factors v

4 T. Götz, A. Bohne-Lang, M. Frank, K. Lohmann, A. Loss, T. Lütteke, C.-W. v.d. Lieth glycosciences.de: An Internet Portal for Glyco-related Data from Open Access Resources Gert Vriend Invited Talk: Information Flux Through Proteins F. Bös, N. Currle-Linde, P. Lindner, R.D. Schmid, J. Pleiss High-throughput molecular dynamics simulations: Long and short range effects of mutations on substrate specificity N. Weskamp, E. Hüllermeier, D. Kuhn, G. Klebe Graph Alignments: A New Concept to Detect Conserved Regions in Protein Active Sites J.E. Gewehr, N. v. Öhsen, R. Zimmer Combining Secondary Structure Element Alignment and Profile-Profile Alignment for Fold Recognition G. Dieterich, M. Kvesic, D. Schomburg, D.W. Heinz, J. Reichelt Integrating public databases into an existing protein visualization and modeling program BRAGI Michael Gagen Invited Talk: Inherent Size and Complexity Constraints in Prokaryote Gene Regulatory Networks C. Best, R. Zimmer, J. Apostolakis Probabilistic methods for predicting protein functions in protein-protein interaction networks R. Delfs, A. Doms, A. Kozlenkov, M. Schroeder GoPubMed: ontology-based literature search applied to Gene Ontology and PubMed 169 M. Beckstette, A. Sczyrba, P.M. Selzer Genlight: An Interactive System for High-throughput Sequence Analysis and Comparative Genomics Walter Schubert Invited Talk: Fast Track to Disease-Specific Drugs? The Impact of In-Situ Proteomics Imaging (Toponomics) A. Kel, N. Voss, T. Konovalova, D. Tchekmenev, P. Wabnitz, O. Kel-Margoulis, E. Wingender From Composite Patters to Pathways Prediction of Key Regulators of Gene Expression D. Koschützki, F. Schreiber Comparison of Centralities for Biological Networks C. Thurner, I.L. Hofacker, P.F. Stadler Conserved RNA Pseudoknots vi

5 H. Wang, C.J. Benham Superhelically Destabilized Sites in the E. coli Genome: Implications for Promoter Prediction in Prokaryotes P.F. Arndt Identification and Measurement of Neigbor Dependent Nucleotide Substitution Processes vii

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7 Preface This volume contains the papers presented at the German Conference on Bioinformatics, GCB 2004, held in Bielefeld, October 4 6, GCB is an annual international conference providing a forum for the presentation of research results in Bioinformatics and Computational Biology. The conference is organized on behalf of the Fachgruppe Informatik in den Biowissenschaften (BIOINF) of the German Society of Computer Science (GI), the AG Computereinsatz in den Biowissenschaften of the German Society of Chemical Technique and Biotechnology (DECHEMA), and the Studiengruppe Bioinformatik of the German Society for Biological Chemistry and Molecular Biology (GBM). GCB 2004 was preceeded by four tutorials in the afternoon of October 3, 2004: An Introduction to Molecular Phylogeny by K. Hoef-Emden, High Performance Computing in Bioinformatics by T. Ludwig and A. Stamatakis, RNA Mediated Regulation by D. Staiger, D. Evers and R. Giegerich, and Index Structures in Bioinformatics by K.- B. Schürmann, K. R. Rasmussen and J. Stoye. The technical program consisted of four invited keynote lectures and 30 contributing talks. The keynotes were given by Dan Gusfield (Davis) on Phylogenetic Networks with Constrained and Unconstrained Recombination, by Gert Vriend (Nijmegen) on Information Flux Through Proteins, by Michael Gagen (Brisbane) on Inherent Size and Complexity Constraints in Prokaryote Gene Regulatory Networks, and by Walter Schubert (Magdeburg) on Fast Track to Disease-Specific Drugs? The Impact of In-Situ Proteomics Imaging (Toponomics). This year, three types of contributing paper submissions were considered, all three of them peer-reviewed by members of the program committee and sub-referees: Research papers (8-10 page extended abstracts of technical up-to-date research results), software demos (4-6 pages abstracts describing new bioinformatics software developments), and discovery notes (1-2 page abstracts describing recent findings of biological results by means of bioinformatics techniques). The research papers and software demos are contained in this proceedings volume, discovery notes are printed in the book of poster abstracts. The program committee received an overall number of 69 submissions (47 research papers, 14 discovery notes, 8 software demos) from which 30 (20, 6, 4) were selected for presentation at the conference. Additionally, about 80 poster presentations were accepted for the conference. We heartily thank the members of the program committee and their subreferees for their efforts in reviewing the papers. Bielefeld, August 2004 Robert Giegerich Jens Stoye ix