GCB 1998: Cologne, Germany

Lectures

• Alexander E. Kel, Olga V. Kel-Margoulis, Vladimir N. Babenko, Nikolay A. Kolchanov, Edgar Wingender: Combinatorial identification of promoters induced upon immune cell activation. BibTeX
• Alvis Brazma, Inge Jonassen, Jaak Vilo, Esko Ukkonen: Predicting gene regulatory elements from their expression data in the complete yeast genome. BibTeX
• Edgar Wingender, Xin Chen, T. Heinemeyer, Alexander E. Kel, Ines Liebich, T. Meinhardt: A hierarchy of databases for modeling gene regulatory mechanisms. BibTeX
• Thomas Werner, Andreas Klingenhoff, Kornelie Frech, Kerstin Quandt: Modular modeling correlates with functional promoter diversification of human MHC class I promoters although nucleotide sequence conservation is not correlated. BibTeX
• Michael Zuker: [Invited Lecture] The other folding problem: Algorithms and thermodynamics for nucleic acid secondary structure. BibTeX
• Uta Bohnebeck, Werner Sälter, Tamás Horváth, Stefan Wrobel, Dietmar Blohm: Measuring similarity of RNA structures by relational instance-based learning: A first step toward detecting RNA signal structures in silico. BibTeX
• Ralf Bundschuh, Terence Hwa: Detectability of Sequence Homology by DNA Hybridization. BibTeX
• Gunnar von Heijne: [Invited Lecture] Picking out membrane proteins. BibTeX
• Dmitrij Frishman, Andrey A. Mironov, Hans-Werner Mewes, Mikhail S. Gelfand: Combining diverse evidence for gene recognition in completely sequenced bacterial genomes. BibTeX
• Christoph Sensen, Terry Gaasterland: [Invited Lecture] Automated genome analysis using MAGPIE. BibTeX
• Steffen Möller, Ulf Leser, Wolfgang Fleischmann, Rolf Apweiler: EDITtoTrEMBL: A distributed approach to high-quality automated protein sequence annotation. BibTeX
• Claire O'Donovan, Maria Jesus Martin, Eric Glémet, Jean-Jacques Codani, Rolf Apweiler: Removing Redundancy in SWISS-PROT and TrEMBL. BibTeX
• Wolfgang Fleischmann, Steffen Möller, Alain Gateau, Rolf Apweiler: A novel method for automatic and reliable functional annotation of proteins. BibTeX
• Eors Szathmary: [Invited Lecture] The Evolution of Information storage and heredity. BibTeX
• Hanspeter Herzel, Olaf Weiss, Edward N. Trifonov: Sequence Periodicities in Complete Genomes Reflect Supercoiling. BibTeX
• Sean R. Eddy: [Invited Lecture] Genome sequence analysis and profile hidden Markov models. BibTeX
• Thomas Dandekar, Stefan Schuster, Martijn A. Huynen, Peer Bork: Pathway alignment: Application in the comparative analysis of glycolysis. BibTeX
• Dietmar Schomburg: BRENDA, Enzyme Data for Metabolic pathways. BibTeX
• S. Lindek, R. Fritsch, Ernst H. K. Stelzer, José María Carazo, A. Engel, I. Fita, C. Henn, P. McNeil, David M. Shotton, J. Machtynger: Biolmage, the database of biological microscopy data. BibTeX
• Jean-Stéphane Varré, Jean-Paul Delahaye, Eric Rivals: The transformation distance: A dissimilarity measure based an movements of segments. BibTeX
• Knut Reinert, Hans-Peter Lenhof, Burkhard Morgenstern: An exact solution for the Segment-to-Segment multiple sequence alignment problem. BibTeX
• Antje Krause, Pierre Nicodème, Marc Rehmsmeier, Martin Vingron: Automatic clustering of large sequence databases. BibTeX
• Janet M. Thornton, Andrew C. R. Martin, Christine A. Orengo, Duncan Milburn, Roman A. Laskowski: [Invited Lecture] Protein Folds and Functions. BibTeX
• Mark Gerstein: [Invited Lecture] A Structural Census of Genomes: Comparing Bacterial, Eukaryotic, and Archaea Genomes in Terms of Protein Structure. BibTeX
• Manfred J. Sippl: [Invited Lecture] Fold Recognition: Techniques, Applications, and Pitfalls. BibTeX
• Alexander Hinneburg, Daniel A. Keim, Wolfgang Brandt: Detecting relationships between amino acid residue sequences and 3D protein structures based on a new class of rotamer libraries. BibTeX
• Finn Drabløs: Clustering of non-polar contacts in proteins. BibTeX
• Rolf Backofen, Sebastian Will: Structure prediction in an HP-type lattice with an extended alphabet. BibTeX
• Ruth Nussinov, Raquel Norel, Bilha Sandak, George Verbitsky, Haim J. Wolfson: [Invited Lecture] Structural motifs in the interior and on the surfaces of protein monomers and at protein-protein interfaces. BibTeX
• Thomas Seidl, Gabi Kastenmüller, Hans-Peter Kriegel: Similarity Search in 3D Protein Databases. BibTeX
• Matthias Rarey, Bernd Kramer, Thomas Lengauer: Docking of hydrophobic ligands with interaction-based matching algorithms. BibTeX

Posters

Regulation

• Niels Grabe, Ralf Hofestädt: A promoter model based on different combinations of binding sites. BibTeX

Nucleotide-Structure

• Dirk Evers, Michael Zuker: European Mfold Server. BibTeX
• Christoph Schneider, Jürgen Sühnel: Unrestrained molecular dynamics simulation of the FMN-RNA Aptamer complex. BibTeX
• Maria Brandl, Michael Meyer, Jürgen Sühnel: Quantum chemical ab initio study on an unusual water-mediated uracil-cytosine base pair. BibTeX

Metabolic Pathways

• Ralf Hofestädt, Manuela Prüß, Uwe Scholz, Holger Urban: The Metabolic Diseases DataBase (MDDB) - A Molecular Database Toolkit for the Detection of Inborne Errors. BibTeX
• Nicole Isermann, Wolfgang Wiechert: Efficient Computer algebraic Methods to analyze carbon labeling experiments. BibTeX
• Ignacio Sánchez-Valdenebro, Thomas Pfeiffer, Juan Carlos Nuño, Francisco Montero, Stefan Schuster: A structural approach to the analysis of metabolic networks illustrated with erythrocyte metabolism. BibTeX

Genome Information & Sequence Data

• Kaj Albermann, Jean Hani, S. Stocker, Alfred Zollner, Hans-Werner Mewes: The MIPS Yeast Genome Database. BibTeX
• Yvonne J. K. Edwards, Martin C. Frith, Greg Elgar, Martin J. Bishop: Theatre: A Novel Tool For The Comparative Investigation and Display of Evolutionary Diversity of Functional and Structural Features in DNA Sequences. BibTeX
• Greg Elgar, M. S. Clark, Yvonne J. K. Edwards, S. Meek, S. Smith, S. Umrania, S. Warner, WiIliams G, Martin J. Bishop: Characterization of The Compact Model Genome of The Japanese Puffer Fish (Fugu rubripes) Using A Cosmid Sequence Scanning Approach. BibTeX
• Klaus F. X. Mayer, Christine M. Schüller, Larry Parnell: A Statistical Analysis of the success of exon prediction algorithms on the Arabidopsis genome. BibTeX
• Uwe Ohler, Heinrich Niemann: Stochastic Language Models for Content Based DNA Sequence Classification. BibTeX
• Chandra M. Sarkar, J. Flavio R. Ortigao, Ulf Gyllensten, Anthony J. Brookes: HGBase, a database of intra-genic DNA sequence polymorphisms. BibTeX
• Ruben Schattevoy, J. Weber, André Rosenthal: High Throughput Sequence Annotation Server. BibTeX
• Normann Strack, Hans-Werner Mewes: An Object Oriented Approach to Data Handling and Semiautomatic Processing of cDNA Clones. BibTeX
• N. I. Akberova, A. Leontiev: Context-free method of pattern recognition in the genetic texts. BibTeX
• Erich Bornberg-Bauer: Computational approaches to identify Leucine Zippers. BibTeX
• Bastien Chevreux, Thomas Pfisterer, Thomas Wetter, Sándor Suhai: Computer assisted editing of genomic sequences. BibTeX
• Darrell Conklin, Terry Farrah: Protein motif recognition in DNA sequences containing indel errors. BibTeX
• Eivind Coward, Finn Drabløs: A method for detecting periodic patterns in sequences. BibTeX
• Henning Hermjakob, Claire O'Donovan, Maria Jesus Martin, Fiona Lang, Rolf Apweiler: SPTR: A comprehensive, non redundant and up-to-date view of the protein sequence world. BibTeX
• Andreas Kaps, Dirk Haase, Hans-Werner Mewes: Developing a groupware system for annotating Protein Sequences Using Object Oriented Technology. BibTeX
• Philip Lijnzaad, Katarzyna Kruszewska, Nicole Redaschi, Patricia Rodriguez-Tomé: A CORBA server for the EMBL Nucleotide Sequence Database: presentation of a first full implementation (EMCORBA v2). BibTeX
• Niels Mache, Paul Levi: GENIO/frame - Frame Shift Analysis and Sequencing Error Detection of Eukaryotic CDS. BibTeX
• Niels Mache, Paul Levi: GENIO/scan - EST Guided Identification of Genes in Human Genomic DNA. BibTeX
• Peter Sterk, Mary Ann Tuli: The EMBL Nucleotide Sequence Database at the European Bioinformatics Institute (EBI): Data Acquisition. BibTeX
• Mary Ann Tuli, Peter Sterk: The EMBL Nucleotide Sequence Database at the European Bioinformatics Institute (EBI): Sequence Similarity Searching & Database query/retrieval. BibTeX
• Olaf Weiss, Hanspeter Herzel: Property Codes in Sets of Protein Sequences. BibTeX
• Norman A. Doggett, Jonathan Longmire, Alexander Schliep, David C. Torney: Screening large clone libraries efficiently. BibTeX

Sequence Alignment and Homology

• Yvonne Kallberg, Hans Jörnvall, Bengt Persson: Implementing the Boyer-Moore Algorithm. BibTeX
• Burkhard Morgenstern: DIALIGN2: Improvement of the segment to segment approach to multiple sequence alignment. BibTeX
• Bengt Persson, Yvonne Kallberg, Erik Nordling, Jan-Olav Höög, Hans Jörnvall: Studies on the evolution of short-chain and medium-chain dehydrogenases/reductases. BibTeX
• Heiko A. Schmidt, Martin Vingron: pfastDNAml: Using Parallel Computing for Maximum Likelihood Phylogenetic Analysis. BibTeX
• Martin Ebeling, Peter Ernst, Mechthild Falkenhahn, Karl-Heinz Glatting, Agnes Hotz-Wagenblatt, A. Kühl, Ge Zhang, Sándor Suhai: EST Clustering at GENIUSnet, the German EMBnet node. BibTeX

Protein Structure

• Brigitte Altenberg, Gerrit Vriend: Molecular modelling and macromolecular visualisation with WHAT IF. BibTeX
• Sabine Dietmann, Cornelius Frömmel: Prediction of neighboring secondary structure of molecular patches in proteins by artificial neural networks. BibTeX
• Christoph Gille, Andrean Goede, Robert Preissner, Cornelius Frömmel: Atomic patch similarity as a criterion of evolutionary relationship between proteins. BibTeX
• Andrean Goede, Robert Preissner, Cornelius Frömmel: A procedure for superposition of two arbitrary atomic arrangements. BibTeX
• Robert Günther, Kerstin Möhle, Hans-Jörg Hofmann: Secondary structure formation in beta-Peptides. BibTeX
• Jukka V. Lehtonen, Konstantin A. Denessiouk, Mark S. Johnson: An application of genetic algorithm and parallel computing method to the protein structure comparison problem. BibTeX
• Oliver Leven, Dietmar Schomburg: Prediction of Protein Thermostability. BibTeX
• Qianning Liao, Jingchu Luo, Songping Liang, Xiaocheng Gu: A structural motif of three disulfide bridges and three beta strands in peptides. BibTeX
• Michael Meyer, Maria Brandl, Jürgen Sühnel: C-H..0 interactions in proteins and protein complexes. BibTeX
• Ulrich Schieborr: Dynamics in a time averaged stochastic dynamic simulation compared to essential dynamic methods applied to ribonuclease T1. BibTeX
• Fuad Abdallah, Olav Zimmermann, Oliver Leven, Sebastian Schneckener, Jan Kim: A Relational Macromolecular Structure Database. BibTeX

Docking

• Peter Krämer, Dietmar Schomburg: Use of local intermolecular interactions for the prediction of protein/protein binding sites. BibTeX
• Olav Zimmermann, Oliver Martin, Dietmar Schomburg: Geometric Docking of Transmembrane Structures. BibTeX
• Erik Nordling, Udo C. T. Oppermann, Hanns-Ulrich Marschall, Hans Jörnvall, Bengt Persson: Docking of bile acids to [gamma][gamma]alcohol dehydrogenase. BibTeX
• Robert Preissner, Andrean Goede, Cornelius Frömmel: Dictionary of Interfaces in Proteins (DIP). Data Bank of complementary molecular surface patches. BibTeX
• Michael Thormann, Hans-Jörg Hofmann: Docking experiences, AutoDock - a Case Study. BibTeX

Others

• Markus Fischer, Christoph Kaiser, Jürgen Pleiss, Rolf D. Schmid: Lipase Engineering Database. BibTeX
• Markus Kieninger, J. Gohrke, Chandra M. Sarkar, J. Flavio R. Ortigao, Thomas Kämpke: DoPrimer - a modular object oriented application and Java class library for the design of oligonucleotide primers. BibTeX
• Manuel Ruiz, Gérard Mennessier, Véronique Giudicelli, Denys Chaume, Marie-Paule Lefranc: IMGT/Collier de Perles, a LIGM-DB tool for Immunoglobulin and T-Cell Receptor 2D representations. BibTeX
• M. Schilling, Christoph Grunau, André Rosenthal: MethDB - a relational DNA-Methylation-Database. BibTeX
• Jingchu Luo, Christoph Sensen, Tin Wee Tan: Asia Pacific Bioinformatics Network. BibTeX