GCB 1998:
Cologne, Germany
Proceedings of the German Conference on Bioinformatics, GCB '98, University of Cologne, Germany, October 1998, Oxford University Press
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.
- Alvis Brazma, Inge Jonassen, Jaak Vilo, Esko Ukkonen:
Predicting gene regulatory elements from their expression data in the complete yeast genome.
- Edgar Wingender, Xin Chen, T. Heinemeyer, Alexander E. Kel, Ines Liebich, T. Meinhardt:
A hierarchy of databases for modeling gene regulatory mechanisms.
- 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.
- Michael Zuker:
[Invited Lecture] The other folding problem: Algorithms and thermodynamics for nucleic acid secondary structure.
- 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.
- Ralf Bundschuh, Terence Hwa:
Detectability of Sequence Homology by DNA Hybridization.
- Gunnar von Heijne:
[Invited Lecture] Picking out membrane proteins.
- Dmitrij Frishman, Andrey A. Mironov, Hans-Werner Mewes, Mikhail S. Gelfand:
Combining diverse evidence for gene recognition in completely sequenced bacterial genomes.
- Christoph Sensen, Terry Gaasterland:
[Invited Lecture] Automated genome analysis using MAGPIE.
- Steffen Möller, Ulf Leser, Wolfgang Fleischmann, Rolf Apweiler:
EDITtoTrEMBL: A distributed approach to high-quality automated protein sequence annotation.
- Claire O'Donovan, Maria Jesus Martin, Eric Glémet, Jean-Jacques Codani, Rolf Apweiler:
Removing Redundancy in SWISS-PROT and TrEMBL.
- Wolfgang Fleischmann, Steffen Möller, Alain Gateau, Rolf Apweiler:
A novel method for automatic and reliable functional annotation of proteins.
- Eors Szathmary:
[Invited Lecture] The Evolution of Information storage and heredity.
- Hanspeter Herzel, Olaf Weiss, Edward N. Trifonov:
Sequence Periodicities in Complete Genomes Reflect Supercoiling.
- Sean R. Eddy:
[Invited Lecture] Genome sequence analysis and profile hidden Markov models.
- Thomas Dandekar, Stefan Schuster, Martijn A. Huynen, Peer Bork:
Pathway alignment: Application in the comparative analysis of glycolysis.
- Dietmar Schomburg:
BRENDA, Enzyme Data for Metabolic pathways.
- 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.
- Jean-Stéphane Varré, Jean-Paul Delahaye, Eric Rivals:
The transformation distance: A dissimilarity measure based an movements of segments.
- Knut Reinert, Hans-Peter Lenhof, Burkhard Morgenstern:
An exact solution for the Segment-to-Segment multiple sequence alignment problem.
- Antje Krause, Pierre Nicodème, Marc Rehmsmeier, Martin Vingron:
Automatic clustering of large sequence databases.
- Janet M. Thornton, Andrew C. R. Martin, Christine A. Orengo, Duncan Milburn, Roman A. Laskowski:
[Invited Lecture] Protein Folds and Functions.
- Mark Gerstein:
[Invited Lecture] A Structural Census of Genomes: Comparing Bacterial, Eukaryotic, and Archaea Genomes in Terms of Protein Structure.
- Manfred J. Sippl:
[Invited Lecture] Fold Recognition: Techniques, Applications, and Pitfalls.
- 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.
- Finn Drabløs:
Clustering of non-polar contacts in proteins.
- Rolf Backofen, Sebastian Will:
Structure prediction in an HP-type lattice with an extended alphabet.
- 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.
- Thomas Seidl, Gabi Kastenmüller, Hans-Peter Kriegel:
Similarity Search in 3D Protein Databases.
- Matthias Rarey, Bernd Kramer, Thomas Lengauer:
Docking of hydrophobic ligands with interaction-based matching algorithms.
Posters
Regulation
Nucleotide-Structure
Metabolic Pathways
Genome Information & Sequence Data
- Kaj Albermann, Jean Hani, S. Stocker, Alfred Zollner, Hans-Werner Mewes:
The MIPS Yeast Genome Database.
- 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.
- 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.
- Klaus F. X. Mayer, Christine M. Schüller, Larry Parnell:
A Statistical Analysis of the success of exon prediction algorithms on the Arabidopsis genome.
- Uwe Ohler, Heinrich Niemann:
Stochastic Language Models for Content Based DNA Sequence Classification.
- Chandra M. Sarkar, J. Flavio R. Ortigao, Ulf Gyllensten, Anthony J. Brookes:
HGBase, a database of intra-genic DNA sequence polymorphisms.
- Ruben Schattevoy, J. Weber, André Rosenthal:
High Throughput Sequence Annotation Server.
- Normann Strack, Hans-Werner Mewes:
An Object Oriented Approach to Data Handling and Semiautomatic Processing of cDNA Clones.
- N. I. Akberova, A. Leontiev:
Context-free method of pattern recognition in the genetic texts.
- Erich Bornberg-Bauer:
Computational approaches to identify Leucine Zippers.
- Bastien Chevreux, Thomas Pfisterer, Thomas Wetter, Sándor Suhai:
Computer assisted editing of genomic sequences.
- Darrell Conklin, Terry Farrah:
Protein motif recognition in DNA sequences containing indel errors.
- Eivind Coward, Finn Drabløs:
A method for detecting periodic patterns in sequences.
- 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.
- Andreas Kaps, Dirk Haase, Hans-Werner Mewes:
Developing a groupware system for annotating Protein Sequences Using Object Oriented Technology.
- 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).
- Niels Mache, Paul Levi:
GENIO/frame - Frame Shift Analysis and Sequencing Error Detection of Eukaryotic CDS.
- Niels Mache, Paul Levi:
GENIO/scan - EST Guided Identification of Genes in Human Genomic DNA.
- Peter Sterk, Mary Ann Tuli:
The EMBL Nucleotide Sequence Database at the European Bioinformatics Institute (EBI): Data Acquisition.
- Mary Ann Tuli, Peter Sterk:
The EMBL Nucleotide Sequence Database at the European Bioinformatics Institute (EBI): Sequence Similarity Searching & Database query/retrieval.
- Olaf Weiss, Hanspeter Herzel:
Property Codes in Sets of Protein Sequences.
- Norman A. Doggett, Jonathan Longmire, Alexander Schliep, David C. Torney:
Screening large clone libraries efficiently.
Sequence Alignment and Homology
- Yvonne Kallberg, Hans Jörnvall, Bengt Persson:
Implementing the Boyer-Moore Algorithm.
- Burkhard Morgenstern:
DIALIGN2: Improvement of the segment to segment approach to multiple sequence alignment.
- Bengt Persson, Yvonne Kallberg, Erik Nordling, Jan-Olav Höög, Hans Jörnvall:
Studies on the evolution of short-chain and medium-chain dehydrogenases/reductases.
- Heiko A. Schmidt, Martin Vingron:
pfastDNAml: Using Parallel Computing for Maximum Likelihood Phylogenetic Analysis.
- 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.
Protein Structure
- Brigitte Altenberg, Gerrit Vriend:
Molecular modelling and macromolecular visualisation with WHAT IF.
- Sabine Dietmann, Cornelius Frömmel:
Prediction of neighboring secondary structure of molecular patches in proteins by artificial neural networks.
- Christoph Gille, Andrean Goede, Robert Preissner, Cornelius Frömmel:
Atomic patch similarity as a criterion of evolutionary relationship between proteins.
- Andrean Goede, Robert Preissner, Cornelius Frömmel:
A procedure for superposition of two arbitrary atomic arrangements.
- Robert Günther, Kerstin Möhle, Hans-Jörg Hofmann:
Secondary structure formation in beta-Peptides.
- Jukka V. Lehtonen, Konstantin A. Denessiouk, Mark S. Johnson:
An application of genetic algorithm and parallel computing method to the protein structure comparison problem.
- Oliver Leven, Dietmar Schomburg:
Prediction of Protein Thermostability.
- Qianning Liao, Jingchu Luo, Songping Liang, Xiaocheng Gu:
A structural motif of three disulfide bridges and three beta strands in peptides.
- Michael Meyer, Maria Brandl, Jürgen Sühnel:
C-H..0 interactions in proteins and protein complexes.
- Ulrich Schieborr:
Dynamics in a time averaged stochastic dynamic simulation compared to essential dynamic methods applied to ribonuclease T1.
- Fuad Abdallah, Olav Zimmermann, Oliver Leven, Sebastian Schneckener, Jan Kim:
A Relational Macromolecular Structure Database.
Docking
- Peter Krämer, Dietmar Schomburg:
Use of local intermolecular interactions for the prediction of protein/protein binding sites.
- Olav Zimmermann, Oliver Martin, Dietmar Schomburg:
Geometric Docking of Transmembrane Structures.
- Erik Nordling, Udo C. T. Oppermann, Hanns-Ulrich Marschall, Hans Jörnvall, Bengt Persson:
Docking of bile acids to [gamma][gamma]alcohol dehydrogenase.
- Robert Preissner, Andrean Goede, Cornelius Frömmel:
Dictionary of Interfaces in Proteins (DIP). Data Bank of complementary molecular surface patches.
- Michael Thormann, Hans-Jörg Hofmann:
Docking experiences, AutoDock - a Case Study.
Others
- Markus Fischer, Christoph Kaiser, Jürgen Pleiss, Rolf D. Schmid:
Lipase Engineering Database.
- 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.
- 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.
- M. Schilling, Christoph Grunau, André Rosenthal:
MethDB - a relational DNA-Methylation-Database.
- Jingchu Luo, Christoph Sensen, Tin Wee Tan:
Asia Pacific Bioinformatics Network.
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