GCB 2001: Braunschweig, Germany
Edgar Wingender (Ed.): Computer science and biology: Proceedings of the German Conference on Bioinformatics, GCB 2001, October 7-10, 2001, Braunschweig, Germany. German Research Center for Biotechnology 2001 ISBN 3-00-008114-3
Papers
- Masaru Tomita: E-CELL Project: Towards Whole Cell Simulation. 1
- Andrey Rzhetsky, Michael Krauthammer, Tomohiro Koike, Pauline Kra, Shawn M. Gomez, Hong Yu, Pablo Ariel Duboué, Wubin Weng, Steven B. Johnson, Vasileios Hatzivassiloglou, Carol Friedman: GeneWays: A System for Mining Text and for Integrating Data on Molecular Pathways. 2-5
- Franz-Josef Brandenburg, Michael Forster, Andreas Pick, Marcus Raitner, Falk Schreiber: BioPath Visualization of Biochemical Pathways. 11-15
- Hongwu Ma, Xiaofeng Guo, Xue-Ming Zhao: Pathway Analysis of Bacillus subtillis Metabolic Network Based on Genomic Information. 16-20
- John Reinitz: Looking at functional genomics from inside the Drosophila blastoderm. 21
- Andreas Deutsch: Modelling interacting cell systems in biology and medicine with cellular automata. 22-25
- Ingolf Sommer, Niklas von Öhsen, Alexander Zien, Ralf Zimmer, Thomas Lengauer: Confidence Measures for Fold Recognition. 26-33
- Andreas Bohne, Martin Frank, Thomas Wetter, Claus-Wilhelm von der Lieth: Glycosylation of Proteins: A Computer-Based Method for Rapid Exploration of Conformational Space of N-Glycans. 34-39
- Zhi-Ping Feng: Predicting the Subcellular Location of a Protein. 44
- Zhou Yu, Tao Li, Jindong Zhao, Jingchu Luo: PGAAS: A prokaryotic genome assembly assistant system. 45
- Jacob Köhler, Steffen Schulze-Kremer: The Semantic Metadatabase (SEMEDA): Ontology Based Integration of Federated Molecular Biological Data Sources. 47-52
- Ernst Kretschmann, Rolf Apweiler: Automatic rule generation for protein annotation with the C4.5 data-mining algorithm applied on peptides in Ensembl. 53-57
- Daniel Hanisch, Ralf Zimmer, Thomas Lengauer: ProML - the Protein Markup Language for specification of protein sequences, structures and families. 58-67
- Mario Albrecht, Daniel Hanisch, Ralf Zimmer, Thomas Lengauer: Improving Fold Recognition of Protein Threading by Experimental Distance Constraints. 68-77
- Jan Freudenberg, Ralf Zimmer, Daniel Hanisch, Thomas Lengauer: A new Method for Unification of Existing Protein Structure- and Sequence-Families. 78-84
- Martin Dugas, Claudia Schoch, Susanne Schnittger, Wolfgang Kern, Torsten Haferlach, Dorle Messerer, Karl Überla: Impact of integrating clinical and genetic information. 85-88
- Thomas Werner: Finding and decrypting of promoters contributes to the elucidation of gene function. 89
- Jorng-Tzong Horng, Hsien-Da Huang, Cho-Chun Huang, Cheng-Yan Kao: Mining Putative Regulatory Elements in Gene Promoter Regions. 90-95
- Alexander E. Kel, Olga V. Kel-Margoulis, T. G. Ivanova, Edgar Wingender: ClusterScan: A Tool for Automatic Annotation of Genomic Regulatory Sequences by Searching for Composite Clusters. 96-101
- Rainer Spang, Carrie Blanchette, Harry Zuzan, Jeffrey R. Marks, Joseph Nevins, Mike West: Prediction and uncertainty in the analysis of gene expression profiles. 102-111
- Julia V. Ponomarenko, Tatyana I. Merkulova, Galina Orlova, Oleg N. Fokin, Elena Gorshkova, Mikhail P. Ponomarenko: Mining SNPs for Associating Disease Penetration with Transcription Factor Binding Site Alterations. 112-117
- Ewan Birney: Ensembl: Annotating metazoan genomes. 125
- Niko Beerenwinkel, Barbara Schmidt, Hauke Walter, Rolf Kaiser, Thomas Lengauer, Daniel Hoffmann, Klaus Korn, Joachim Selbig: Identifying drug resistance-associated patterns in HIV genotypes. 126-130
- Rolf Backofen, N. S. Narayanaswamy, Firas Swidan: Protein similarity search under mRNA structural constraints: application to selenocysteine incorporation. 135-140
Posters
- Patrizio Arrigo, P. Scartezzini, A. Egeo, Pasquale Paolo Cardo: AGeWa (Automatic Gene Walk): an automatic tool for ASO design. 141
- Constantin Bannert, Marc Rehmsmeier, Rainer Spang, Jens Stoye: Sequence Database Search Using Jumping Alignments. 142
- Ania Barbasiewicz, Lin Liu, B. Franz Lang, Nelli Shimko, Gertraud Burger: Building Organelle Genome Databases using an Object-Oriented Approach. 142-143
- Knut Behrendt, Andreas Politzer, Julio Saez-Rodriguez, Matthias Reuss, Klaus Mauch: Topological Analysis and Visualisation of large Signalling Networks: The TGF-beta Signal Transductionin Eukaryotic Systems. 143-144
- Uta Bohnebeck, Tom Wetjen: Effective Pre- and Post-Processing for the Determination of Highly Sensitive Oligonucleotidesto be Used on DNA Microarrays. 144-145
- Rüdiger Bräuning, Peter Ernst, Mechthild Falkenhahn, Karl-Heinz Glatting, Agnes Hotz-Wagenblatt, Mark van der Linden, Barbara Pardon, Coral del Val, Sándor Suhai: The German EMBnet Node: GENIUSnet. 146-147
- Maria Brandl, M. S. Weiss, Andreas Jabs, Jürgen Sühnel, Rolf Hilgenfeld: C-H...pi Interactions in Proteins: A Structural Bioinformatics Study. 147-148
- Astrid Fleischmann, Michael Darsow, Kirill Degtyarenko, Rolf Apweiler: IntEnz - The Enzyme Database in Oracle. 148-149
- Ellen Fricke, Sigrid Land, Stella Rotert, Dagmar Karas, Edgar Wingender: Cytomer: A database on gene expression sources. 149-151
- Razif R. Gabdoulline, Aitor Gonzalez, Rebecca C. Wade: 3D modeling of macromolecular structures and reactions in the context of genomes. 151-152
- Valérie Gailus-Durner, Rolf Gohla, Torsten Crass: A Question Based Navigator for Exercising Distributed Bioinformatics Tasks. 152-155
- Ulrike Göbel, Steffi Gebauer-Jung, Thomas Wiehe: A Program for the Construction of a Promoter Model From a Set of Upstream Sequences of Coregulated Genes. 157
- Ellen Gößling, Olga V. Kel-Margoulis, Alexander E. Kel, Edgar Wingender: MATCHTM - a tool for searching transcription factor binding sites in DNA sequences. Application for the analysis of human chromosomes. 158-161
- S. Goetze, A. Knopp, Craig J. Benham, Stephen A. Krawetz, Jürgen Bode: Biomathematical and in vitro analysis of destabilized regions in the interferon gene cluster. 161
- Ulrike Götze, Susanne Pistor, Claudia Choi, Mathias Krull, Frank Schacherer, Nico Voss, Edgar Wingender: TRANSPATH - a database on signal transduction networks. 162-163
- Juergen Haas: Flexible Web-Controlled Pipelining of Stand-Alone Windows Data Analysis Applications. 163-165
- K. Hafez, Jens G. Reich: Modeling of the Human Lipoprotein Metabolism - metabolic fluxes and genetic variations involved in exchange and transfer processes. 166-167
- Jorng-Tzong Horng, Ching-Mei Lin, Bing-He Yang, Cheng-Yan Kao: A Genetic Algorithm for Multiple Sequence Alignment. 167-170
- Hsien-Da Huang, Shu-Fen Fang, Jorng-Tzong Horng: Mining Combinations of Structural Motif from SSU 16 S Ribosomal RNA Secondary Structures. 170-173
- Johannes Hüsing, Michael Zeschnigk, Tanja Hölter, Karl-Heinz Jöckel: Using expression arrays to investigate deletion of chromosomal strands. 173-175
- Hui-Chih Hung, Guang-Yaw Liu, Gu-Gang Chang: Computer Data Fitting in the Equilibrium Protein Folding Process Involving Multiple Intermediates. 176-178
- Jochen Hurlebaus, Wolfgang Wiechert, Ralf Takors: MMT - A Metabolic Modeling Tool for Metabolic Engineering. 178-182
- Dirk Husmeier, Frank Wright: Approximate Bayesian Discrimination between Alternative DNA Mosaic Structures. 182-184
- Olga V. Kel-Margoulis, Igor Deineko, Ingmar Reuter, Edgar Wingender, Alexander E. Kel: TRANSCompel® - a professional database on composite regulatory elements in eukaryotic genes. 185-187
- Jan T. Kim: Modelling the Organization of Flower Morphogenesis by Transcription Factor Networks Using Lindenmayer Systems. 190-191
- Jan T. Kim, Thomas Martinetz, Daniel Polani: On the Effects of Transcription Factor Properties on the Information Content of Binding Sites. 192-194
- Steffen Klamt, Ernst Dieter Gilles: FluxAnalyzer: A Graphical User Interface for Analyzing Structural Properties and Fluxes in Balanced Metabolic Networks. 194-197
- Dorothee-U. Kloos, Claudia Choi, Edgar Wingender: The SMAD-TGF-beta SignallingNetwork: TRANSFAC meets TRANSPATH. 198-199
- A. Knopp, S. Goetze, Craig J. Benham, Matthias Frisch, Stephen A. Krawetz, Jürgen Bode: Analysis of biomathematically predicted Scaffold / Matrix Attached Regions (S/MARs) by three different approaches. 200
- Kerstin Koch, Frank Zöllner, Gerhard Sagerer: Building a new Rotamer Library for Protein-Protein Docking using energy calculations and statistical approaches. 201-202
- Matthias Lange, Andreas Freier, Uwe Scholz, Andreas Stephanik: A Computational Support for the Access to Integrated Molecular Biology Data. 203-205
- Wolfram Liebermeister: Independent component analysis of gene expression data. 205-206
- Ines Liebich, Maik Christensen, Edgar Wingender: ReAlSplice: A database on regulated alternative splicing. 206-207
- Wei Liu, Andy Woodward, Douglas B. Kell: Compression of proteome gel images using complex wavelet transform. 207
- Steffen Möller, Marcus Bantscheff, Michael O. Glocker, Dirk Koczan, Peter Lorenz, Hans-Jürgen Thiesen: Correlation of Gene Expression as Measured by Different Assays. 209
- Ferdinand Moldenhauer, Ionela Zevedei-Oancea, Stefan Schuster: Pathway Analysis of Metabolic Networks: New version of METATOOL and convenient classification of metabolites. 210
- Yuri L. Orlov, V. P. Filippov, V. N. Potapov, Nikolay A. Kolchanov: Construction of stochastic context trees for genetical texts. 212-215
- Yuri L. Orlov, Eugenii E. Vityaev, Oleg V. Vishnevsky, A. S. Belenok, Boris Kovalerchuk, Mikhail A. Pozdnyakov, Nikolay A. Kolchanov: Program "Gene Discovery" for Pattern Matching in Promoter Sequences. 215-217
- Jürgen Pleiss, Christian Gentner, Holger Scheib, Tanja Schulz, Rolf D. Schmid: From sequence to function: a quantitative model of lipase enantioselectivity. 217
- Anatolij Potapov, Klaus Seidl, Maik Christensen, Volker Drewes, Frank Schacherer, Edgar Wingender: The integrated TRANSFAC system as a basis for modeling the architecture of gene regulatory networks. 218
- Jan Reichert, K. Mehliss, Jürgen Sühnel: The IMB Jena Image Library of Biological Macromolecules - New Features. 219
- Kai J. Runte, Henning Hermjakob, Rolf Apweiler: Towards a New Curation Environment for the TrEMBL Database. 220
- Christoph Schneider, Maria Brandl, Michael Meyer, Jürgen Sühnel: Water-Mediated Uracil-Cytosine Base Pairs in RNA - A Computational Study. 221
- Dietmar Schomburg, Ida Schomburg, Antje Chang, Oliver Hofmann, Christian Ebeling, F. Ehrentreich: BRENDA a resource for Enzyme data and metabolic pathway information. 222
- Markus Schwehm: Fast Stochastic Simulation of Metabolic Networks. 223-226
- Klaus Seidl, Edgar Wingender: -PheGe- a novel concept for in-silico analyses of genotype/phenotype relations. 226-227
- J. Sun, J. van den Heuvel, A.-P. Zeng: Reconstruction of metabolic and regulatory networks of Klebsiella pneumoniae from genome data. 227-228
- Thoralf Töpel, Uwe Scholz, Ulrike Mischke, Dagmar Scheible, Ralf Hofestädt, Friedrich Trefz: RAMEDIS - Rare Metabolic Diseases Publishing Tool for Genotype-Phenotype Correlation. 228-231
- Ana Tereza R. Vasconcelos, L. Gonzaga, Rangel C. Souza, D. Q. Mendes, Roger F. C. Paixão, R. Kersanach, M. Oliveira, S. M. Martins, Andrew J. G. Simpson: A Tool for Automatic Genome Annotation. 231-232
- Martin Werber, Bernd Weisshaar: F-Workbench: a database-driven environment for the analysis of transcription factors. 233
- Karin Wieligmann, Luis Felipe Pineda De Castro, Martin Zacharias: Conformational preferences of SH2 domains in free and ligand-bound states studied by molecular dynamics simulations. 234
- Luzie U. Wingen, Jan T. Kim, Heinz Saedler, Koen Dekker: ZIGIA-DB: A versatile database for handling complex functional genomic data of Arabidopsisthaliana. 234-235
- E. W. Wolski, Christoph K. Wierling, Thomas Kreitler, Szymon M. Kielbasa, U. Schneider, Johan Gobom, Hans Lehrach, Holger Eickhoff: Visualization and analysis of gene expression data using freeware and GPL-Software. 236-237
- Li-Cheng Wu, Jorng-Tzong Horng, Feng-Mao Lin: An Approach to Finding Short Tandem Repeats in Complete Genomes. 238-241
- Ionela Zevedei-Oancea, Stefan Schuster: Treatment of multifunctional enzymesin metabolic pathway analysis. 241-242
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