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
- Anatolij Potapov, Edgar Wingender:
Modeling the Architecture of Regulatory Networks.
6-10
- 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
- Takako Takai-Igarashi, Toshihisa Takagi:
Ontology and functional genomics.
46
- 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
- Dirk Evers, Robert Giegerich:
Reducing the Conformation Space in RNA Structure Prediction.
118-124
- 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
- Oliver Rinner, Burkhard Morgenstern:
Gene prediction by comparative sequence analysis.
131-134
- 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
- Änne Glass, Lothar Gierl:
Designing GENESYS - a software system for mining chip data.
155-157
- 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
- Nawaz Khan, Shahedur Rahman:
A Conceptual Object Model of Gene Mutation Data.
187-190
- 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
- Holger Michael, S. Thiele, Edgar Wingender:
TRANSFAC®_YEAST.
208
- 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
- Arne Müller, Michael J. E. Sternberg:
Structural annotation of the human genome.
211-212
- 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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