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Julio Collado-Vides, Ralf Hofestadt, Michael Mavrovouniotis, Gerhard Michal (Editors)

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Julio Collado-Vides, Ralf Hofestadt, Michael Mavrovouniotis, Gerhard Michal (Editors) Julio Collado-Vides, Ralf Hofestadt, Michael Mavrovouniotis, Gerhard Michal (editors): Modeling and Simulation of Gene and Cell Regulation and Metabolic Pathways Dagstuhl-Seminar-Report; 215 21.06.1998-26.06.1998(98251) UiWERS'TATSSiBLIOTHEK HANNOVER TECHNiSCHE iNFORMATIONSBIBLIOTHEK UB/TIB Hannover 89 119 169 916 TOG Contents Preface 3 John Reinitz Solving the Inverse Problem in Gene Expression: Lessons from Drosophila 11 Gary Stormo Discovering Regulatory Sites from Expression Data 12 Edgar Wingender Database Modeling of Gene Regulatory Pathways 13 Thomas Werner Promoter classification by functional organizational models 14 Andreas Dress The Family of bHLH-Proteins 15 Michael Savageau Development of Fractal Kinetic Theory for Enzyme-Catalyzed Reactions and Implications for the Design of Biochemical Pathways 17 Michael Kohn Identifying Sites of Metabolic Regulation by Graph Theoretical Modeling 18 Wolf-D. Ihlenfeldt A General System for the Simulation of Organic Reactions 19 Gerhard Michal Regulation of Metabolic Pathways 19 Stevo Bozinovski Protein Biosynthesis: The Flexible Manufacturing Metaphor 20 Edgar Wingender The TRANSFAC-Database 21 Michael Kohn A Demonstration of MetaNet Graph Drawing and Analysis Software 21 Jacky Snoep A Control of DNA supercoiling in the complex cell 22 Jay Mittenthal Designing metabolism: Alternative connectivities for the pentose phosphate pathway 23 Rolf Apweiler The SWISS-PROT and TrEMBL Protein Sequence Database as a Tool to Model Regulatory and Metabolic Pathways 23 Bruno Sobral A Plant Metabolism Database 26 Minoru Kanehisa Regulatory Pathways in KEGG 27 Dominique Bergeron The death factors: a combinatorial analysis 28 Terry Gaasterland Multi-Genome Views of Whole Genomes with a focus on E.coli global reg- ulatory proteins 29 Julio Collado-Vides Regulatory Predictions in the Complete E.coli Genome 31 Pedro Mendes Integration of gene expression with metabolism in kinetic simulations 32 Luis Mendoza The regulatory network that controls flowering in Arabidopsis 34 Takako Takai-Igarashi Cell Signaling Networks Database 35 Pedro Mendes Exploring biochemical models with Gepasi, a kinetics simulator 35 Uwe Scholz Molecular Database Integration: Analysis of Metabolic Network Control 37 Thomas Muck Indexing and Retrieval of Complex Data Sets or Is it a good idea to store metabolic data in an ooDB? 38 Vladimir Babenko Databases integration and automatic knowledge acquisition on regulatory regions of eukaryotic genome 38 Daniel Kahn Integration of protein data : ProDom, XDOM and genome projects 39 Fedor Kolpakov GeneNet: a Database for Gene Networks and its Automated Visualization through the Internet 40 Hiroyuki Ogata Integrated Analysis of Metabolic Pathways, Sequence Evolution and Genome Organization 42 Manuela Priifi The Metabolic Diseases Database 44 John Reinitz The GeNet Database 44 Thomas Dandekar Examples on post-transkriptional reguation and metabolic pathways 45 Klaus-Peter Zauner Simulation Experiments on the Role of Spatial Arrangement in Enzymatic Networks 45 Tom Shimizu E-CELL vs StochSim: System-wide and molecularly-detailed approaches to simulation of cellular processes 46 Masahiro Okamoto Towards a Virtual-Lab-System for Metabolic Engineering: Development of Biochemical Engineering System Analyzing Tool-Kit (BEST-KIT) 47 Simone Bentolila Modeling signal pathways 49 Ralf Zimmer Mapping Metabolic Networks and Gene Expression Data via Protein Struc- ture Prediction 51 Jacques van Helden Computer tools for the analysis of yeast regulatory sequences 52 Edda Klipp Evolutionary Optimization and Metabolic Control Analysis 53 Stig Omholt Why and how to build a conceptual bridge between mechanistic regulatory biology and quantitative genetics 55 Stefan Schuster Computer-aided Structural Analysis of Biochemical Reaction Systems 56 Takayoshi Shoudai Parallel Knowledge Discovery System for Amino Acid Sequences - BON- SAI Garden 57 Patrizio Arrigo Application of Conceptual Clustering to the Recognition of the Hierarchical Structure of Transcriptional Control Domains 58 Jiirgen Siihnel Hydrogen Bonds in Biopolymer Structures - Variations on an Old Theme 58 Jaime Lagunez-Otero The Cell as an Expert System 60 Falk Schreiber Visualization of Biochemical Pathways 60 10.
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