Genome Informatics 2008

This volume contains 25 peer-reviewed papers based on the presentations at the 8th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2008) held at the Teikyo Hotel, Zeuten Lake, near Berlin, from June 9 to June 10, 2008. This workshop started in 2001 as an event for doctoral students and young researchers to present and discuss their research results and approaches in bioinformatics and systems biology. It is part of a collaborative educational program involving leading institutions and leaders committed to the following programs and partner institutions: Boston (Gary Benson) - Graduate Program in Bioinformatics, Boston University, Berlin (Herman-Georg Holzhütter) - The International Research Training Group (IRTG) "Genomics and Systems Biology of Molecular Networks", Kyoto/Tokyo (Minoru Kanehisa/Satoru Miyano) - Joint Bioinformatics Education Program of Kyoto University and University of Tokyo.

Preface	p. ix
Program Committee	p. xi
Exploring the Effect of Variable Enzyme Concentrations in a Kinetic Model of Yeast Glycolysis	p. 1
The Role of IP3R Clustering in Ca2+ Signaling	p. 15
Rule-Based Reasoning for System Dynamics in Cell Systems	p. 25
Estimation of Nonlinear Gene Regulatory Networks via L1 Regularized NVAR from Time Series Gene Expression Data	p. 37
ModelMage: A Tool for Automatic Model Generation, Selection and Management	p. 52
A Framework for Determining Outlying Microarray Experiments	p. 64
Exploring the Impact of Osmoadaptation on Glycolysis Using Time-Varying Response-Coefficients	p. 77
Comparing Flux Balance Analysis to Network Expansion: Producibility, Sustainability and the Scope of Compounds	p. 91
Semi-Supervised Graph Partitioning with Decision Trees	p. 102
Measuring Correlations in Metabolomic Networks with Mutual Information	p. 112
Optimality Criteria for the Prediction of Metabolic Fluxes in Yeast Mutants	p. 123
Biosynthetic Potentials from Species-Specific Metabolic Networks	p. 135
Generalized Reaction Patterns for Prediction of Unknown Enzymatic Reactions	p. 149
Optimal Metabolic Regulation Using a Constraint-Based Model	p. 159
Comparative Determination of Biomass Composition in Differentially Active Metabolic States	p. 171
Suffix Techniques as a Rapid Method for RNA Substructure Search	p. 183
The Relationship between Fine Scale DNA Structure, GC Content, and Functional Elements in 1% of the Human Genome	p. 199
A Novel Strategy to Search Conserved Transcription Factor Binding Sites Among Coexpressing Genes in Human
Modeling IL-2 Gene Expression in Human Regulatory T Cells	p. 222
Toxicity versus Potency: Elucidation of Toxicity Properties Discriminating between Toxins, Drugs, and Natural Compounds	p. 231
Comparative VEGF Receptor Tyrosine Kinase Modeling for the Development of Highly Specific Inhibitors of Tumor Angiogenesis	p. 243
Network Analysis of Adverse Drug Interactions	p. 252
Sampling Geometries of Protein-Protein Complexes	p. 260
Computer Aided Optimization of Carbon Atom Labeling for Tracer Experiments	p. 270
Web-Links as a Means to Document Annotated Sequence and 3D-Structure Alignments in Systems Biology	p. 277
Author Index	p. 285
Table of Contents provided by Ingram. All Rights Reserved.

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Genome Informatics 2008

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