Genome Informatics 2008: Genome Informatics Series Volume 20: Proceedings of the 8th International Workshop on Bioinformatics and Systems Biology (Ibsb 2008)

Overview

This volume contains 25 peer-reviewed papers based on the presentations at the 8th International Annual Workshop on Bioinformatics and Systems Biology (IBSB 2008) held at the Teikyo Hotel, Zeuten Lake near Berlin, from June 9 to June 11, 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 ...

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Overview

This volume contains 25 peer-reviewed papers based on the presentations at the 8th International Annual Workshop on Bioinformatics and Systems Biology (IBSB 2008) held at the Teikyo Hotel, Zeuten Lake near Berlin, from June 9 to June 11, 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 Holzh&uumlet;tter) - 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.

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Product Details

  • ISBN-13: 9781848162990
  • Publisher: Imperial College Press
  • Publication date: 10/6/2008
  • Pages: 300
  • Product dimensions: 6.60 (w) x 9.80 (h) x 0.70 (d)

Table of Contents

Preface ix

Program Committee xi

Exploring the Effect of Variable Enzyme Concentrations in a Kinetic Model of Yeast Glycolysis J. Bruck W. Liebermeister E. Klipp 1

The Role of IP3R Clustering in Ca2+ Signaling A. Skupin M. Falcke 15

Rule-Based Reasoning for System Dynamics in Cell Systems E. Jeong M. Nagasaki S. Miyano 25

Estimation of Nonlinear Gene Regulatory Networks via L1 Regularized NVAR from Time Series Gene Expression Data K. Kojima A. Fujita T. Shimamura S. Imoto S. Miyano 37

ModelMage: A Tool for Automatic Model Generation, Selection and Management M. Fl&oumlet;ttmann J. Schaber S. Hoops E. Klipp P. Mendes 52

A Framework for Determining Outlying Microarray Experiments R. Wan Å. M. Wheelock H. Mamitsuka 64

Exploring the Impact of Osmoadaptation on Glycolysis Using Time-Varying Response-Coefficients C. K&uumlet;hn E. Petelenz B. Nordlander J. Schaber S. Hohmann E. Klipp 77

Comparing Flux Balance Analysis to Network Expansion: Producibility, Sustainability and the Scope of Compounds K. Kruse O. Ebenh&oumlet;h 91

Semi-Supervised Graph Partitioning with Decision Trees T. Hancock H. Mamitsuka 102

Measuring Correlations in Metabolomic Networks with Mutual Information J. Numata O. Ebenh&oumlet;h E.-W. Knapp 112

Optimality Criteria for the Prediction of Metabolic Fluxes in Yeast Mutants E. S. Snitkin D. Segrè 123

Biosynthetic Potentials from Species-Specific Metabolic Networks G. Basler Z. Nikoloski O. Ebenh&oumlet;h T. Handorf 135

Generalized Reaction Patterns for Prediction of Unknown Enzymatic Reactions Y. Shimizu M. Hattori S. Goto M. Kanehisa 149

Optimal Metabolic Regulation Using a Constraint-Based Model W. J. Riehl D. Segè159

Comparative Determination of Biomass Composition in Differentially Active Metabolic States H.-C. Chiu D. Segrè 171

Suffix Techniques as a Rapid Method for RNA Substructure Search R. A. Bauer K. Rother J. M. Bujnicki R. Preissner 183

The Relationship between Fine Scale DNA Structure, GC Content, and Functional Elements in 1% of the Human Genome S. C. J. Parker E. H. Margulies T. D. Tullius 199

A Novel Strategy to Search Conserved Transcription Factor Binding Sites Among Coexpressing Genes in Human Y. Hatanaka M. Nagasaki R. Yamaguchi T. Obayashi K. Numata A. Fujita T. Shimamura Y. Tamada S. Imoto K. Kinoshita K. Nakai S. Miyano|p212

Modeling IL-2 Gene Expression in Human Regulatory T Cells M. Benary H. Bendfeldt R. Baumgrass H. Herzel 222

Toxicity versus Potency: Elucidation of Toxicity Properties Discriminating between Toxins, Drugs, and Natural Compounds S. Struck U. Schmidt B. Gruening I. S. Jaeger J. Hossbach R. Preissner 231

Comparative VEGF Receptor Tyrosine Kinase Modeling for the Development of Highly Specific Inhibitors of Tumor Angiogenesis U. Schmidt J. Ahmed E. Michalsky M. Hoepfner R. Preissner 243

Network Analysis of Adverse Drug Interactions M. Takarabe S. Okuda M. Itoh T. Tokimatsu S. Goto M. Kanehisa 252

Sampling Geometries of Protein-Protein Complexes A. Guerler S. Lorenzen F. Krull E.-W. Knapp 260

Computer Aided Optimization of Carbon Atom Labeling for Tracer Experiments B. S. Menk&uumlet;c C. Gille H.-G. Holzh&uumlet;tter 270

Web-Links as a Means to Document Annotated Sequence and 3D-Structure Alignments in Systems Biology C. Gille A. Hoppe H.-G. Holzh&uumlet;tter 277

Author Index 285

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