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Genome Informatics 2008 cover
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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.


Contents:
  • Exploring the Effect of Variable Enzyme Concentrations in a Kinetic Model of Yeast Glycolysis (J Bruck et al.)
  • Estimation of Nonlinear Gene Regulatory Networks via L1 Regularized NVAR from Time Series Gene Expression Data (K Kojima et al.)
  • Comparing Flux Balance Analysis to Network Expansion: Producibility, Sustainability and the Scope of Compounds (K Kruse & O Ebenhöh)
  • Biosynthetic Potentials from Species-Specific Metabolic Networks (G Basler et al.)
  • Comparative Determination of Biomass Composition in Differentially Active Metabolic States (H-C Chiu & D Segrè)
  • The Relationship between Fine Scale DNA Structure, GC Content, and Functional Elements in 1% of the Human Genome (S C J Parker et al.)
  • Toxicity versus Potency: Elucidation of Toxicity Properties Discriminating between Toxins, Drugs, and Natural Compounds (S Struck et al.)
  • Comparative VEGF Receptor Tyrosine Kinase Modeling for the Development of Highly Specific Inhibitors of Tumor Angiogenesis (U Schmidt et al.)
  • Network Analysis of Adverse Drug Interactions (M Takarabe et al.)
  • Web-Links as a Means to Document Annotated Sequence and 3D-Structure Alignments in Systems Biology (C Gille et al.)

Readership: Researchers and graduate students in bioinformatics and computational biology.
You have access to thisebook
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FRONT MATTER
  • Pages:i–xi

https://doi.org/10.1142/9781848163003_fmatter

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EXPLORING THE EFFECT OF VARIABLE ENZYME CONCENTRATIONS IN A KINETIC MODEL OF YEAST GLYCOLYSIS
  • Pages:1–14

https://doi.org/10.1142/9781848163003_0001

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THE ROLE OF IP3R CLUSTERING IN Ca2+ SIGNALING
  • Pages:15–24

https://doi.org/10.1142/9781848163003_0002

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RULE-BASED REASONING FOR SYSTEM DYNAMICS IN CELL SYSTEMS
  • Pages:25–36

https://doi.org/10.1142/9781848163003_0003

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ESTIMATION OF NONLINEAR GENE REGULATORY NETWORKS VIA L1 REGULARIZED NVAR FROM TIME SERIES GENE EXPRESSION DATA
  • Pages:37–51

https://doi.org/10.1142/9781848163003_0004

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ModelMage: A TOOL FOR AUTOMATIC MODEL GENERATION, SELECTION AND MANAGEMENT
  • Pages:52–63

https://doi.org/10.1142/9781848163003_0005

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A FRAMEWORK FOR DETERMINING OUTLYING MICROARRAY EXPERIMENTS
  • Pages:64–76

https://doi.org/10.1142/9781848163003_0006

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EXPLORING THE IMPACT OF OSMOADAPTATION ON GLYCOLYSIS USING TIME-VARYING RESPONSE-COEFFICIENTS
  • Pages:77–90

https://doi.org/10.1142/9781848163003_0007

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COMPARING FLUX BALANCE ANALYSIS TO NETWORK EXPANSION: PRODUCIBILITY, SUSTAINABILITY AND THE SCOPE OF COMPOUNDS
  • Pages:91–101

https://doi.org/10.1142/9781848163003_0008

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SEMI-SUPERVISED GRAPH PARTITIONING WITH DECISION TREES
  • Pages:102–111

https://doi.org/10.1142/9781848163003_0009

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MEASURING CORRELATIONS IN METABOLOMIC NETWORKS WITH MUTUAL INFORMATION
  • Pages:112–122

https://doi.org/10.1142/9781848163003_0010

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OPTIMALITY CRITERIA FOR THE PREDICTION OF METABOLIC FLUXES IN YEAST MUTANTS
  • Pages:123–134

https://doi.org/10.1142/9781848163003_0011

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BIOSYNTHETIC POTENTIALS FROM SPECIES-SPECIFIC METABOLIC NETWORKS
  • Pages:135–148

https://doi.org/10.1142/9781848163003_0012

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GENERALIZED REACTION PATTERNS FOR PREDICTION OF UNKNOWN ENZYMATIC REACTIONS
  • Pages:149–158

https://doi.org/10.1142/9781848163003_0013

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OPTIMAL METABOLIC REGULATION USING A CONSTRAINT-BASED MODEL
  • Pages:159–170

https://doi.org/10.1142/9781848163003_0014

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COMPARATIVE DETERMINATION OF BIOMASS COMPOSITION IN DIFFERENTIALLY ACTIVE METABOLIC STATES
  • Pages:171–182

https://doi.org/10.1142/9781848163003_0015

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SUFFIX TECHNIQUES AS A RAPID METHOD FOR RNA SUBSTRUCTURE SEARCH
  • Pages:183–198

https://doi.org/10.1142/9781848163003_0016

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THE RELATIONSHIP BETWEEN FINE SCALE DNA STRUCTURE, GC CONTENT, AND FUNCTIONAL ELEMENTS IN 1% OF THE HUMAN GENOME
  • Pages:199–211

https://doi.org/10.1142/9781848163003_0017

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A NOVEL STRATEGY TO SEARCH CONSERVED TRANSCRIPTION FACTOR BINDING SITES AMONG COEXPRESSING GENES IN HUMAN
  • Pages:212–221

https://doi.org/10.1142/9781848163003_0018

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MODELING IL-2 GENE EXPRESSION IN HUMAN REGULATORY T CELLS
  • Pages:222–230

https://doi.org/10.1142/9781848163003_0019

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TOXICITY VERSUS POTENCY: ELUCIDATION OF TOXICITY PROPERTIES DISCRIMINATING BETWEEN TOXINS, DRUGS, AND NATURAL COMPOUNDS
  • Pages:231–242

https://doi.org/10.1142/9781848163003_0020

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COMPARATIVE VEGF RECEPTOR TYROSINE KINASE MODELING FOR THE DEVELOPMENT OF HIGHLY SPECIFIC INHIBITORS OF TUMOR ANGIOGENESIS
  • Pages:243–251

https://doi.org/10.1142/9781848163003_0021

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NETWORK ANALYSIS OF ADVERSE DRUG INTERACTIONS
  • Pages:252–259

https://doi.org/10.1142/9781848163003_0022

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SAMPLING GEOMETRIES OF PROTEIN-PROTEIN COMPLEXES
  • Pages:260–269

https://doi.org/10.1142/9781848163003_0023

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COMPUTER AIDED OPTIMIZATION OF CARBON ATOM LABELING FOR TRACER EXPERIMENTS
  • Pages:270–276

https://doi.org/10.1142/9781848163003_0024

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WEB-LINKS AS A MEANS TO DOCUMENT ANNOTATED SEQUENCE AND 3D-STRUCTURE ALIGNMENTS IN SYSTEMS BIOLOGY
  • Pages:277–284

https://doi.org/10.1142/9781848163003_0025

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BACK MATTER
  • Pages:285–286

https://doi.org/10.1142/9781848163003_bmatter

You have access to thisebook