Genome Informatics Vol. 20 (2008)

Presented at the The Eighth Annual International Workshop on Bioinformatics and Systems Biology
June 9 - 11, 2007, Berlin, Germany

Published as: E.-W. Knapp, G. Benson, H.-G. Holzh├╝tter, M. Kanehisa, S. Miyano
"Genome Informatics Vol. 20"
Imperial College Press, London

Preface by Ernst-Walter Knapp, Gary Benson, Hermann-Georg Holzh├╝tter, Minoru Kanehisa and Satoru Miyano

Program Committee


Papers

Exploring the Effect of Variable Enzyme Concentrations in a Kinetic Model of Yeast Glycolysis
József Bruck, Wolfram Liebermeister, Edda Klipp
Genome Informatics 20: 1-14 (2008)
[Abstract]   [Full-text HTML]   [Full-text PDF]

The Role of IP3R Clustering in Ca2+ Signaling
Alexander Skupin, Martin Falcke
Genome Informatics 20: 15-24 (2008)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Rule-Based Reasoning for System Dynamics in Cell Systems
Euna Jeong, Masao Nagasaki, Satoru Miyano
Genome Informatics 20: 25-36 (2008)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Estimation of Nonlinear Gene Regulatory Networks via L1 Regularized NVAR from Time Series Gene Expression Data
Kaname Kojima, André Fujita, Teppei Shimamura, Seiya Imoto, Satoru Miyano
Genome Informatics 20: 37-51 (2008)
[Abstract]   [Full-text HTML]   [Full-text PDF]

ModelMage: A Tool for Automatic Model Generation, Selection and Management
Max Flötmann, Jörg Schaber, Stephan Hoops, Edda Klipp, Pedro Mendes
Genome Informatics 20: 52-63 (2008)
[Abstract]   [Full-text HTML]   [Full-text PDF]

A Framework for Determining Outlying Microarray Experiments
Raymond Wan, Åsa M. Wheelock, Hiroshi Mamitsukal
Genome Informatics 20: 64-76 (2008)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Exploring the Impact of Osmoadaptation on Glycolysis Using Time-Varying Reponse-Coefficients
Clemens Kühn, Elzbieta Petelenz, Bodil Nordlander, Jörg Schaber, Stefan Hohmann, Edda Klipp
Genome Informatics 20: 77-90 (2008)
[Abstract]   [Full-text HTML]   [Full-text PDF]   [Supplementary Data]

Comparing Flux Balance Analysis to Network Expansion: Producibility, Sustainability and the Scope of Compounds
Kai Kruse, Oliver Ebenhöh
Genome Informatics 20: 91-101 (2008)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Semi-Supervised Graph Partitioning with Decision Trees
Timothy Hancock, Hiroshi Mamitsuka
Genome Informatics 20: 102-111 (2008)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Measuring Correlations in Metabolomic Networks with Mutual Information
Jorge Numata, Oliver Ebenhöh, Ernst-Walter Knapp
Genome Informatics 20: 112-122 (2008)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Optimality Criteria for the Prediction of Metabolic Fluxes in Yeast Mutants
Evan S. Snitkin, Daniel Segré
Genome Informatics 20: 123-134 (2008)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Biosynthetic Potentials from Species-Specific Metabolic Networks
Georg Basler, Zoran Nikoloski, Oliver Ebenhöh, Thomas Handorf
Genome Informatics 20: 135-148 (2008)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Generalized Reaction Patterns for Prediction of Unknown Enzymatic Reactions
Yugo Shimizu, Masahiro Hattori, Susumu Goto, Minoru Kanehisa
Genome Informatics 20: 149-158 (2008)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Optimal Metabolic Regulation Using a Constraint-Based Model
William J. Riehl, Daniel Segré
Genome Informatics 20: 159-170 (2008)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Comparative Determination of Biomass Composition in Differentially Active Metabolic States
Hsuan-Chao Chiu, Daniel Segré
Genome Informatics 20: 171-182 (2008)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Suffix Techniques as a Rapid Method for RNA Substructure Search
Raphael A. Bauer, Kristian Rother, Janusz M. Bujnicki, Robert Preissner
Genome Informatics 20: 183-198 (2008)
[Abstract]   [Full-text HTML]   [Full-text PDF]

The Relationship between Fine Scale DNA Structure, GC Content, and Functional Elements in 1% of the Human Genome
Stephen C.J. Parker, Elliott H. Margulies, Thomas D. Tullius
Genome Informatics 20: 199-211 (2008)
[Abstract]   [Full-text HTML]   [Full-text PDF]

A Novel Strategy to Search Conserved Transcription Factor Binding Sites among Coexpressing Genes in Human
Yosuke Hatanaka, Masao Nagasaki, Rui Yamaguchi, Takeshi Obayashi, Kazuyuki Numata, André Fujita, Teppei Shimamura, Yoshinori Tamada, Seiya Imoto, Kengo Kinoshita, Kenta Nakai, Satoru Miyano
Genome Informatics 20: 212-221 (2008)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Modeling IL-2 Gene Expression in Human Regulatory T Cells
Manuela Benary, Hanna Bendfeldt, Ria Baumgrass, Hanspeter Herzel
Genome Informatics 20: 222-230 (2008)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Toxicity vs Potency: Elucidation of Toxicity Properties Disscriminating between Toxins, Drugs, and Natural Compounds
Swantje Struck, Ulrike Schmidt, Bjoern Gruening, Ines S. Jaeger, Julia Hossbach, Robert Preissner
Genome Informatics 20: 231-242 (2008)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Comparative VEGF Receptor Tyrosine Kinase Modeling for the Development of Highly Specific Inhibitors of Tumor Angiogenesis
Ulrike Schmidt, Jessica Ahmed, Elke Michalsky, Michael Hoepfner, Robert Preissner
Genome Informatics 20: 243-251 (2008)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Network Analysis of Adverse Drug Interactions
Masataka Takarabe, Shujiro Okuda, Masumi Itoh, Toshiaki Tokimatsu, Susumu Goto, Minoru Kanehisa
Genome Informatics 20: 252-259 (2008)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Sampling Geometries of Protein-Protein Complexes
Aysam Guerler, Stephan Lorenzen, Floran Krull, Ernst-Walter Knapp
Genome Informatics 20: 260-269 (2008)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Computer Aided Optimization of Carbon Atom Labeling for Tracer Experiments
Benjamin Sefa Menküc, Christoph Gille, Hermann-Gorge Holzhütter
Genome Informatics 20: 270-276 (2008)
[Abstract]   [Full-text HTML]   [Full-text PDF]

Web-links as a Means to Document Annotated Sequence and 3D Structure Alignments in Systems Biology
Christoph Gille, Andreas Hoppe, Hermann-Georg Holzhütter
Genome Informatics 20: 277-284 (2008)
[Abstract]   [Full-text HTML]   [Full-text PDF]