Front matter
1-3
Cells as Computation
Amitai Regev and Ehud Shapiro
4-20
Formal Modeling of C. elegans Development: A Scenario-Based Approach
Na’aman Kam, David Harel, Hillel Kugler, Rami Marelly and Amir Pnueli, et al.
21-34
Causal π-Calculus for Biochemical Modelling
Michele Curti, Pierpaolo Degano and Cosima Tatiana Baldari
34-46
Graphs for Core Molecular Biology
Vincent Danos and Cosimo Laneve
47-56
Contribution of Computational Tree Logic to Biological Regulatory Networks: Example from Pseudomonas Aeruginosa
Sabine Peres and Comet Jean-Paul
57-74
Modeling Cellular Behavior with Hybrid Automata: Bisimulation and Collapsing
Marco Antoniotti, Bhubaneswar Mishra, Carla Piazza, Alberto Policriti and Marta Simeoni
75-87
Multiscale Modeling of Alternative Splicing Regulation
Damien Eveillard, Delphine Ropers, Hidde de Jong, Christiane Branlant and Alexander Bockmayr
88-103
A Method for Estimating Metabolic Fluxes from Incomplete Isotopomer Information
Juho Rousu, Ari Rantanen, Hannu Maaheimo, Esa Pitkänen and Katja Saarela, et al.
104-113
Dynamic Bayesian Network and Nonparametric Regression for Nonlinear Modeling of Gene Networks from Time Series Gene Expression Data
SunYong Kim, Seiy Imoto and Satoru Miyano
114-126
Discrete Event Simulation for a Better Understanding of Metabolite Channeling - A System Theoretic Approach
Daniela Degenring, Mathias Röhl and Adelinde M. Uhrmacher
127-141
Mathematical Modeling of the Influence of RKIP on the ERK Signaling Pathway
Cho Kwang-Hyun, Shin Sung-Young, Kim Hyun-Woo, Olaf Wolkenhauer and Brian McFerran, et al.
142-148
A Method to Identify Essential Enzymes in the Metabolism: Application to
Escherichia Coli
Ney Lemke, Fabiana Herédia, Cláudia K. Barcellos and José C. M. Mombach
149-162
Symbolic Model Checking of Biochemical Networks
Nathalie Chabrier and François Fages
163
Coupled Oscillator Models for a Set of Communicating Cells
Will Casey
164-165
Representing and Simulating Protein Functional Domains in Signal Transduction Using Maude
Steven Eker, Keith Laderoute, Patrick Lincoln, M.G. Sriram and Carolyn Talcott
166
A Core Modeling Language for the Working Molecular Biologist (Abstract)
Marc Chiaverini and Vincent Danos
167
Integrating Simulation Packages via Systems Biology Mark-Up Language
Manuel Corpas
168-169
Recreating Biopathway Databases towards Simulation
Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno and Satoru Miyano
170
How to Synthesize an Optimized Genetic λ-Switching System? A System-Theoretic Approach Based on SQP
Kwang-Hyun Cho, Jong-Ho Cha and Olaf Wolkenhauer
171
Simulation Sudy of the TNFα Mediated NF-κB Signaling Pathway
Kwang-Hyun Cho, Sung-Young Shin, Hyeon-Woo Lee and Olaf Wolkenhauer
172
Detection and Analysis of Unexpected State Components in Biological Systems
Anastasia Pagnoni and Andrea Visconti
173
Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis
Monika Heiner, Ina Koch and Jürgen Will
174
An Overview of Data Models for the Analysis of Biochemical Pathways
Yves Deville, David Gilbert, Jacques van Helden and Shoshana Wodak
175-177
Discrete Event Systems and Client-Server Model for Signaling Mechanisms
Gabriel Ciobanu and Dorin Huzum
178-181
Enhanced Operational Semantics in Systems Biology
Pierpaolo Degano and Corrado Priami
182-186
Issues in Computational Methods for Functional Genomics and Systems Biology
Magali Roux-Rouquié, Leroy Hood, Sandrine Imbeaud and Charles Auffray
187-193
Integrating Biological Process Modelling with Gene Expression Data and Ontologies for Functional Genomics (Position Paper)
Liviu Badea and Doina Tilivea
194-197
Computer Simulation of Protocells
Doron Lancet
198-201
How to Solve Semantic Puzzles of Systems Biology
Olaf Langmack
202-206
Evolution as Design Engineer
David L. Dill and Patrick Lincoln
207-211
Inference, Modeling and Simulation of Gene Networks
Satoru Miyano
Back matter