COMPUTATIONAL SYSTEMS BIOLOGY

Introducing Computational Systems Biology. A Kriete and R Eils I. Enabling Information and Integration Technologies for Systems Biology: 2. Databases for Systems Biology. J Eils, C Lawerenz, K Astrahantseff, M Ginkel, and R Eils Natural Language Processing and Ontology-enhanced Biomedical Literature Mining for Systems Biology. X Hu Integrated Imaging Informatics. B Parvin, G Fontenay, Q Yang, and MH Barcellos-Hoff Simpathica: A Computational Systems Biology Tool within the Valis BioinformaticsEnvironment. B Mishra, M Antoniotti, S Paxia and N Ugel Standards, Platforms and Applications. HM Sauro II. Foundations of Biochemical Network Analysis and Modeling 7. Introduction to Computational Models of Biochemical Reaction Networks. FJ Bruggeman, BM Bakker, JJ Hornberg, and HV Westerhoff 8. Biological Foundations of Signal Transduction and the Systems Biology Perspective. U Klingmüller 9. Reconstruction of Metabolic Network from Genome Information and Its Structural and Functional Analysis. H-W Ma and A-P Zeng 10. Integrated Regulatory and Metabolic Models. M.W. Covert III. Computer Simulations of Dynamic Networks 11. A Discrete Approach to Network Modeling. R Laubenbacher and P Mendes 12. Gene Networks: Estimation, Modeling and Simulation. S Imoto, H Matsuno, and S Miyano 13. Computational models for circadian rhythms: Deterministic versus stochastic approaches. J-C Leloup, D Gonze, and A Goldbeter IV. Multi-Scale Representations of Cells and Emerging Phenotypes 14. Multistability and Multicellularity: Cell Fates as High-dimensional Attractors of Gene Regulatory Networks. S Huang 15. Spatio-Temporal Systems Biology. A Ghosh, D Miller, R Zou, B Sokhansanj,and A Kriete 16. Cytomics from cell states to predictive medicine. G Valet, RF Murphy, JP Robinson, A Tárnok, A Kriete 17. The IUPS Physiome Project: Progress and Plans. P Hunter, K Burrowes, J Fernandez, P Nielsen, N Smith, and M Tawhai Subject Index