Systems Biology

Part I. Foundation of Systems Biology, Integrative Biology and Issues of Biosystem Complexity, Redundancy and of Other Network Properties

1. Functional Genomics, Proteomics, Metabolomics and Bioinformatics for Systems Biology
Stéphane Ballereau, Enrico Glaab, Alexei Kolodkin, Amphun Chaiboonchoe, Maria Biryukov, Nikos Vlassis, Hassan Ahmed, Johann Pellet, Nitin Baliga, Leroy Hood, Reinhard Schneider, Rudi Balling, Charles Auffray

2. Comparing Biological Networks: A Survey on Graph Classifying Techniques
Laurin A. J. Mueller, Matthias Dehmer, Frank Emmert-Streib

3. Emergent Properties of Gene Regulatory Networks: Models and Data
Roberto Serra, Marco Villani

4. Regulatory Crosstalk Analysis of Biochemical Networks in the Hippocampus and Nucleus Accumbens
Shinichi Kikuchi, Eberhard O. Voit

5. Properties of Biological Networks
Vlado Dančík, Amrita Basu, Paul Clemons

Part II. Modeling of Ill-Defined, Lack of Knowledge (Experimental) Problems in the Field of Complex Biosystems Including Identification and Validation: A Review of Enabling Technologies

6. On Different Aspects of Network Analysis in Systems Biology
Amphun Chaiboonchoe, Wiktor Jurkowski, Johann Pellet, Enrico Glaab, Alexey Kolodkin, Antonio Raussel, Antony Béchec, Stéphane Ballereau, Laurene Meyniel, Isaac Crespo, Hassan Ahmed, Vitaly Volpert, Vincent Lotteau, Nitin Baliga, Leroy Hood, Antonio del Sol, Rudi Balling, Charles Auffray

7. Computational Approaches for Reconstruction of Time-Varying Biological Networks from Omics Data
Vinay Jethava, Chiranjib Bhattacharyya, Devdatt Dubhashi

8. Probabilistic Graphical Modeling in Systems Biology: A Framework for Integrative Approaches
Christine Sinoquet

9. Innovations of the Rule-Based Modeling Approach
Lily A. Chylek, Edward C. Stites, Richard G. Posner, William S. Hlavacek

10. Reproducibility of Model-Based Results in Systems Biology
Dagmar Waltemath, Ron Henkel, Felix Winter, Olaf Wolkenhauer

11. Parameter Identifiability and Redundancy, with Applications to a General Class of Stochastic Carcinogenesis Models
Mark P. Little, Wolfgang F. Heidenreich, Guangquan Li

12. Semantic Systems Biology: Formal Knowledge Representation in Systems Biology for Model Construction, Retrieval, Validation and Discovery
Michel Dumontier, Leonid L. Chepelev, Robert Hoehndorf

Part III. Critical Analysis of Multi-Scale Computational Methods and Tools, Computational Tools for Crossing Levels and Applications

13. Computational Infrastructures for Data and Knowledge Management in Systems Biology
Fotis Georgatos, Stéphane Ballereau, Johann Pellet, Moustafa Ghanem, Nathan Price, Leroy Hood, Yi-Ke Guo, Dominique Boutigny, Charles Auffray, Rudi Balling, Reinhard Schneider

14. Computational Tools and Resources for Integrative Modeling in Systems Biology
Christoph Wierling, Hendrik Hache

15. Agent-Based Modeling Approaches to Multi-Scale Systems Biology: An Example Agent-Based Model of Acute Pulmonary Inflammation
Gary An, Michael Wandling, Scott Christley

16. Reconstruction and Comparison of Cellular Signaling Pathway Resources for the Systems-Level Analysis of Cross-Talks
Máté Pálfy, László Földvári-Nagy, Dezső Módos, Katalin Lenti, Tamás Korcsmáros

17. A Survey of Current Integrative Network Algorithms for Systems Biology
Andrew K. Rider, Nitesh V. Chawla, Scott J. Emrich

18. Direct Computer Mapping Based Modeling of a Multiscale Process Involving p53/miR-34a Signaling
Béla Csukás, Mónika Varga, Aleš Prokop

Keywords: Biomedicine, Biomedicine general, Microbial Genetics and Genomics, Simulation and Modeling, Biomedical Engineering