Systems Biology for Signaling Networks

1. Systems Biology Approaches: Solving New Puzzles in a Symphonic Manner
Sangdun Choi

2. Current Progress in Static and Dynamic Modeling of Biological Networks
Bernie J. Daigle, Balaji S. Srinivasan, Jason A. Flannick, Antal F. Novak, Serafim Batzoglou

3. Getting Started in Biological Pathway Construction
Rebecca A. Sealfon, Stuart C. Sealfon

4. From Microarray to Biology
Mikhail Dozmorov, Robert E. Hurst

5. Computational Procedures for Model Identification
Eva Balsa-Canto, Julio R. Banga

6. Assembly of Logic-Based Diagrams of Biological Pathways
Tom C. Freeman

7. Automating Mathematical Modeling of Biochemical Reaction Networks
Andreas Dräger, Adrian Schröder, Andreas Zell

8. Strategies to Investigate Signal Transduction Pathways with Mathematical Modelling
Julio Vera, Svetoslav Nikolov, Olaf Wolkenhauer

9. Inferring Transcriptional Regulatory Network
Ming Zhan

10. Finding Functional Modules
Mutlu Mete, Fusheng Tang, Xiaowei Xu, Nurcan Yuruk

11. Modeling the Dynamics of Biological Networks from Time Course Data
Sašo Džeroski, Ljupčo Todorovski

12. Decision Making in Cells
Tomáš Helikar, Naomi Kochi, John Konvalina, Jim A. Rogers

13. Robustness of Neural Network Models
Daniel W. Franks, Graeme D. Ruxton

14. Functional Modules in Protein–Protein Interaction Networks
Tobias Müller, Marcus Dittrich

15. Mixture Model on Graphs: A Probabilistic Model for Network-Based Analysis of Proteomic Data
Josselin Noirel, Guido Sanguinetti, Phillip C. Wright

16. Integration of Network Information for Protein Function Prediction
Xiaoyu Jiang, Eric D. Kolaczyk

17. Cellular-Level Gene Regulatory Networks: Their Derivation and Properties
Benjamin Bivort

18. Tyrosine-Phosphoproteome Dynamics
Masaaki Oyama, Shinya Tasaki, Hiroko Kozuka-Hata

19. Systems Biology of the MAPK1,2 Network
Melissa Muller, Prahlad T. Ram

20. Pathway Crosstalk Network
Yong Li

21. Crosstalk Between Mitogen-Activated Protein Kinase and Phosphoinositide-3 Kinase Signaling Pathways in Development and Disease
Jijun Hao, Marie A. Daleo, Charles C. Hong

22. Systems-Level Analyses of the Mammalian Innate Immune Response
David J. Lynn, Jennifer L. Gardy, Christopher D. Fjell, Robert E.W. Hancock, Fiona S.L. Brinkman

23. Molecular Basis of Protective Anti-Inflammatory Signalling by Cyclic AMP in the Vascular Endothelium
Claire Rutherford, Timothy M. Palmer

24. Construction of Cancer-Perturbed Protein–Protein Interaction Network of Apoptosis for Drug Target Discovery
Liang-Hui Chu, Bor-Sen Chen

25. Transcriptional Changes in Alzheimer’s Disease
Jeremy A. Miller, Daniel H. Geschwind

26. Pathogenesis of Obesity-Related Chronic Liver Diseases as the Study Case for the Systems Biology
Ancha Baranova, Aybike Birerdinc, Michael Estep, Zobair M. Younossi

27. The Evolving Transcriptome of Head and Neck Squamous Cell Carcinoma
Yau -Hua Yu

28. Peptide Microarrays for a Network Analysis of Changes in Molecular Interactions in Cellular Signalling
Michael D. Sinzinger, Roland Brock

29. A Primer on Modular Mass-Action Modelling with CellML
Michael T. Cooling

30. FERN – Stochastic Simulation and Evaluation of Reaction Networks
Florian Erhard, Caroline C. Friedel, Ralf Zimmer

31. Programming Biology in BlenX
Lorenzo Dematté, Roberto Larcher, Alida Palmisano, Corrado Priami, Alessandro Romanel

32. Discrete Modelling: Petri Net and Logical Approaches
Ina Koch, Claudine Chaouiya

33. ProteoLens: A Database-Driven Visual Data Mining Tool for Network Biology
Jake Yue Chen, Tianxiao Huan

34. MADNet: A Web Server for Contextual Analysis and Visualization of High-Throughput Experiments
Igor Šegota, Petar Glažar, Kristian Vlahoviček

Nyckelord: Biomedicine, Human Genetics, Bioinformatics, Cell Biology, Computer Appl. in Life Sciences, Immunology