Elements of Computational Systems Biology

Preface.
Contributors.
PART I: OVERVIEW.
1 Advances in Computational Systems Biology (Huma M.Lodhi).
PART II: BIOLOGICAL NETWORK MODELING.
2 Models in Systems Biology: The Parameter Problem and theMeanings of Robustness (Jeremy Gunawardena).
3 In Silico Analysis of Combined Therapeutics Strategy forHearth Failure (Sung-Young Shin, Tae-Hwan Kim, Kwang-Hyun Cho,and Sang-Mok Choo).
4 Rule-Based Modeling and Model Refinement (Elaine Murphy,Vincent Danos, Jerome Feret, Jean Krivine, and RussellHarmer).
5 A (Natural) Computing Perspective on Cellular Processes(Mateo Cavaliere and Tommaso Mazza).
6 Simulating Filament Dynamics in Cellular Systems (Wilbur E.Channels and Pablo A. Iglesias).
PART III: BIOLOGICAL NETWORK INFERENCE.
7 Reconstruction of Biological Networks by Supervised MachineLearning Approaches (Jean-Philippe Vert).
8 Supervised Inference of Metabolic Networks from theIntegration of Genomic Data and Chemical Information (YoshihiroYamanishi).
9 Integrating Abduction and Induction in Biological InferenceUsing CF-Induciton (Yoshitaka Yamamoto, Katsumi Inoue, andAndrei Doncescu).
10 Analysis and Control of Deterministic and ProbabilisticBoolean Networks (Tatsuya Akutsu and Wai-Ki Ching).
11 Probabilistic Methods and Rate Heterogeneity (Tal Pupkoand Itay Mayrose).
PART IV: GENOMICS AND COMPUTATIONAL SYSTEMS BIOLOGY.
12 From DNA Motifs to Gene Networks: A Review of PhysicalInteraction Models (Panayiotis V. Benos and Alain B.Tchagang).
13 The Impact of Whole Genome In Silico Screening forNuclear Receptor-Binding Sites in Systems Biology (CarstenCarlberg and Merja Heinaniemi).
14 Environmental and Physiological Insights from MicrobialGenome Sequences (Alessandra Carbone and AnthonyMathelier).
PART V: SOFTWARE TOOLS FOR SYSTEMS BIOLOGY.
15 Ali Baba: A Text Mining Tool for Systems Biology (JorgHakenberg, Conrad Plake, and Ulf Leser).
16 Validation Issues in Regulatory Module Discovery (AlokMishra and Duncan Gillies).
17 Computational Imaging and Modeling for Systems Biology(Ling-Yun Wu, Xiaobo Zhou, and Stephen T.C. Wong).
Index.
Series Information.