Preface xvii
Contributors xix
A METHODOLOGICAL CHAPTERS 1
1 Two Challenges of Systems Biology 3
William S. Hlavacek
2 Introduction to Statistical Methods for Complex Systems 15
Tristan Mary-Huard and Stéphane Robin
3 Bayesian Inference and Computation 39
Christian P. Robert, Jean-Michel Marin and Judith Rousseau
4 Data Integration: Towards Understanding Biological Complexity 66
David Gomez-Cabrero and Jesper Tegner
5 Control Engineering Approaches to Reverse Engineering Biomolecular Networks 83
Francesco Montefusco, Carlo Cosentino and Declan G. Bates
6 Algebraic Statistics and Methods in Systems Biology 114
Carsten Wiuf
B TECHNOLOGY-BASED CHAPTERS 133
7 Transcriptomic Technologies and Statistical Data Analysis 135
Elizabeth Purdom and Sach Mukherjee
8 Statistical Data Analysis in Metabolomics 163
Timothy M.D. Ebbels and Maria De Iorio
9 Imaging and Single-Cell Measurement Technologies 181
Yu-ichi Ozaki and Shinya Kuroda
10 Protein Interaction Networks and Their Statistical Analysis 200
Waqar Ali, Charlotte Deane and Gesine Reinert
C NETWORKS AND GRAPHICAL MODELS 235
11 Introduction to Graphical Modelling 237
Marco Scutari and Korbinian Strimmer
12 Recovering Genetic Network from Continuous Data with Dynamic Bayesian Networks 255
Gaëlle Lelandais and Sophie Lèbre
13 Advanced Applications of Bayesian Networks in Systems Biology 270
Dirk Husmeier, Adriano V. Werhli and Marco Grzegorczyk
14 Random Graph Models and Their Application to Protein-Protein Interaction Networks 290
Desmond J. Higham and Natasa Przulj
15 Modelling Biological Networks via Tailored Random Graphs 309
Anthony C.C. Coolen, Franca Fraternali, Alessia Annibale, Luis Fernandes and Jens Kleinjung
D DYNAMICAL SYSTEMS 331
16 Nonlinear Dynamics: A Brief Introduction 333
Alessandro Moura and Celso Grebogi
17 Qualitative Inference in Dynamical Systems 339
Fatihcan M. Atay and Jurgen Jost
18 Stochastic Dynamical Systems 359
Darren J. Wilkinson
19 Gaussian Process Inference for Differential Equation Models of Transcriptional Regulation 376
Neil Lawrence, Magnus Rattray, Antti Honkela and Michalis Titsias
20 Model Identification by Utilizing Likelihood-Based Methods 395
Andreas Raue and Jens Timmer
E APPLICATION AREAS 417
21 Inference of Signalling Pathway Models 419
Tina Toni, Juliane Liepe and Michael P. H. Stumpf
22 Modelling Transcription Factor Activity 440
Martino Barenco, Daniel Brewer, Robin Callard and Michael Hubank
23 Host-Pathogen Systems Biology 451
John W. Pinney
24 Bayesian Approaches for Mass Spectrometry-Based Metabolomics 467
Simon Rogers, Richard A. Scheltema, Michael Barrett and Rainer Breitling
25 Systems Biology of microRNAs 477
Doron Betel and Raya Khanin
References 491
Index 495