Systems Biology is the systematic study of the interactions between the components of a biological system and studies how these interactions give rise to the function and behavior of the living system. Through this, a life process is to be understood as a whole system rather than the collection of the parts considered separately. Systems Biology is therefore more than just an emerging field: it represents a new way of thinking about biology with a dramatic impact on the way that research is performed. The logical approach provides an intuitive method to provide explanations based on an expressive relational language.
This book covers various aspects of logical modeling of biological systems, bringing together 10 recent logic-based approaches to Systems Biology by leading scientists. The chapters cover the biological fields of gene regulatory networks, signaling networks, metabolic pathways, molecular interaction and network dynamics, and show logical methods for these domains based on propositional and first-order logic, logic programming, answer set programming, temporal logic, Boolean networks, Petri nets, process hitting, and abductive and inductive logic programming.
It provides an excellent guide for all scientists, biologists, bioinformaticians, and engineers, who are interested in logic-based modeling of biological systems, and the authors hope that new scientists will be encouraged to join this exciting scientific endeavor.
Tabela de Conteúdo
Foreword xiii
Luis Fariñas Del Cerro
Chapter 1 Symbolic Representation and Inference or Regulatory
Network Structures 1
Nataly Maimari, Krysia Broda, Antonis Kakas, Rob Krams and
Alessandra Russo
Chapter 2 Reasoning on the Response of Logical Signaling
Networks with ASP 49
Torsten Schaub, Anne Siegek and Santiago Videla
Chapter 3 A Logical Model for Molecular Interaction Maps
93
Robert De Molombe, Luis Farinas Del Cerro and Naji Obeid
Chapter 4 Analyzing Large Network Dynamics with Process Hitting
125
Loic Paulevé, Courtney Chancellor, Maxime Folschette, Morgan
Magnin and Olivier Roux
Chapter 5 ASP for Construction and Validation of Regulatory
Biological Networks
Alexandre Rocca, Nicolas Mobilia, Éric Fanchon, Tony
Ribeiro, Laurent Trilling and Katsumi Inoue
Chapter 6 Simulation-Based Reasoning about Biological Pathways
Using Petri Nets and ASP 207
Saadat Anwar, Chitta Barbal and Katsumi Inoue
Chapter 7 Formal Methods Applied to Gene Networks Modeling
245
Gilles Bernot, Jean-Paul Comet and El Houssine Snaussi
Chapter 8 Temporal Logic Modeling of Dynamical Behaviors:
First-Order Patterns and Solvers 291
François Fages and Pauline Traynard
Chapter 9 Analyzing SBGN-AF Networks Using Normal Logic Programs
325
Adrien Rougny, Christine Froidevaux, Yoshitaka Yamamoto and
Katsumi Inoue
Chapter 10 Machine Learning of Biological Networks Using
Abductive ILP 363
Alireza Tamassoni, Diahuan Lin, Hiroaki Watanabe, Jianzhong Chen
and Stephen Muggleton
List of Authors 403
Index 407
Sobre o autor
Luis Fariñas del Cerro, Professor, IRIT, Toulouse, France.
Katsumi Inoue, Professor, NII, Tokyo, Japan.
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