Systems Biology is an approach to biology that involves understanding the complexity of interactions among biological entities within a systemic whole. The goal is to understand the emergence of physiological or functional properties.
Symbolic Approaches to Modeling and Analysis of Biological Systems presents contributions of formal methods from computer science for modeling the dynamics of biological systems. It deals more specifically with symbolic methods, i.e. methods that can establish the qualitative properties of models.
This book presents different approaches related to semantics, language, modeling and their link with data, and allows us to examine the fundamental problems and challenges that biological systems are facing. The first part of the book presents works that rely on various available data to build models, while the second part gathers contributions surrounding issues of semantics and formal methods.
Part 1. Models and Data.
1. Inference of Gene Regulatory Networks from Multi-scale Dynamic Data, Arnaud Bonnaffoux.
2. Combinatorial Optimization Problems for Studying Metabolism, Clémence Frioux and Anne Siegel.
3. The Challenges of Inferring Dynamic Models from Time Series, Tony Ribeiro, Maxime Folschette, Laurent Trilling, Nicolas Glade, Katsumi Inoue, Morgan Magnin and Olivier Roux.
4. Connecting Logical Models to Omics Data, Jonas Béal, Élisabeth Remy and Laurence Calzone.
Part 2. Formal and Semantic Methods.
5. Boolean Networks: Formalism, Semantics and Complexity, Loïc Paulevé.
6. Computational Logic for Biomedicine and Neurosciences, Elisabetta De Maria, Joëlle Despeyroux, Amy Felty, Pietro Lio, Carlos Olarte and Abdorrahim Bahrami.
7. The Cell: A Chemical Analog Calculator, François Fages and Franck Molina.
8. Formal Verification Methods for Modeling in Biology: Biological Regulation Networks, Gilles Bernot, Hélène Collavizza and Jean-Paul Comet.
9. Accessible Pattern Analyses in Kappa Models, Jérôme Fret.
Cédric Lhoussaine is a professor at the Université de Lille and head of the BioComputing team at the Research Center in Computer Science, Signal and Automatic Control of Lille (CRIStAL), France.
Élisabeth Remy is a CNRS research director at the Mathematics Institute of Marseille and head of the Mathematics and Algorithms for Biological Systems team (MABioS) at Aix Marseille Université, France.
Table of Contents
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