Computational Systems Biology

Systems Biology is concerned with the quantitative study of complex biosystems at the molecular, cellular, tissue, and systems scales. Its focus is on the function of the system as a whole, rather than on individual parts. This exciting new arena applies mathematical modeling and engineering methods to the study of biological systems. This book is the first of its kind to focus on the newly emerging field of systems biology with an emphasis on computational approaches. The work covers new concepts, methods for information storage, mining and knowledge extraction, reverse engineering of gene and metabolic networks, as well as modelling and simulation of multi-cellular systems. Central themes include strategies for predicting biological properties and methods for elucidating structure-function relationships. Introducing computational systems biology / Andres Kriete and Roland Eils Enabling information and integration technologies for systems biology. Databases for systems biology / Jürgen Eils ... [et al.] Natural language processing and ontology-enhanced biomedical literature mining for systems biology / Xiaohua Hu Integrated imaging informatics / Barham Parvin ... [et al.] Simpathica : a computational systems biology tool within the valis bioinformatics environment / Bud mishra ... [et al.] Standards, platforms, and applications / Herbert M. Sauro Foundations of biochemical network analysis and modeling. Introduction to computational models of biochemical reaction networks / F.J. Bruggeman ... [et al.] Biological foundations of signal transduction and the systems biology perspective / Ursula Klingmüller Reconstruction of metabolic network from genome information and its structural and functional analysis / Hong-Wu Ma and An-Ping Zeng Integrated regulatory and metabolic models / Markus W. Covert Computer simulations of dynamic networks. A discrete approach to network modeling / Reinhard Laubenbacher and Pedro Mendes Gene networks : estimation, modeling and simulation / Seiya Imoto, Hiroshi Matsuno, and Satoru Miyano Computational models for circadian rhythms : deterministic versus stochastic approaches / Jean-Christophe Leloup, Didier Gonze, and Albert Goldbeter Multi-scale representations of cells and emerging phenotypes. Multistability and multicellularity : cell fates as high-dimensional attractors of gene regulatory networks / Sui Huang Spatio-temporal systems biology / Avijit ghosh ... [et al.] Cytomics from cell states to predictive medicine / Günter Valet ... [et al.] The IUPS Physiome Project : progress and plans / Peter Hunter ... [et al.] Computational systems biology is a field that aims to develop a systems level understanding of biological processes using computational techniques. This book presents a compendium of the state-of-the-art in this new era of biological understanding. The contributors review bioinformation engineering and data integration technologies along with biomedical applications. Different computational approaches to model and simulate biological systems are discussed. Current computational research efforts, comprehensively covered in this volume, are focused on regulatory, signaling and metabolic networks. New concepts for computer representations on multi-scales predicting emergent properties of biological systems are introduced.