Computational Systems Biology

Network Components.- Identification of cis-Regulatory Elements in Gene Co-expression Networks Using A-GLAM.- Structure-Based Ab Initio Prediction of Transcription Factor-Binding Sites.- Inferring Protein-Protein Interactions from Multiple Protein Domain Combinations.- Prediction of Protein-Protein Interactions: A Study of the Co-evolution Model.- Computational Reconstruction of Protein-Protein Interaction Networks: Algorithms and Issues.- Prediction and Integration of Regulatory and Protein-Protein Interactions.- Detecting Hierarchical Modularity in Biological Networks.- Network Inference.- Methods to Reconstruct and Compare Transcriptional Regulatory Networks.- Learning Global Models of Transcriptional Regulatory Networks from Data.- Inferring Molecular Interactions Pathways from eQTL Data.- Methods for the Inference of Biological Pathways and Networks.- Network Dynamics.- Exploring Pathways from Gene Co-expression to Network Dynamics.- Network Dynamics.- Kinetic Modeling of Biological Systems.- Guidance for Data Collection and Computational Modelling of Regulatory Networks.- Function and Evolutionary Systems Biology.- A Maximum Likelihood Method for Reconstruction of the Evolution of Eukaryotic Gene Structure.- Enzyme Function Prediction with Interpretable Models.- Using Evolutionary Information to Find Specificity-Determining and Co-evolving Residues.- Connecting Protein Interaction Data, Mutations, and Disease Using Bioinformatics.- Effects of Functional Bias on Supervised Learning of a Gene Network Model.- Computational Infrastructure for Systems Biology.- Comparing Algorithms for Clustering of Expression Data: How to Assess Gene Clusters.- The Bioverse API and Web Application.- Computational Representation of Biological Systems.- Biological NetworkInference and Analysis Using SEBINI and CABIN.

From the reviews: "The new volume of the Humana Press 'Methods in Molecular Biology' series, entitled 'Computational Systems Biology,' consists of 25 chapters authored by 57 specialists in the field. ... This book contains a wide collection of methods that ... gives a broad review of this fascinating and quickly developing field. ... for a computational biologist, it is a fascinating read, a broad and comprehensive resource on the current methods and approaches." (Borys Wróbel, Acta Biochimica Polonica, Vol. 56, December, 2009)