Computational Systems Biology

Table of Contents

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   Book Overview
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   Chapter 1 Identification of cis -Regulatory Elements in Gene Co-expression Networks Using A-GLAM
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   Chapter 2 Structure-Based Ab Initio Prediction of Transcription Factor–Binding Sites
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   Chapter 3 Inferring Protein–Protein Interactions from Multiple Protein Domain Combinations
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   Chapter 4 Prediction of Protein–Protein Interactions: A Study of the Co-evolution Model
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   Chapter 5 Computational Reconstruction of Protein–Protein Interaction Networks: Algorithms and Issues
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   Chapter 6 Prediction and Integration of Regulatory and Protein–Protein Interactions
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   Chapter 7 Detecting hierarchical modularity in biological networks.
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   Chapter 8 Methods to Reconstruct and Compare Transcriptional Regulatory Networks
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    Chapter 9 Learning Global Models of Transcriptional Regulatory Networks from Data
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    Chapter 10 Inferring Molecular Interactions Pathways from eQTL Data
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    Chapter 11 Methods for the Inference of Biological Pathways and Networks
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    Chapter 12 Exploring Pathways from Gene Co-expression to Network Dynamics
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    Chapter 13 Network Dynamics
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    Chapter 14 Kinetic Modeling of Biological Systems
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    Chapter 15 Guidance for Data Collection and Computational Modelling of Regulatory Networks
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    Chapter 16 A Maximum Likelihood Method for Reconstruction of the Evolution of Eukaryotic Gene Structure
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    Chapter 17 Enzyme Function Prediction with Interpretable Models
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    Chapter 18 Using Evolutionary Information to Find Specificity-Determining and Co-evolving Residues
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    Chapter 19 Connecting Protein Interaction Data, Mutations, and Disease Using Bioinformatics
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    Chapter 20 Effects of Functional Bias on Supervised Learning of a Gene Network Model
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    Chapter 21 Comparing Algorithms for Clustering of Expression Data: How to Assess Gene Clusters
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    Chapter 22 The Bioverse API and Web Application
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    Chapter 23 Computational Representation of Biological Systems
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    Chapter 24 Biological Network Inference and Analysis Using SEBINI and CABIN