Computational Systems Biology

ISBN: 978-1-58829-905-5 (Print) 978-1-59745-243-4 (Online)

Table of contents (24 protocols)

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  1. Front Matter

    Pages i-xviii

  2. Network Components

    1. Front Matter

      Pages 1-1

    2. No Access

      Book Protocol

      Pages 3-22

      Identification of cis-Regulatory Elements in Gene Co-expression Networks Using A-GLAM

    3. No Access

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      Pages 23-41

      Structure-Based Ab Initio Prediction of Transcription Factor–Binding Sites

    4. No Access

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      Pages 43-59

      Inferring Protein–Protein Interactions from Multiple Protein Domain Combinations

    5. No Access

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      Pages 61-88

      Prediction of Protein–Protein Interactions: A Study of the Co-evolution Model

    6. No Access

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      Pages 89-100

      Computational Reconstruction of Protein–Protein Interaction Networks: Algorithms and Issues

    7. No Access

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      Pages 101-143

      Prediction and Integration of Regulatory and Protein–Protein Interactions

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      Pages 145-160

      Detecting Hierarchical Modularity in Biological Networks

  3. Network Inference

    1. Front Matter

      Pages 1-1

    2. No Access

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      Pages 163-180

      Methods to Reconstruct and Compare Transcriptional Regulatory Networks

    3. No Access

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      Pages 181-210

      Learning Global Models of Transcriptional Regulatory Networks from Data

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      Pages 211-223

      Inferring Molecular Interactions Pathways from eQTL Data

    5. No Access

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      Pages 225-245

      Methods for the Inference of Biological Pathways and Networks

  4. Network Dynamics

    1. Front Matter

      Pages 1-1

    2. No Access

      Book Protocol

      Pages 249-267

      Exploring Pathways from Gene Co-expression to Network Dynamics

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      Pages 269-309

      Network Dynamics

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      Pages 311-335

      Kinetic Modeling of Biological Systems

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      Pages 337-354

      Guidance for Data Collection and Computational Modelling of Regulatory Networks

  5. Function and Evolutionary Systems Biology

    1. Front Matter

      Pages 1-1

    2. No Access

      Book Protocol

      Pages 357-371

      A Maximum Likelihood Method for Reconstruction of the Evolution of Eukaryotic Gene Structure

    3. No Access

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      Pages 373-420

      Enzyme Function Prediction with Interpretable Models

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      Pages 421-448

      Using Evolutionary Information to Find Specificity-Determining and Co-evolving Residues

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      Pages 449-461

      Connecting Protein Interaction Data, Mutations, and Disease Using Bioinformatics

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      Pages 463-475

      Effects of Functional Bias on Supervised Learning of a Gene Network Model

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