1st Edition

Systems Biology and Bioinformatics A Computational Approach

    190 Pages 23 B/W Illustrations
    by CRC Press

    190 Pages 23 B/W Illustrations
    by CRC Press

    The availability of molecular imaging and measurement systems enables today’s biologists to swiftly monitor thousands of genes involved in a host of diseases, a critical factor in specialized drug development. Systems Biology and Bioinformatics: A Computational Approach provides students with a comprehensive collection of the computational methods used in what is being coined the digital era of biology.

    Written by field experts with proven track records, this authoritative textbook first provides an introduction to systems biology and its impact on biology and medicine. The book then reviews the basic principles of molecular and cell biology using a system-oriented approach, with a brief description of the high-throughput biological experiments that produce databases.

    The text includes techniques to discover genes, perform nucleotide and amino acid sequence matching, and estimate static gene dynamic pathways. The book also explains how to use system-oriented models to predict the behavior of biological systems for important applications such as rational drug design. 

    The numerous examples and problem sets allow students to confidently explore practical systems biology applications using real examples with real biological data, making Systems Biology and Bioinformatics: A Computational Approach an ideal text for senior undergraduate and first-year graduate students.

    Cell Biology

    An Introduction to Cell Structure

    Proteins as Tools of the Cell

    Genes: Directors of the Cell

    Cell Cycle

    Bioassays

    Southern Blotting

    Fluorescent In Situ Hybridization

    Sanger (Dideoxy) Method

    Polymerase Chain Reaction

    Analyzing Protein Structure and Function

    Studying Gene Expression and Function—DNA Microarrays

    Review of Some Computational Methods

    Introduction to Probability and Stochastic Processes Theories

    Bayesian Theory

    Test of Hypothesis

    Expectation Maximization Method

    Maximum Likelihood Theory

    System Identification Theory

    Computational Structural Biology: Protein Structure Prediction

    Protein Structure Prediction Methods

    Data Resources

    Computational Structural Biology: Protein Sequence Analysis

    Pairwise Sequence Matching

    Multiple Sequence Alignment

    Genomics and Proteomics

    Genomics

    Proteomics

    Methods for Identification of Differentially Expressed Genes or Proteins

    Why t Test Is Not Enough?

    Mixture Model Method

    Genes Involved in Leukemia: A Case Study

    Binary and Bayesian Networks as Static Models of Regulatory Pathways

    Binary Regulator Pathways

    Bayesian Networks: Algorithm

    Applications and Practical Considerations

    Metabolic Control Theory for Static Modeling of Metabolic Pathways

    Basic Ideas

    Main Concepts in Metabolic Control Theory

    Mason Method

    Metabolic Control Model for Galactose Regulation Pathway: A Case Study

    System Identification and Control Theory for Dynamic Modeling of Biological Pathways

    Methodology

    Modeling of Cell Cycle: A Case Study

    Gene Silencing for Systems Biology

    A Brief Review of RNA Interference, Small Interfering RNA, and Gene Silencing Mechanisms

    Pathway Perturbation Using Gene Silencing

    Simulation and Systems Biology

    What Is Simulation?

    Challenges to Effective Simulation

    Case Studies

    Software, Databases, and Other Resources for Systems Biology

    Databases

    Scoring Matrix

    Analysis Software

    Bioinformatics in MATLAB

    Future Directions

    Single-Cell Microarray and Systems Biology

    High-Throughput Protein Assays and Systems Biology

    Integration of Molecular Data with Higher-Level Datasets

    Identifying Genes Controlling Macrolevel Changes

    Molecular-Level Image Systems and Systems Biology

    Index

    Biography

    Kayvan Najarian, Siamak Najarian, Shahriar Gharibzadeh, Christopher N. Eichelberger