Systems Biology and Bioinformatics

About this book

Emphasizing computational methods, "Systems Biology and Bioinformatics" provides an introduction to system biology and its impact on biology and medicine. The book 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 methods presented in the text include 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.

Contents

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

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Biography

Virginia Commonwealth University, Richmond, VA, USA Amirkabir University of Technology, Tehran, Iran University of North Caroline, Charlotte, USA