1st Edition
Systems Biology and Bioinformatics A Computational Approach
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
