Bioinformatics for Systems Biology - Editor Krawetz, Stephen, 2nd Edition (2009)

With continued informatic and biological cross-fertilization, advancements in Systems Biology will revolutionize personalized medicine answering questions by integrating information in unexpected ways.

Table of Contents

Part I - Life of a Cell and Its Analysis

- Structure and Function of the Nucleus and Cell Organelles
- Transcription and the Control of Gene Expression
- RNA Processing and Translation
- DNA Replication, Recombination, and Repair
- Cell signalling
- Epigenetics of Spermiogenesis -- combining in silico and proteomic approaches in the mouse model
- Genomic Tools for Analyzing Transcriptional Regulatory Networks

Part II - Statistical Tools and Their Application

- Probability and Hypothesis Testing
- Stochastic Models for Biological Patterns
- Population Genetics
- Statistical tools for gene expression analysis and system biology and related web resources

Part III - Transcriptome Analysis

- What goes in is what comes out -- How to design and implement a successful microarray experiment
- Tools and Approaches for an End-to-End Expression Array Analysis
- Analysis of alternative splicing with microarrays

Part IV - Structural and Functional Sequence Analysis

- An Introduction to Multiple Sequence Alignment — and the T-Coffee Shop. Beyond just aligning sequences: how good can you make your alignment, and so what?
- A spectrum of phylogenetic-based approaches for predicting protein functional sites
- The role of Transcription Factor Binding Sites in Promoters and Their In Silico Detection
- In silico Discovery of DNA Regulatory Sites and Modules

Part V - Literature Mining for Association and Meaning

- Mining the Research Literature in Systems Biology
- GoPubMed: Exploring PubMed with Ontological Background Knowledge
- BiblioSphere - Hypothesis Generation in Regulatory Network Analysis
- Biological Knowledge Extraction

Part VI - Genomic Databases

- Using KEGG in the Transition from Genomics to Chemical Genomics
- Ensembl: Open-Source Software for Large-Scale Genome Analysis
- Management of spatially organised biological data using EMAGE
- Equality of the sexes? Parent-of-origin effects on transcription and de novo mutations

Part VII - Biological Networks

- Methods for Structural Inference and Functional Module Identification in Intracellular Networks
- Methods for Dynamical Inference in Intracellular Networks
- ASIAN: Network Inference Web Server

Part VIII Bridging the Gap

- Bioinformatics for Metabolomics
- Virtual Reality Meets Functional Genomics
- Systems Biology of Personalized Medicine