Bioinformatics for Systems Biology (eBook)

Preface 4
Contents 6
Contributors 9
Life of a Cell and Its Analysis 12
Structure and Function of the Nucleus and Cell Organelles 13
Transcription and the Control of Gene Expression 42
RNA Processing and Translation 59
DNA Replication, Recombination, and Repair 75
Cell Signaling 96
Epigenetics of Spermiogenesis 112
Genomic Tools for Analyzing Transcriptional Regulatory Networks 125
Statistical Tools and Their Application 143
Probability and Hypothesis Testing 144
Stochastic Models for Biological Patterns 156
Population Genetics 168
Statistical Tools for Gene Expression Analysis and Systems Biology and Related Web Resources 186
Transcriptome Analysis 211
What Goes in is What Comes Out: How to Design and Implement a Successful Microarray Experiment 212
Tools and Approaches for an End-to-End Expression Array Analysis 229
Analysis of Alternative Splicing with Microarrays 268
Structural and Functional Sequence Analysis 281
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? 282
A Spectrum of Phylogenetic-Based Approaches for Predicting Protein Functional Sites 313
The Role of Transcription Factor Binding Sites in Promoters and Their In Silico Detection 336
In Silico Discovery of DNA Regulatory Sites and Modules 350
Literature Mining for Association and Meaning 364
Mining the Research Literature in Systems Biology 365
GoPubMed: Exploring PubMed with Ontological Background Knowledge 380
BiblioSphere — Hypothesis Generation in Regulatory Network Analysis 395
Biological Knowledge Extraction 407
Genomic Databases 428
Using KEGG in the Transition from Genomics to Chemical Genomics 429
Ensembl 445
Management of Spatially Organized Biological Data using EMAGE 460
Equality of the Sexes? Parent-of-Origin Effects on Transcription and de novo Mutations 476
Biological Networks 505
Methods for Structural Inference and Functional Module Identification in Intracellular Networks 506
Methods for Dynamical Inference in Intracellular Networks 529
ASIAN: Network Inference Web Server 550
Bridging the Gap 565
Bioinformatics for Metabolomics 566
Virtual Reality Meets Functional Genomics 585
Systems Biology of Personalized Medicine 598
Index 614