Bioinformatics for Systems Biology

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 Signaling.- Epigenetics of Spermiogenesis.- Genomic Tools for Analyzing Transcriptional Regulatory Networks.- Statistical Tools and Their Application.- Probability and Hypothesis Testing.- Stochastic Models for Biological Patterns.- Population Genetics.- Statistical Tools for Gene Expression Analysis and Systems Biology and Related Web Resources.- 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.- 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.- 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.- Genomic Databases.- Using KEGG in the Transition from Genomics to Chemical Genomics.- Ensembl.- Management of Spatially Organized Biological Data using EMAGE.- Equality of the Sexes? Parent-of-Origin Effects on Transcription and de novo Mutations.- BiologicalNetworks.- Methods for Structural Inference and Functional Module Identification in Intracellular Networks.- Methods for Dynamical Inference in Intracellular Networks.- ASIAN: Network Inference Web Server.-