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 signalling.- Epigenetics of Spermiogenesis: combining in silico and proteomic approaches in the mouse model.- 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 system 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: 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.- Biological Networks: Methods for Structural Inference and Functional Module Identification inIntracellular Networks.- Methods for Dynamical Inference in Intracellular Networks.- ASIAN: Network Inference Web Server.- Bridging the Gap: Bioinformatics for Metabolomics.- Virtual Reality Meets Functional Genomics.- Systems Biology of Personalized Medicine.