Preliminary -- Introduction BIOSAPIENS: A European Network of Excellence to develop genome annotation resources -- Section 1 / Gene definition -- State of the art in eukaryotic gene prediction -- Quality control of gene predictions -- Section 2 / Gene regulation and expression -- Evaluating the prediction of cis-acting regulatory elements in genome sequences -- A biophysical approach to large-scale protein-DNA binding data -- From gene expression profiling to gene regulation -- Section 3 / Annotation and genetics -- Annotation, genetics and transcriptomics -- Section 4 / Functional annotation of proteins -- Resources for functional annotation -- Annotating bacterial genomes -- Data mining in genome annotation -- Modern genome annotation: the BioSapiens network -- Structure to function -- Harvesting the information from a family of proteins -- Section 5 / Protein structure prediction -- Structure prediction of globular proteins -- The state of the art of membrane protein structure prediction: from sequence to 3D structure -- Section 6 / Protein-protein complexes, pathways and networks -- Computational analysis of metabolic networks -- Protein-protein interactions: analysis and prediction -- Section 7 / Infrastructure for distributed protein annotation -- Infrastructure for distributed protein annotation -- Section 8 / Applications -- Viral bioinformatics -- Alternative splicing in the ENCODE protein complement -- Back matter.