BIOSAPIENS: A European Network of Excellence to develop genome annotation resources -- BIOSAPIENS: A European Network of Excellence to develop genome annotation resources -- Gene definition -- State of the art in eukaryotic gene prediction -- Quality control of gene predictions -- 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 -- Annotation and genetics -- Annotation, genetics and transcriptomics -- 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 -- Protein structure prediction -- Structure prediction of globular proteins -- The state of the art of membrane protein structure prediction: from sequence to 3D structure -- Protein-protein complexes, pathways and networks -- Computational analysis of metabolic networks -- Protein-protein interactions: analysis and prediction -- Infrastructure for distributed protein annotation -- Infrastructure for distributed protein annotation -- Applications -- Viral bioinformatics -- Alternative splicing in the ENCODE protein complement.