D. Frishman & Alfonso Valencia 
Modern Genome Annotation [PDF ebook] 
The Biosapiens Network

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 Bio Sapiens 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.