The ISMB conference series provides a general forum for disseminating the latest developments in bioinformatics. ISMB is a multidisciplinary conference that brings together scientists from computer science, mathematics, molecular biology and statistics. Its scope includes the development and application of advanced computational methods for biological problems. Relevant computational techniques include, but are not limited to: machine learning, pattern recognition, knowledge representation, databases, combinatorics, stochastic modeling, string and graph algorithms, linguistic methods, robotics, constraint satisfaction, and parallel computation. Biological areas of interest include biomolecular structure, genomics, biomolecular sequence analysis, evolution and phylogenetics, biomolecular interactions, metabolic pathways, regulatory networks, developmental control, and molecular biology generally. Emphasis is placed on the validation of methods using real data sets, on practical applications in the biological sciences, and on development of novel computational techniques.