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This book constitutes the refereed proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2005, held in Cambridge, MA, USA in May 2005.§§The 39 revised full papers presented together with abstracts of keynote talks were carefully reviewed and selected from 217 submissions. As the top conference in computational molecular conference, RECOMB addresses all current issues in algorithmic and theoretical bioinformatics.