First of all, we would like to thank the authors for their efforts in preparing their manuscripts. We also appreciate the great efforts made by the program committee members and the external reviewers in the reviewing process. We further acknowledge the assistance from the local organizing committee members for arranging the conference venue. Special thanks are due to the conference editorial staff for their excellent work, especially, Emi Ikeda, Ayumu Saito, and Asako Suzuki. Finally, GIW 2009 was sponsored by the Human Genome Center of the Institute of Medical Science at the University of Tokyo, and the Japanese Society for Bioinformatics.