This volume of Genome Informatics contains the full papers presented at the Fifth International Workshop on Bioinformatics and Systems Biology held in Berlin (Germany) from 22 - 25 August, 2005. This student-focused series of workshops is held annually since 2001 with an ever increasing number of participants. It is part of a collaborative program in bioinformatics and computational biology involving three leading research institutes: Boston University in the U.S., Kyoto University in Japan, and Humboldt University Berlin in Germany. Its main aim is to provide doctoral students and other young researchers with opportunities to present and discuss their research objectives, approaches and new results. The submissions were pre-screened by the scientific committee members and all papers were peer-reviewed. 30 papers were accepted after revision. It is for the second time that papers presented at our Workshop series are published (for the papers presented at the Fourth International Workshop, held 2004 in Kyoto, see Genome Informatics Series, Vol. 15, No. 1). The papers reflect the broad spectrum of workshop topics reaching from large scale data analysis to mechanism based modelling of cellular processes. The papers will soon be indexed in Medline, and their electronic versions are freely available from the website of the Japanese Society for Bioinformatics (

Reinhart Heinrich
Charles DeLisi
Minoru Kanehisa
Program Committee Co-Chairs


We would like to thank all authors for preparing their manuscripts and for performing the revisions within a tight time schedule. We appreciate the program committee members for making suggestions for the scientific program of the workshop and for their effort devoted to the process of selecting papers. We thank all scientists contributing to the reviewing process. We further appreciate the local organizing committee members for assisting us in the arrangements for the workshop venue. Special thanks are due to the workshop editorial office members for their excellent work, especially, Emi Ikeda, Seiya Imoto and Masao Nagasaki of Human Genome Center, University of Tokyo.
This event would not have been possible without the support of Humboldt-University (Berlin), the sponsorship of the Bioinformatics Center (Kyoto University), the Human Genome Center (University of Tokyo), the Bioinformatics Program (Boston University), the Graduate Program ``Dynamics and Evolution of Cellular and Macromolecular Processes" (German Research Foundation), the Education and Research Organization for Genome Information Science (Japan), the Kyoto University 21st Century COE Program ``Knowledge Information Infrastructure for Genome Science" and the Japanese Society for Bioinformatics.