This volume contains 25 peer-reviewed papers based on the presentations at the 8th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2008) held at the Teikyo Hotel, Zeuten Lake, near Berlin, from June 9 to June 10, 2008. This workshop started in 2001 as an event for doctoral students and young researchers to present and discuss their research results and approaches in bioinformatics and systems biology. It is part of a collaborative educational program involving leading institutions and leaders committed to the following programs and partner institutions:

Boston (Gary Benson) Graduate Program in Bioinformatics, Boston University

Berlin (Herman-Georg Holzhtter) The International Research Training Group (IRTG) "Genomics and Systems Biology of Molecular Networks"

Kyoto/Tokyo (Minoru Kanehisa/Satoru Miyano) Joint Bioinformatics Education Program of Kyoto University and University of Tokyo.

We are pleased to present the proceedings of the Third Workshop on Algorithms in Bioinformatics (WABI 2003), which took place on September 15-20, 2003 in Budapest, Hungary. The WABI workshop was part of the four-conference meeting, ALGO 2003, which was locally organized by Dr. Jan ' os Csirik, Head of the Department of Computer Science, J' ozsef Attila University, Budapest. See http://www. conferences. hu/ALGO2003/algo_2003. htmfor more details. WABI focuses on discrete algorithms that address important problems in molecular biology, genomics, and genetics, that are founded on sound models, that are computationally e?cient, that have been implemented and tested in simulations and on real datasets, and that provide new biological results. The workshopgoalsareto presentrecentresearchandidentify andexploredirections for future research. We received78 submissionsin responseto the call for papers and 36 were- cepted. We wouldliketo sincerelythank the authorsof allsubmitted papers and the conference participants. We especially thank a terri?c program committee for their diligent and thorough work in reviewing and selecting the papers.