This volume contains the papers presented at the 10th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2006), which was held in Venice, Italy, on April 2-5, 2006. The RECOMB conference serieswasstartedin1997bySorinIstrail,PavelPevznerandMichaelWaterman. The table on p. VIII summarizes the history of the meetings. RECOMB 2006 was hosted by the University of Padova at the Cinema Palace of the Venice Convention Center, Venice Lido, Italy. It was organized by a committee chaired by Concettina Guerra. A special 10th Anniversary Program Committee was formed, by including the members of the Steering Committee and inviting all Chairs of past editions. The Program Committee consisted of the 38 members whose names are listed on a separate page. From212submissionsofhighquality,40paperswereselectedforpresentation atthemeeting,andtheyappearintheseproceedings.Theselectionwasbasedon reviewsandevaluationsproducedbytheProgramCommitteemembersaswellas byexternalreviewers,andonasubsequentWeb-basedPCopenforum.Following thedecisionmadein2005bytheSteeringCommittee,RECOMBProceedingsare published as a volume of Lecture Notes in Bioinformatics (LNBI), which is - editedbythefoundersofRECOMB. Traditionally,theJournalofComputational Biology devotes a special issue to the publication of archival versions of selected conference papers. RECOMB 2006 featured seven keynote addresses by as many invited spe- ers: Anne-Claude Gavin (EMBL, Heidelberg, Germany), David Haussler (U- versity of California, Santa Cruz, USA), Ajay K. Royyuru (IBM T.J. Watson ResearchCenter, USA), David Sanko? (University of Ottawa,Canada), Michael S. Waterman (University of Southern California, USA), Carl Zimmer (Science Writer, USA), Roman A. Zubarev (Uppsala University, Sweden). The Stanislaw Ulam Memorial Computational BiologyLecture was given by Michael S. Wat- man. A special feature presentation was devoted to the 10th anniversary and is included in this volume.

This volume contains the papers presented at the 9th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2005), which was held in Cambridge, Massachusetts, on May 14-18, 2005. The RECOMB conference series was started in 1997 by Sorin Istrail, Pavel Pevzner and Michael Waterman. The list of previous meetings is shown below in the s- tion "Previous RECOMB Meetings. " RECOMB 2005 was hosted by the Broad Institute of MIT and Harvard, and Boston University's Center for Advanced - nomic Technology, and was excellently organized by the Organizing Committee Co-chairs Jill Mesirov and Simon Kasif. This year, 217 papers were submitted, of which the Program Committee - lected 39 for presentation at the meeting and inclusion in this proceedings. Each submission was refereed by at least three members of the Program Committee. After the completion of the referees' reports, an extensive Web-based discussion took place for making decisions. From RECOMB 2005, the Steering Committee decided to publish the proceedings as a volume of Lecture Notes in Bioinf- matics (LNBI) for which the founders of RECOMB are also the editors. The prominent volume number LNBI 3500 was assigned to this proceedings. The RECOMB conference series is closely associated with the Journal of Compu- tional Biology which traditionally publishes special issues devoted to presenting full versions of selected conference papers. The RECOMB Program Committee consistedof42members, aslistedonaseparatepage. Iwouldliketothank the RECOMB 2005 Program Committee members for their dedication and hard work.

The revised lectures presented in this volume are based on a course given by leading scholars at the C.I.M.E. Summer School held in Martina Franca, Italy, in July 2000.The 11 revised chapters presented were carefully revised and cross-reviewed in order to provide competent coverage of mathematical methods for protein structure analysis and design. The topics addressed pinpoint major issues arising in the development and analysis of models, algorithms, and software tools devoted to the structure of proteins, all of which play crucial roles in structural genomics and proteomics.

This book constitutes the post-proceedings of the DIMACS/RECOMB Satellite Workshop on Computational Methods for SNPs and Haplotype Inference held in Piscataway, NJ, USA, in November 2002.

The book presents ten revised full papers as well as abstracts of the remaining workshop papers. All relevant current issues in computational methods for SNP and haplotype analysis and their applications to disease associations are addressed.