This volume contains the papers presented at the 12th Annual International ConferenceonREsearchin COmputationalMolecularBiology(RECOMB2008) held in Singapore, March 30-April 2, 2008. The RECOMB conference series was founded in 1997 by Sorin Istrail, Pavel Pevzner and Michael Waterman. Its history is summarized in the table herein. The general development of the RECOMB conference series is guided by a Steering Committee. RECOMB 2008 was hosted by the National University of Singapore and held at the University Cultural Centre. The Conference Chair was Limsoon Wong, who was supported by a 16-member-strong Organizing Committee. Out of 193 papers submitted to RECOMB 2008, the Program Committee (PC) selected 34 papers for presentation at the conference. The PC consisted of 46 members, who could further draw on the help of subreviewers. Three PC members with possible help of the external reviewers ?rst reviewed each paper, subsequently a Web-based discussion led to the ?nal selection of papers. This year, RECOMB and the journal Genome Research teamed up to - fer authors Genome Research as an alternative forum for publication. Appro- mately 55 of the RECOMB submissions, selected by a subset of the PC headed by Sera?m Batzoglou, were forwarded to Genome Research for consideration.