Algorithms in Bioinformatics

Abstract

These proceedings contain papers from the 2009 Workshop on Algorithms in Bioinformatics (WABI), held at the University of Pennsylvania in Philadelphia, Pennsylvania during September 12–13, 2009. WABI 2009 was the ninth annual conference in this series, which focuses on novel algorithms that address important problems in genomics, molecular biology, and evolution. The conference emphasizes research that describes computationally efficient algorithms and data structures that have been implemented and tested in simulations and on real data. WABI is sponsored by the European Association for Theoretical Computer Science (EATCS) and the International Society for Computational Biology (ISCB). WABI 2009 was supported by the Penn Genome Frontiers Institute and the Penn Center for Bioinformatics at the University of Pennsylvania. For the 2009 conference, 90 full papers were submitted for review by the Program Committee, and from this strong field of submissions, 34 papers were chosen for presentation at the conference and publication in the proceedings. The final program covered a wide range of topics including gene interaction networks, molecular phylogeny, RNA and protein structure, and genome evolution. Extended versions of selected papers will appear in a special issue of the journal Algorithms for Molecular Biology, published by BiomedCentral. We thank all the members of the Program Committee for their detailed and timely reviews, and we also thank the authors of all the papers, whose contributions made the workshop possible. Thanks also to the 2009 Keynote speakers, Shelley Berger of the Wistar Institute (Philadelphia, Pennsylvania) and Elchanan Mossel of the Weizmann Institute of Science (Rehovot, Israel). Above all, we want to extend our appreciation to the Organizing Committee at the University of Pennsylvania – Junhyong Kim (Chair), Stephen Fisher, and Li-San Wang – who handled all of the local arrangements, the conference website, and many other details that made the conference a success.