Scope

All research on algorithmic work in bioinformatics and systems biology. The emphasis is on discrete algorithms and machine-learning methods that address important problems in molecular biology, that are founded on sound models, that are computationally efficient, and that have been implemented and tested in simulations and on real datasets. The goal is to present recent research results, including significant work-in-progress, and to identify and explore directions of future research.

The Workshop on Algorithms in Bioinformatics (WABI) is sponsored by EATCS (the European Association for Theoretical Computer Science) and ISCB (the International Society for Computational Biology). WABI09 is supported by the Penn Genome Frontiers Institute and the Penn Center for Bioinformatics.

Topics

Original research papers (including significant work-in-progress) are solicited in all aspects of algorithms in bioinformatics, including, but not limited to:

Exact, approximate, and machine-learning algorithms for sequence analysis, gene and signal recognition, alignment and assembly, molecular evolution, structure determination or prediction, gene expression, pathways, gene networks, proteomics, functional genomics, and drug design.
High-performance computing approaches to computationally hard learning and optimization problems in bioinformatics.
Methods, software and dataset repositories for development and testing of such algorithms and their underlying models.
Submissions

Submission must be formatted in the Springer LNCS style (http://www.springer.de/comp/lncs/authors.html) and not exceed 12pp. Each paper must contain a succinct statement of the issues and of their motivation, a summary of the main results, and a brief explanation of their significance, all accessible to a non-specialist reader.

Electronic submission is required; procedures for submission can be found in the WABI'09 web site. In case of problems, authors may, by prior arrangement, email a PDF to the chairs, Steven Salzberg and Tandy Warnow.

Simultaneous submission to another conference with published proceedings is not permitted, but simultaneous submission to a journal is allowed, provided that the authors notify the program chairs and: (1) if published in a journal before the conference date, such a contribution will be published as a short abstract (1 page) in the WABI proceedings, (2) if published in a journal after the conference date, the journal version must carry as a footnote to the title "A preliminary version of this work appeared in the WABI'09 proceedings."

Proceedings

Accepted papers will be published in the Springer series Lecture Notes in Bioinformatics and will be allotted 12 pages. Previous proceedings of WABI appeared in LNCS/LNBI volumes 2149 (Aarhus 2001), 2452 (Rome 2002), 2812 (Budapest 2003), 3240 (Bergen 2004), 3692 (Mallorca 2005), 4175 (Zurich 2006) and 4645 (Philadelphia 2007). By arrangements with the Editor-in-Chief, selected papers from WABI will be invited for an extended publication in a special issue of IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Address any questions to the program committee chairs, Steven Salzberg and Tandy Warnow.

Important Dates

Submission deadline May 8, 2009
Notification to authors May 29, 2009
Final version due June 15, 2009
Symposium September 12-13, 2009
Keynote Speakers

TBA
Program Committee

Tanya Berger-Wolf (University of Illinois, USA)
Paola Bonizzoni (Università Degli Studi di Milano-Bicocca, Italy)
Dan Brown (University of W aterloo, Canada)
Rita Casadio (Università Degli Studi di Milano-Bicocca, Italy)
Mark Clement (Brigham Young University, USA)
Maxime Crochemore (Université Paris-Est, Marne-la-Vallée, France)
Miklos Csuros (University of Montreal, Canada)
Aaron Darling (UC Davis, USA)
Nadia El-Mabrouk (Université de Montréal, Canada)
Eleazar Eskin (UCLA, USA)
Liliana Florea (University of Maryland, USA)
Ganesh Ganapathy
Olivier Gascuel (LIRMM-CNRS, France)
Raffaele Giancarlo (Università degli Studi di Palermo, Italy)
Concettina Guerra (Università di Padova, Italy)
Sridhar Hannenhalli (University of Pennsylvania, USA)
Daniel Huson (Universität Tübingen, Germany)
Shane Jensen (University of Pennsylvania -- Wharton, USA)
Carl Kingsford (University of Maryland, USA)
Ming Li (University of Waterloo, Canada)
Randy Linder (University of Texas, USA)
Stefano Lonardi (University of California, USA)
Jian Ma (UC Santa Cruz, USA)
Istvan Miklos (Rényi Institute, Hungarian Academy of Sciences, Hungary)
Bernard Moret (Swiss Federal Institude of Technology, Switzerland)
Burkhard Morgenstern (University of Gottingen, Germany)
Elchanan Mossel (UC Berkeley, USA)
Luay Nakhleh (Rice University, USA)
Macha Nikolski (Université Bordeaux, France)
Uwe Ohler (Duke University, USA)
Laxmi Parida (IBM T.J. Watson Research Center, USA)
Kunsoo Park (Seoul National University, Korea)
Cinzia Pizzi (University of Padova, Italy)
David Posada (University of Vigo, Spain)
Sven Rahmann (U. Dortmund, Germany)
Knut Reinert (Freie Universität Berlin, Germany)
Allen Rodrigo (U. Auckland, NZ)
Mikhail Roytberg (Russian Academy of Sciences, Russia)
David Sankoff (University of Ottawa, Canada)
Mona Singh (Princeton University, USA)
Steven Salzberg (University of Mariland, USA) (co-chair)
Steven Skiena (SUNY Stony Brook, USA)
Alexis Stamatakis (Ludwig-Maximilians Universität, Germany)
Jens Stoye (Universität Bielefeld, Germany)
Jijun Tang (University of South Carolina, USA)
Glenn Tesler (UCSD, USA)
Alfonso Valencia (Structural and Computational Biology Programme, Spain)
Li-San Wang (University of Pennsylvania, USA)
Lusheng Wang (City University of Hong Kong, HK)
Tandy Warnow (University of Texas, USA) (co-chair)
Chris Workman (Technical University of Denmark, Denmark)
Organizing Committee (University of Pennsylvania)

Junhyong Kim (chair) Biology & Penn Genome Frontiers Institute
Li-San Wang Penn Institute on Aging