New: List of accepted papers!

WABI will be part of ALGO 2011, hosted by the Max-Planck-Institute für Informatics, Saarbrücken. WABI is sponsored by the European Association for Theoretical Computer Science (EATCS), and the International Society for Computational Biology (ISCB). A printed version of this Call for Papers may be recovered here.


All research in algorithmic work in bioinformatics, computational biology and systems biology. The emphasis is mainly 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.


Original research papers (including significant work-in-progress) or state-of-the-art surveys are solicited in all aspects of algorithms in bioinformatics, computational biology and systems biology including, but not limited to:

  • Exact and approximate algorithms for sequence analysis, gene and signal recognition, alignment and assembly, molecular evolution, structure determination or prediction, gene expression, molecular pathways and network, proteomics, functional genomics, and drug design.
  • Methods, software, and dataset repositories for development and testing of such algorithms and their underlying models, as well as high-performance computing approaches to computationally hard learning and optimization problems.
  • Novel approaches to analyzing and modeling next-generation sequence data, including sequence assembly, population genomics, metagenomics, metatranscriptomics and ncRNA sequencing.

Call for Papers

Submissions must be formatted in LaTeX using the Springer LNCS style and must not exceed 12 pages. 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 non-specialist readers. All submissions must be made online, through the EasyChair submission system within the WABI'11 submission site. You need to register on that web site before submitting; you may update your submission(s) up to the last minute. A standard PDF file must be received by 23:59 (GMT) on May 10, 2011 in order for your submission to be considered. In case of problems, authors may, by prior arrangement, email a PDF file to the chairs, Teresa Przytycka and Marie-France Sagot.

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; if published in a journal, such a contribution will be published as a short abstract in the WABI proceedings.


Proceedings will be published in the Springer series Lecture Notes in Bioinformatics; papers 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), 4645 (Philadelphia 2007), 5251 (Karlsruhe 2008), 5724 (Philadelphia 2009), and 6293 (Liverpool 2010).

By arrangement with the Editor-in-Chief, selected papers from WABI will be invited for an extended publication in a special issue of the BMC Algorithms for Molecular Biology.

Key dates

Submission deadline: 13 May, 2011 Closed
Notification to authors: 2 June, 2011
Final version due: 14 June, 2011
Workshop: 5 - 7 September, 2011

Invited Speaker

Vincent Moulton, University of East Anglia, UK

Program Committee

Tatsuya Akutsu, Kyoto U., Japan
Jan Baumbach, Max-Planck-Institut für Informatik, Saarbrücken, Germany
Tanya Berger-Wolf, U. Illinois, Chicago, USA
Sebastian Böcker, U. Jena, Germany
Paola Bonizzoni, Università Degli Studi di Milano-Bicocca, Italy
Dan Brown, U. Waterloo, Canada
Michael Brudno, University of Toronto, Canada
Robert Castelo, Universitat Pompeu Fabra, Spain
Benny Chor, Tel Aviv University, Israel
Lenore Cowen, Tufts University, USA
Nadia El-Mabrouk, University of Montreal, Canada
Eleazar Eskin, UCLA, USA
Liliana Florea, U. Maryland, USA
Ana Teresa Freitas, INESC-ID/IST Technical University of Lisbon, Portugal
Anna Gambin, Warsaw University, Poland
Olivier Gascuel, University of Montpellier, France
Raffaele Giancarlo, Università degli Studi di Palermo, Italy
Dan Gusfield, University of California, Davis, USA
Ivo Hofacker, Universität Wien, Austria
Barbara Holland, University of Tasmania, Australia
Daniel Huson, Universität Tübingen, Germany
Igor Jurisica, University of Toronto, Canada
Carl Kingsford, University of Maryland, College Park, USA
Gunnar Klau, CWI Amsterdam, The Netherlands
Mehmet Koyuturk, Case Western Reserve University, USA
Jens Lagergren, KTH, Sweden
Hans-Peter Lenhof, University of Saarbrücken, Germany
Stefano Lonardi, UC Riverside, USA
Christine Leslie, Memorial Sloan-Kettering Cancer Center, New York, USA
Ion Mandoiu, U. Connecticut, USA
Satoru Miyano, Human Genome Center, Univ. of Tokyo, Japan
Bernard M.E. Moret, Swiss Federal Institute of Technology (EPFL), Switzerland
Burkhard Morgenstern, U. Göttingen, Germany
Vincent Moulton, University of East Anglia, UK
Gene W. Myers, Janelia Farms Research Campus, USA
Itsik Pe’er, Columbia University, New York, USA
Nadia Pisanti, U. Pisa, Italy
Teresa Przytycka, NCBI, NLM, NIH, USA (co-chair)
Knut Reinert, Freie Universität Berlin, Germany
Juho Rousu, University of Helsinki, Finland
Yvan Saeys, Ghent University, Belgium
Marie-France Sagot, INRIA, U. Lyon, France (co-chair)
Cenk Sahinalp, Simon Fraser University, Canada
David Sankoff, University of Ottawa, Canada
Thomas Schiex, INRA Toulouse, France
Russell Schwartz, Carnegie Mellon University, USA
Stefan Schuster, U. Jena, Germany
Charles Semple, Canterbury U., New Zealand
Mona Singh, Princeton University, USA
Saurabh Sinha, University of Illinois, USA
Jörg Stelling, Swiss Federal Institute of Technology Zurich, Switzerland
Leen Stougie, Free University Amsterdam, The Netherlands
Jens Stoye, University of Bielefeld, Germany
Michael Stumpf, Imperial College London, UK
Jerzy Tiuryn, University of Warsaw, Poland
Hélène Touzet, LIFL Université de Lille 1, France
Alfonso Valencia, Structural and Computational Biology Group, Spain
Lusheng Wang, City University of Hong Kong, Hong Kong
Chris Workman, Technical University of Denmark, Denmark
Alex Zelikovsky, Georgia State University, USA
Louxin Zhang, National University of Singapore, Singapore
Michal Ziv-Ukelson, Ben Gurion University of the Negev, Israel
Elena Zotenko, Garvan Institute, Australia