First RECOMB Satellite Conference on
Open Problems in Algorithmic Biology
(RECOMB-AB)
August 27-29, 2012
St. Petersburg, Russia

OVERVIEW:

The First RECOMB Satellite Conference on Open Problems in Algorithmic Biology (RECOMB-AB) will be held August 27-29, 2012 in St. Petersburg, Russia. This workshop brings together leading researchers in the mathematical, computational, and life sciences to discuss current challenges in computational biology, with an emphasis on open algorithmic problems. The program will consist of invited speakers, contributed speakers, posters, and discussion panels.

Saint Petersburg (formerly known as Leningrad) is Russia's second largest city. The large historic center of Saint Petersburg, threaded with canals dotted with baroque bridges, is a UNESCO World Heritage site. Its Hermitage Museum, housed in the Winter Palace (formerly called the Palace of the Russian Tsars), is one of the world's greatest collections of art.

THEME AND SCOPE:

RECOMB-AB aims to discuss recent advances and present open algorithmic problems in different areas of life sciences. Today, life sciences are in the midst of a major paradigm shift driven by computational sciences. RECOMB-AB emphasizes that this is a two-way street: while life sciences have greatly benefited from new computational ideas, they also are a major source of new open problems and inspiration for computational sciences. RECOMB-AB brings together leading researchers in the mathematical, computational, and life sciences to discuss interesting, challenging, and well-formulated open problems in algorithmic biology.

Many areas of computational sciences started as an attempt to solve applied problems and later became more theoretically-oriented. These theoretical aspects may be very valuable even if they stray away from the applied problems that originally motivated them. Thus, RECOMB-AB is interested in a wide range of well-formulated open problems. Some of them may be rather theoretical and have limited biological application. The solutions of others might provide valuable tools for biologists or might lead to new biological discoveries. This blend of theoretical and applied problems is a fascinating feature of algorithmic biology.

The discussion panels at RECOMB-AB will also address the worrisome proliferation of ill-formulated computational problems in bioinformatics. While some biological problems can be translated into well-formulated computational problems, others defy all attempts to bridge biology and computing. This may result in computational biology papers that lack a formulation of a computational problem they are trying to solve. While some such papers may represent valuable biological contributions (despite lacking a well-defined computational problem), others may represent computational “pseudoscience.” RECOMB-AB will address the difficult question of how to evaluate computational papers that lack a computational problem formulation.

Open problems should address a problem of interest in Biology, whose solution may depend on development of new ideas in Computing, or problems of interest in Computing that were initially motivated by Biology. Open problems may be completely new; they may be problems that were studied in the past but without a precise formulation as an algorithmic problem; or they may be new and improved self-contained formulations of previously published problems.

Topics of interest include, but are not limited to,

• Machine learning, statistical, combinatorial, and other algorithms in biology
• Molecular sequence analysis
• Molecular evolution
• Gene expression
• Biological networks
• Sequencing and genotyping techniques
• Genomics
• Population genetics
• Systems biology
• Bio-imaging
• Molecular structural biology
• Proteomics

OPEN PROBLEMS IN ALGORITHMIC BIOLOGY PROJECT:

Selected speakers (invited and contributed) will be invited to participate in an article on Open Problems in Algorithmic Biology, to be published in the Journal of Computational Biology in Fall 2012. This multi-author article will be a compilation of the problems posed in the abstracts and invited talks.

CALL FOR PARTICIPATION:

RECOMB-AB will have a somewhat unusual format. In addition to research abstracts, RECOMB-AB will showcase open problems in algorithmic biology. We invite submissions in two categories: Algorithmic Biology Open Problems, and Algorithmic Biology Research Abstracts. Submissions should be submitted through the links provided on the RECOMB-AB website and must be received by April 27, 2012.

Algorithmic Biology Open Problems. Each submission should cover a single well-formulated open problem in algorithmic biology. Each submission should be self-contained and should start from a statement of biological problem and end with a well-formulated computational problem addressing the biological problem. Authors should include the motivation for studying the problem and any known partial or conjectured solutions of the problem. A single submission may include multiple computational problems motivated by the same biological problem. Authors of selected papers will be invited to present their problem at RECOMB-AB either as a talk or as a poster. Selected authors will also be invited to participate in a multi-author article on Open Problems in Algorithmic Biology, to be published in the Journal of Computational Biology.

Algorithmic Biology Research Abstracts. Unpublished work and recently published work will both be considered. If the work is published, please include it in the references. Authors of selected papers will be invited to present their paper at RECOMB-AB either as a talk or as a poster. Abstracts will be distributed to conference participants, but there is no formal publication through the conference.

PREPARATION OF ABSTRACTS:

Abstracts should be submitted via the conference website in PDF format. All abstracts should be in English. Abstracts consist of up to two pages of text (plus cover page, references, figures, and tables, which do not count towards the two pages). Please see the conference website for further details.