CALL FOR PAPERS
RECOMB Satellite Conference on Open Problems in Algorithmic Biology
(RECOMB-AB)
August 27-29, 2012
St. Petersburg, Russia
http://bioinf.spbau.ru/ab2012
recombab2012 at gmail dot com
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.
KEYNOTE SPEAKERS:
Max Alekseyev (University of South Carolina)
Vineet Bafna (University of California, San Diego)
Mikhail Gelfand (Russian Academy of Sciences and Moscow State University)
Sorin Istrail (Brown University)
Richard Karp (University of California, Berkeley)
Bernard Moret (École Polytechnique Fédérale de Lausanne)
Stephen O’Brien (Saint Petersburg University)
Pavel Pevzner (University of California, San Diego)
Marie-France Sagot (INRIA, Université Lyon 1)
Cenk Sahinalp (Simon Fraser University)
Ron Shamir (Tel Aviv University)
Glenn Tesler (University of California, San Diego)
Tandy Warnow (The University of Texas at Austin)
Michael S. Waterman (University of Southern California)
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.
KEY DATES:
Abstract submission deadline Friday April 27, 2012
Notification of acceptance Friday May 18, 2012
Request for visa Friday May 25, 2012
Final abstract due Friday June 15, 2012
Registration period To be announced
Conference August 27-29, 2012
(arrival on August 26)
PROGRAM COMMITTEE:
Glenn Tesler (University of California, San Diego) (Chair)
Pavel Pevzner (University of California, San Diego) (Co-chair)
Max Alekseyev (University of South Carolina)
Guillaume Bourque (McGill University)
Michael Brudno (University of Toronto)
Mark Chaisson (Pacific Biosciences)
Francis Chin (University of Hong Kong)
Dannie Durand (Carnegie Mellon University)
Eran Halperin (Tel Aviv University)
Uri Keich (University of Sydney)
Alexander Kulikov (Steklov Institute of Mathematics at St. Petersburg and St. Petersburg Academic University)
Laxmi Parida (IBM Research)
Alkes Price (Harvard University)
Mona Singh (Princeton University)
Jens Stoye (Bielefeld University)
Haixu Tang (Indiana University)
Olga Troyanskaya (Princeton University)
Nikolay Vyahhi (St. Petersburg Academic University)
Kira Vyatkina (St. Petersburg Academic University)
ORGANIZING COMMITTEE:
Alexander Kulikov (Steklov Institute of Mathematics at St. Petersburg and St. Petersburg Academic University) (Chair)
Nikolay Vyahhi (St. Petersburg Academic University) (Co-chair)
Max Alekseyev (University of South Carolina)
Mikhail Gelfand (Moscow State University)
Alexander Omelchenko (St. Petersburg Academic University)
Kira Vyatkina (St. Petersburg Academic University)