Call for Papers and Posters
Beyond gap models: reconstructing alignments and phylogenies under genomic-scale events
A Pacific
Symposium on Biocomputing 2008
Session
January 4-8, 2008
Fairmont Orchid, The Big Island of Hawaii
Hawaii, U.S.A.
Multiple sequence alignment (MSA) has long been a mainstay of bioinformatics and has proved quite useful in the alignment of well conserved protein and DNA sequences; some of these sequences have also been used with great success in phylogenetic reconstruction. Sequences with low percentage identity, on the other hand, typically yield poor alignments. Now that researchers want to produce alignments among widely divergent genomes, including both coding and noncoding sequences we need to revisit both multiple alignment and phylogenetic reconstruction under more ambitious models, ones that take into account the plethora of genomic events rather than just substitutions and insertions/deletions (indels). We also need to revisit multiple sequence alignment and phylogeny reconstruction for datasets currently beyond the capability of existing methods, due to high rates of site substitution, high indel rates, and large numbers of taxa or sites.
Most current methods postulate only two types of events: substitutions (modeled with a transition matrix, such as PAM or BLOSUM matrices for protein data) and indels (rarely modelled beyond a simple affine cost function for the size of the gaps). While these two events can indeed transform any sequence into any other, their model of genomic events is far too simplistic: substitutions are not location- or neighbor-independent and indels can be caused by a variety of complex events, such as uneven recombination, insertion of transposable elements, gene duplication/loss, lateral transfer, etc. Moreover, genomic rearrangement events can completely mislead procedures based on most current models, resulting in a total loss of alignment when a homologous element has undergone an inversion or a duplication.
Computational biologists have been studying genome rearrangements for 20 years and have started work on duplication and loss events. Taking these events into account in a multiple alignment will require the simultaneous construction of the alignment and of the phylogenetic tree -- an approach also known as phylogenetic alignment. Up to very recently, the computational complexity of phylogenetic alignment was widely viewed as too high, but the state of the art in phylogenetic reconstruction has advanced significantly over the last 10 years, both in terms of accuracy and in terms of computational efficiency, so that what was then impossible is now merely difficult.
Session Topics
We would like to invite contributions presenting new methods for multiple sequence alignment, new simulation software for evolving sequences under complex models of evolution, or evaluations of existing methods for multiple sequence alignment or phylogenetic reconstruction under such models. Papers presenting new methods should provide experimental or empirical evidence of the performance of the new methods. In addition, papers that present novel empirical evidence of complex evolutionary processes operating on molecular sequences are welcome. In this context, submission topics can include, but are not limited to:
• Methods for simultaneous alignment and phylogeny reconstruction under site substitutions and indels that demonstrate clear benefits over independent MSA and phylogeny reconstruction.
• Methods and models for genomic-scale alignment and phylogenetic reconstruction, including the handling of gene families.
• Comparisons of existing MSA and phylogeny reconstruction methods under complex models.
• Molecular evolution relevant to the above topics.
Other topics within the subject area are welcome. Note that all submitted papers should demonstrate the relevance to this topic. If unsure whether your paper fits the session theme, please contact one of the co-chairs.
Session
Co-chairs
University of Toronto
Randy Linder, Ph.D.
University of Texas
Bernard Moret, Ph.D.
Ecole Polytechnique Federeale de Lausanne
Tandy Warnow, Ph.D.
University of Texas
Submission
Information
Please
note that the submitted papers are reviewed and accepted on a
competitive basis. At least three reviewers will be assigned to each
submitted manuscript.
Important
Dates
•
Paper submission
deadline: July 16, 2007
•
Notification of paper
acceptance: September 5, 2007
•
Camera-ready copy
deadline: September 24, 2007
•
Abstract deadline (for
non-reviewed posters): November 9, 2007
All deadlines are at midnight
Pacific Standard Time .
Paper Format
All papers must be
submitted to psb-submit @ helix.stanford.edu
in electronic format with PSB in the subject line. The file formats we accept are: postscript
(*.ps) and Adobe Acrobat (*.pdf).
Attached files should be named with the last name of the first author
(e.g. altman.ps, altman.pdf, or altman.ps). Hardcopy submissions or
unprocessed TEX or LATEX files will be rejected without review.
• The email address
of the corresponding author
Michael Brudno, Ph.D.
Each paper must be accompanied by a cover letter. The cover letter must
state the following:
• The specific PSB session that should review the paper or
abstract
• The submitted paper contains original, unpublished results, and
is not currently under consideration elsewhere.
• All co-authors concur with the contents of the paper.
Submitted papers are limited to twelve (12) pages in our publication
format. Please format your paper according to instructions found at
http://psb.stanford.edu/psb-online/psb-submit/.
If figures can not be easily resized and placed precisely in the text,
then it should be clear that with appropriate modifications, the total
manuscript length would be within the page limit.
Color pictures can be printed at the expense of the authors. The fee is
$500 per page of color pictures, payable at the time of camera ready
submission.
Contact Russ Altman (psb-submit @ helix.stanford.edu) for
additional information about paper submission requirements.