Call for Papers and Posters
Computational Challenges in Comparative Genomics:
Gene Family Evolution, Ancestral Genome Reconstruction,
and Applications to Human Genetics
A Pacific
Symposium on Biocomputing 2009
Session
January 5-9, 2009
Fairmont Orchid, The Big Island of Hawaii
Hawaii, U.S.A.
Background
Comparative genomics has become a valuable tool in the study of
cancer, of genetic diseases, of infertility, of pathogenicity and
virulence of microbial parasites and of the evolution of species
important to agriculture, agronomy, forestry and fishery. While
pairwise comparisons of organisms and their genomes have long been a
crucial tool in gene hunting and genome annotation, comparing several
genomes at once only became possible in the last few years as
sufficient numbers of genomes were released. The computational
challenges are many and often very hard: almost every computational
question about genomes is much more complex than analogous questions
about DNA or protein sequences.
Research areas include construction of syntenic blocks from genome
data; gene family evolution, including duplication and loss models,
detection of horizontal transfer, and assignment of orthologs;
identification of whole-genome duplication events; models and
algorithms for genome rearrangements; reconstruction of ancestral
genomes; detection of reticulation events; phylogenetic
reconstruction from whole genomes; and uses of comparative genomic
methods in evolution and systematics, in population genetics and
genetic screening, in research into cancer, inherited disorders and
human pathogens, and in agriculturally significant organisms. Such
research includes model development, algorithm design, high-performance
computing implementations, machine learning, data integration,
analysis pipelines, and, of course, new insights into biology.
Session Theme
We invite contributions with a substantial and innovative computational
component (such as computational models, algorithms, simulation studies, and
computationally innovative analyses of biological data) in all areas
of comparative genomics, with a particular emphasis on gene family
evolution, ancestral genome reconstruction, and integration with
population genetics.
Note that all submissions must demonstrate the relevance to the session theme.
If unsure whether your paper fits the session theme, please contact
Bernard Moret or one
of the co-chairs.
Session Co-chairs
Pennsylvania State University
Bernard Moret, Ph.D.
Ecole Polytechnique Fédérale de Lausanne (EPFL)
Pavel Pevzner, Ph.D.
University of California at San Diego
David Sankoff, Ph.D.
University of Ottawa
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, 2008 (for this session only)
•
Notification of paper
acceptance: September 8, 2008
•
Camera-ready copy
deadline: September 22, 2008
•
Abstract deadline (for
non-reviewed posters): November 7, 2008
All deadlines are at midnight
Pacific Standard Time .
Paper Format
Papers must be submitted to the PSB 2009 paper management system at
• The email address
of the corresponding author
Webb Miller, Ph.D.
http://acamedics.com/submissions/index.php/psb/psb2009/login
Please click the "Not a user? Create an account with this site" link to create an author account and upload your paper.
All papers must be submitted in electronic format to the paper management system.
The file formats we accept are: Postscript
(*.ps) and Portable Document Format (*.pdf).
Attached files should be named with the last name of the first author
(e.g. altman.ps or altman.pdf). Hardcopy submissions or
unprocessed TEX or LATEX files or electronic submissions not submitted through the paper management system will be rejected without review.
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 and submit 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.hawaii @ gmail.com) for
additional information about paper submission requirements.