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.





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

Webb Miller, Ph.D.

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

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. 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 email address of the corresponding author
•  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 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 @ for additional information about paper submission requirements.