Call For Papers: “Phylogenomics & Population Genomics: Models, Algorithms, & Analytical Tools” Session at PSB 2013]

Call for papers

Phylogenomics and Population Genomics: Models, Algorithms, and Analytical Tools Co-chairs: Luay Nakhleh (Rice U.), Noah Rosenberg (Stanford U.), and Tandy Warnow (U. Texas)

A session at the Pacific Symposium on Biocomputing (PSB 2013)

January 3-7, 2013
The Big Island of Hawaii


The increasing availability of whole-genome data from diverse species across the Tree of Life has propelled phylogenomics, the evolutionary analysis of genomes and their relationships, to the forefront of research. Research in phylogenomics has contributed to fundamental questions in biology including, but not limited to: orthology identification, species evolution, the extent and role of horizontal gene transfer, and protein function prediction. Further, as sequencing techniques continue to improve in efficiency and cost, whole-genome data is becoming available for many individuals within populations. This has given rise to interesting questions and problems in population genomics, such as comparative analysis of conserved and ultra-conserved regions, the interplay between adaptive and
non-adaptive evolutionary forces, and the detection of regulatory regions.

Research areas targeted in this session encompass mathematical models and computational tools that enable and/or utilize phylogenomic analyses. These include, but are not limited to: orthology detection, gene tree incongruence and its reconciliation (incomplete lineage sorting, gene duplication and loss, and horizontal gene transfer), protein function prediction, ancestral genome reconstruction, and elucidating the adaptive roles of evolutionary events such as gene duplication and horizontal gene transfer.

Session theme:

We invite contributions with a substantial and innovative mathematical or computational component (such as computational models, algorithms, simulation studies, and computationally innovative analyses of biological data) in all areas of phylogenomics, including, but not limited to, gene tree incongruence, species phylogeny inference, ancestral genome reconstruction, and integration with population genetics.

Important Dates
• Paper submission deadline: July 31, 2012
• Notification of paper acceptance: September 10, 2012
• Camera-ready copy deadline: October 1, 2012

All deadlines are at midnight Pacific Standard Time.

Paper Format
Please see the PSB paper format template and instructions at

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 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 your paper according to instructions found at If figures cannot 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.

Contact PSB (psb.hawaii @ for additional information about paper submission requirements.

Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

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