Phylogenetics in the Post-Genomic Era
Pacific Symposium on Biocomputing 2001
January 3-7, 2001, Honolulu, Hawaii
(Sheraton Waikiki)

This session focuses on topics of immediate and emerging importance to the phylogenetic analysis of molecular data in the post-genomic era. The session will bring together researchers from the biological, computational and mathematical sciences with the goal of achieving a better understanding of the current issues and challenges in phylogenetics.

Solicited are papers and posters including, but not limited to, the following topics:

1. Large Phylogeny Analysis
   Sample topics:
   
   • decomposition and assembly of large data sets
     
   • integrating domain knowledge into large phylogeny construction
     
   • reliable integration of heterogeneous data sets
     
   
   
2. Genome Evolution
   Sample Topics:
   • using gene order, gene content, G+C content, and other sources of information to understand genome evolution
     
   • emerging whole genome approaches
     
   • applications of comparative genome analysis to drug discovery
     
   
   
3. Techniques for Evaluating Phylogenetic Methods
   Sample Topics:
   • characterizing "easy" and "difficult" data sets
     
   • designing simulation studies for evaluating phylogenetic methods
     
   • developing a comprehensive benchmark data set
     
   • statistical comparisons of trees produced by different methods
     
   
   
4. Other Highly Relevant Topics
   The above topics do not capture all of the current relevant topics in phylogenetics. Other important topics include:
   • statistical methods including Bayesian inference
     
   • statistical models appropriate to large data sets, large evolutionary distances and whole genomes
     
   • using secondary and tertiary structure, operon organization, covariance, etc. to infer evolutionary trees
     
   • detecting horizontal gene transfer and lineage specific gene loss
     
   • inferring ligand and compound affinities in drug targets
     

During the session a challenge will be formulated and issued to the community to develop phylogenetic methods that perform well on the usual data sets (e.g., the vertebrate mitochondrial genome data set) in addition to very large data sets such as the Green Plant Project and the Ribosomal Database Project. One of the goals of the session is to develop an appropriate suite of data sets for the challenge in addition to the mechanism for administering and monitoring the challenge. The goal is to develop a challenge that can be objectively used to evaluate the effectiveness of new and existing phyloogenetic methods. We hope that this challenge will develop into an annual competition similar to the CASP challenge for protein structure prediction.

All PSB paper submissions must be submitted electronicly via email to Russ Altman (altman@smi.stanford.edu). We accept postscript, pdf and Microsoft Word format files. We can NOT accept Tex files or other word processors. Please follow the paper formating instructions available from ftp://ftp-smi.stanford.edu/pub/altman/psb. Please note that all submissions must be accompanied by an (email) cover letter that specifies by which specific session (if any) the paper should be reviewed. Please also include a statement in the cover letter that the paper that contains original unpublished results not currently under consideration elsewhere and that all co-authors concur with its contents.

• Paper submissions due: July 17, 2000
  
• Notification of paper acceptance: August 28, 2000
  
• Camera-ready papers due: September 25, 2000
  
• Poster abstract deadline: November 6, 2000
  
• Meeting: January 3-7, 2001