This session will explore the natural partnership between the co-evolving disciplines of phylogenetics and genomics.

Genome structure and function analyses can be strengthened through examining evolutionary history. Phylogenetics is a primary source for methodologies to facilitate these investigations. The analysis of evolutionary history is similarly empowered by a genomic perspective. Phylogenetic systematics increasingly draws upon genomics, both as a vast source of relevant data and as subject matter.

CALL FOR PAPERS

We are currently soliciting papers on subjects in these areas. Manuscripts will be peer-reviewed in a rapid process as indicated in the timeline below. Acceptance will be based on quality and relevance to the session. A subset of the accepted papers will be selected for oral presentation.

This list of relevant topic areas is not intended to be exhaustive. Please contact one of the session cochairs if you have a paper topic you would like to suggest and submit.

1. What makes phylogenetic analyses genomic?
   
   In an effort to be associated with the genomic rage, many geneticist and evolutionary biologists are describing their work as genomic in scale. However, the number of researchers actually using entire genomes in phylogenetic analyses is small, and many researchers are unlikely to ever have access to whole genomes for the organisms they study. We believe that some discussion of what exactly is meant by "phylogenomic" analysis is required if we are to continue to make advances in this field.
   
   Sample topics:
   
   
   • Phylogenomics: a buzz word for comparative genetics?
   
   
2. Phylogenetic analyses of large data sets
   
   This topic covers the generation, assembly, and curation of large amounts of data as well as empirical examples where large data sets are subjected to phylogenetic analysis. Computational methods developed to overcome problems associated with analyzing large numbers of taxa are also solicited.
   
   Sample topics:
   
   
   • assembly and management of large data sets
   • methodological and algorithmic considerations associated with analyzing large data sets
   • high throughput approaches to phylogenetics
   • studies using extremely large taxon samples in both pure research and applied settings
   
   
3. Whole Genome Analyses
   
   Most comparative studies today that include whole genomes focus necessarily on microbial organisms. These systems provide a model for larger, more complex genomes, and have already begun to shed light on many areas in molecular evolution. This topic is intended to bring together those researchers doing truly genomic scale comparative analyses with other investigators working in systematics and computer science.
   
   Sample topics:
   
   
   • whole genome approaches: advances and obstacles
   • applications of comparative genome analysis to solving problems in molecular evolution
   • using microbial genomics to diagnose and classify organisms, including previously unknown forms of life
   
   
4. The Role of Phylogenetic Methods in Analyses of Gene Expression Profiles
   Gene expression data can now be collected rapidly for thousands of genes using DNA microarray technology. The last two years have seen an explosion of microarray data being applied to several areas of biology. The methods of analysis are still in the early stages of development. However, many high profile studies have already applied phylogenetic methods to analyses of expression data. Here we seek to promote discussion of some of the issues that arise when one applies phylogenetics to expression data. The goal is not to simply present trees generated from large expression profiles, but also to consider interactions between the genes in the analysis and to search for improved diagnostic methods using the empirical examples.
   
   
   Sample topics:
   
   
   • tree building methods and the analysis of gene expression data
   • phylogenetic analysis of cancer cell gene expression profiles
   
   

SUBMISSION INFORMATION

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 e-mail cover letter that specifies by which (if any) specific session (e.g., this one) 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.

DATES AND DEADLINES

• Paper submissions due: July 16, 2001
  
• Notification of paper acceptance: August 20, 2001
  
• Camera-ready papers due: September 24, 2001
  
• Poster abstract deadline: November 5, 2001
  
• Meeting: January 3-7, 2002