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Phylogenetic Genomics and Genomic Phylogenetics
Pacific Symposium on Biocomputing 2002
Kauai Marriott Resort and Beach Club, Hawaii
January 3-7, 2002

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.


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:

  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:

  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:

  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:


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.



Scott Stanley
Population Genomics
Genaissance Pharmaceuticals
New Haven, CT

Benjamin Salisbury
Department of Ecology and Evolutionary Biology
Yale University
New Haven, CT