Call for Papers, Posters, and Demonstrations

Session on Genome-wide Analysis and Comparative Genomics


at the Pacific Symposium on Biocomputing 2002



The sequencing of over 800 complete genomes presents unprecedented opportunities for biological discovery as well as new technical challenges for the computational sciences. This session calls for papers on novel computational algorithms and biological applications in genome-wide analysis and comparative genomics. The session will bring together researchers from the biological, computational and mathematical fields with the goal of sharing new research ideas and achieving a better understanding of the current issues and challenges.


The analysis of complete genomes and the comparison of multiple complete genomes are leading to deep biological insights in a variety of areas. However, many of the computational problems in analyzing, aligning and comparing large genomes, and the mathematical questions arising from the interpretation of the analyses and comparisons, have yet to be solved. Research in the area is benefiting from a synergy of computational and biological ideas on how to analyze and compare large sequences. The field is currently exploding with novel research and many unsolved questions. A session dedicated to these topics, bringing together talents from different disciplines, should help to accelerate discoveries and disseminate ideas.


Possible topics:


Topics relevant to this session include, but are not limited to,


        Gene finding using multiple organisms.

        Alignment techniques for large sequences and whole genomes.

        Comparative study of orthologous genes and biological discovery.

        Evaluation of evolutionary distance and alignment matrices.

        Regulatory elements, transcription factor binding sites, and other motif recognition through comparative genomics.

        Sequence assembly and error correction using sequence comparison.

        Database design for efficient storage and retrieval of whole genomes.

        Visualization of whole genomes; visualization of results of genome-wide analysis.

        Non-homology approaches to finding patterns in a genome and to comparing two or more genomes.

        Genome-wide prediction of gene function and gene interaction

        Study of synteny and genome rearrangement.

        Phylogenetic relationship based on molecular and morphological analyses, using genome comparison of gene maps.

        Understanding of evolution.


Papers, posters, and demonstrations addressing any of the mentioned areas, or any other questions related to whole genome analysis or comparative genomics are welcome. We are especially interested in new results on the analyses of actual experimental data such as results that relate specifically to any of the sequenced genomes.


Referees willing to contribute expertise in genome analysis and related topics should contact one of the session chairs.


Session Co-chairs (in alphabetical order):


Inna Dubchak, Ph.D.

Lawrence Berkeley National Laboratory

Lior Pachter, Ph.D.

Univ. of California, Berkeley


Liping Wei, Ph.D.

Nexus Genomics, Inc.


General Information on Papers, Abstracts and Demonstrations

The core of the conference consists of rigorously peer-reviewed full-length papers reporting on original work. Accepted papers will be published in a hard-bound archival proceedings, and the best of these will be presented orally to the entire conference. Researchers wishing to present their research without official publication are encouraged to submit a one page abstract, and present their work in discussion, poster and demonstration sessions. Workstations and internet connections will be available for demonstrations. Please submit detailed requests for demonstration facilities along with your paper or abstract.

Important dates

Paper submissions due: July 16, 2001
Notification of paper acceptance: August 20, 2001
Final paper deadline: September 24, 2001
Abstract deadline: November 5, 2001
Meeting: January 3-7, 2002

Paper format

All papers must be submitted to in electronic format. The file formats we accept are: postscript (*.ps), adobe acrobat (*.pdf) and Microsoft Word documents (*.doc). Attached files should be named with the last name of the first author (e.g., altman.pdf, or altman.doc). 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 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 ( for additional information about paper submission requirements.

    Travel support
    We have been able to offer partial travel support to many PSB attendees in the past, including most authors of accepted full papers who request support and many graduate students. However, please note that no one is guaranteed travel support. Travel support applications will be available on the web site soon.