PSB Session on Genome-wide Analysis and Comparative Genomics

Inna Dubchak ildubchak at
Thu May 16 21:07:10 EST 2002

Call for Papers, Posters, and Demonstrations

           Session on Genome-wide Analysis and Comparative Genomics

                      at the Pacific Symposium on Biocomputing 2003

      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.
         ·         Development of reliable gene sets for sequenced
         ·        Approaches to discover alternative gene structures
generated by alternative promoters, alternative
           splicing and alternative polyadenilation.
         ·        Alignment techniques for large sequences and whole
         ·        Comparative study of orthologous genes and biological
         ·        Evaluation of evolutionary distance and alignment
         ·        Promoters, regulatory elements, transcription factor
binding sites, and other motif recognition
           through comparative genomics.
         ·        Sequence assembly and error correction using sequence
         ·        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
         ·         Study of synteny and genome rearrangement.

      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
      ildubchak at

      Victor Solovyev, Ph.D.
      EOS Biotechnology
      solovyev at

      Liping Wei, Ph.D.
      Nexus Genomics, Inc.
      wei at

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 15, 2002
Notification of paper acceptance: August 19, 2002
Final paper deadline: September 23, 2002
Abstract deadline: November 1, 2002
Meeting: January 3-7, 2003

Paper format

 All papers must be submitted to russ.altman at in electronic
format. The file formats we accept are:
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 (russ.altman at 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

Inna Dubchak, Ph.D.
Staff Scientist
National Energy Research Scientific Computing Center (Mail Stop 84-171)
Lawrence Berkeley National Laboratory, Berkeley, CA 94720
Email:  ildubchak at   Tel: (510)495-2419    Fax: (510)486-5717


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