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.
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.
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 russ.altman@stanford.edu 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.ps, 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:
Submitted papers are limited to twelve (12) pages in our publication format. Please format your paper according to instructions found at ftp://ftp-smi.stanford.edu/pub/altman/psb/. 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@stanford.edu) 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.