CFP: Workshop on Gene-Finding and Gene Structure Prediction

Michiel noordewi at cs.rutgers.edu
Fri Apr 21 18:58:58 EST 1995

                           CALL FOR PAPERS
        Workshop on Gene-Finding and Gene Structure Prediction
                        October 13-14, 1995
                     University of Pennsylvania
                          Philadelphia, PA


The Workshop on Gene-Finding and Gene Structure Prediction will be
concerned with the increasingly important activity in computational
biology of discovering protein-encoding genes in otherwise
uncharacterized primary sequence data.  This has traditionally been
done in genomic sequence by discriminating likely coding regions based
on a variety of statistical analyses and by detection of landmark
sequences such as splice junctions.  Recent approaches have involved
combination of such evidence using rule-based and/or connectionist
architectures, and have dealt in a variety of ways with the
combinatorial problem of exon assembly (dynamic programming,
clustering, etc.)  The recent profusion of expressed-sequence data and
related techniques has also raised new issues and opportunities.  In
this workshop we will explore topics such as compositional measures of
exonic tendency (including approaches founded in statistics,
information theory, and signal processing), the effects of genome
heterogeneity, the role of models of biological signals and processes,
dealing with incomplete and error-prone sequence data, algorithmic and
probabilistic techniques, and similarity-based gene prediction.
Problems of interest include detecting coding sequences and assembling
gene models from large-scale genomic sequence, collections of expressed
sequence fragments, and sets of putative exons from a region.
Practical issues of interest include dataset and performance metric
standardization, annotation of genome databases, and software


The workshop is part of the DIMACS Special Year on Mathematical Support
for Molecular Biology, and is sponsored by DIMACS, SmithKline Beecham
Pharmaceuticals, and the Penn Computational Biology Research Training
Program (funded by the National Science Foundation).  It will be held
at the Penn Tower Hotel and Conference Center, in close proximity to
the facilities of the Computational Biology and Informatics Laboratory
and the Human Genome Center for Chromosome 22.  


A number of invited talks are planned, and in addition short papers and
posters are solicited from participants.  Anyone wishing to present
should plan to submit a one-page abstract giving sufficient detail to
allow the work to be evaluated for relevance and originality.  The
Program Committee will make decisions as to which submissions are
appropriate, and whether they should be presented in oral or poster
form.  Authors will be asked to submit papers for an informal workshop
proceedings, and certain of these may then be selected by the Program
Committee to appear in revised form in a volume to appear later.  This
will be published by the American Mathematical Society, which issues
Proceedings from DIMACS workshops, based on refereed, camera-ready
papers submitted within a few months after the conference.  The
schedule is as follows;  NOTE THE REVISED DEADLINES:

          June 1, 1995           One-page abstracts due
          July 1, 1995           Notification to authors
          September 1, 1995      Final short papers due
          October 13-14, 1995    Workshop

Abstracts should be mailed to the address given at the bottom of this
announcement.  Limited travel funds will be available for presenters
who would otherwise be unable to attend.  They should indicate this in
a cover letter, stating also whether they are a student, woman, or


David Searls, University of Pennsylvania, Chair
Jim Fickett, Los Alamos National Laboratory, Co-Chair
Gary Stormo, University of Colorado, Boulder, Co-Chair
Mick Noordewier, Rutgers University, Co-Chair


Howard Bilofsky, SmithKline Beecham Pharmaceuticals
Jean-Michel Claverie, CNRS-E.P.91 Information Genetique et Structurale
Misha Gelfand, Institute of Protein Research, Russian Academy of Sciences
Roderic Guigo, Institut Municipal d'Investigacio Medica, Barcelona
David Haussler, University of California at Santa Cruz
Stephen Mount, University of Maryland
Pavel Pevzner, Penn State University
Bruce Roe, University of Oklahoma
Victor Solovyev, Baylor College of Medicine
Ed Uberbacher, Oak Ridge National Laboratory
Owen White, Institute for Genome Research


To express interest in the Workshop and to receive further mailings
directly, send e-mail to dsearls at cbil.humgen.upenn.edu, or contact

          David Searls
          Department of Genetics, CRB475
          University of Pennsylvania School of Medicine
          422 Curie Boulevard
          Philadelphia, PA 19104-6145
          Voice: (215)573-3107
          FAX: (215)573-3111

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