DIMACS Mini-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 interoperability.


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 minority.


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, 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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Document last modified on April 25, 1995