Mini-Workshop on Gene-Finding and Gene Structure Prediction

October 13-14, 1995
Genome Center at the University of Pennsylvania
Philadelphia, PA

David Searls (Genome Center, Univ. of Pennsylvania),

Principal Advisor:
Jim Fickett (Los Alamos)

Organization Committee:
Michiel Noordewier (CS & Waksman, Rutgers)
Gary Stormo (Biology, Colorado)


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.


A strong program of oral and poster presentations is planned. Speakers will include the Organizing and Program Committee, listed below, as well as approximately 10 additional talks and 20 posters based on refereed abstract submissions. Some of the speakers include:


Attendees are responsible for making their own travel and hotel reservations. A limited number of rooms have been reserved as a block at the conference hotel, at a conference rate of $95 per night. (The conference will run from approximately 8:30am to 5:30pm on both October 13 and 14.) To reserve a room call the Penn Tower Hotel, Civic Center Blvd. at 34th Street, Philadelphia, PA 19104-4385, at (215)387-8333. Mention that you are with the Gene-Finding Workshop.


Return the following information, by e-mail if at all possible, to Mick Noordewier ( Registration will be cut off at approximately 100 so please submit your registration and wait for an acknowledgement before making definite travel plans. Your registration must then be followed within two weeks by a check, made out to The Trustees of the University of Pennsylvania, in the amount of $95, mailed to David Searls, Department of Genetics 475 CRB, University

of Pennsylvania School of Medicine, 415 Curie Boulevard, Philadelphia, PA 19104-6145. If payment is not received by that time your position will be released. Any questions regarding registration or other aspects of conference attendance should be directed to Dr. Noordewier.

Gene-Finding and Gene Structure Prediction Workshop Registration




E-mail address:

Physical Address:

Phone Number:

FAX Number:

Indicate if presenting a paper or poster:


David Searls, University of Pennsylvania/SmithKline Beecham Pharmaceuticals, 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

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Document last modified on September 11,1995