Mini-Workshop on Gene-Finding and Gene Structure Prediction
October 13-14, 1995
Genome Center at the University of Pennsylvania
- David Searls (Genome Center, Univ. of Pennsylvania), email@example.com
- 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
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:
- Jean-Michel Claverie, "Gene Identification by Database Lookup:
Principle, Problems, and Limits... and Working Solutions"
- Jim Fickett, "Identification of Muscle-Specific Transcriptional
- Mike Gelfand, "Dynamic Programming for Gene Recognition"
- Roderic Guigo, "Evaluation of Gene Structure Prediction Programs"
- David Haussler, "Generalized Hidden Markov Models for DNA Parsing"
- Steve Mount, "Some Nasty Little Facts to Bear in Mind when Predicting
- Mick Noordewier, "On the Entropy of DNA: Algorithms and Measurements
based on Memory and Rapid Convergence"
- Pavel Pevzner, "Spliced Alignment: A New Approach to Gene Recognition"
- Bruce Roe, "Lessons from Over One Million Bases of Human Genomic DNA
- Victor Solovyev, "Recognition of Promoter, Coding and Poly-A Signal
Regions of Eukaryotic Genes by Oligonucleotide Composition and
Functional Motifs Characteristics"
- Gary Stormo, "The GeneParser Approach to Finding Genes"
- Ed Uberbacher, "Gene Discovery and Sequence Annotation in GRAIL 1.3"
- Owen White, "A Highly Curated Set of Non-Redundant, Alternatively
Spliced Human Genes for Optimal Training of Gene-Finding Algorithms"
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 (firstname.lastname@example.org). 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
Indicate if presenting a paper or poster:
David Searls, University of Pennsylvania/SmithKline Beecham
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
Next: Call for Participation
Contacting the Center
Document last modified on September 11,1995