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IMA Hot Topics Workshop
Challenges and Opportunities in Genomics: Production, Storage, Mining and Use
April 24-27, 1999

  Schedule   Participants   1998-1999 Mathematics in Biology 

with partial support from 3M

Organizers:

Sangtae Kim
Parke-Davis Pharmaceutical Research
kim01@aa.WL.com

Vipin Kumar
Department of Computer Science
University of Minnesota
http://www.cs.umn.edu/~kumar
kumar@cs.umn.edu

David Misemer
3M
dkmisemer@mmm.com

Dennis Polla
Electrical & Computer Engineering
University of Minnesota
polla@ee.umn.edu

and

Isidore Rigoutsos
Computational Biology Center
IBM Thomas J. Watson Research Center
http://www.research.ibm.com/people/r/rigoutso/home.html
rigoutso@us.ibm.com


Spurred by progress in the Human Genome Project, and driven by the need for cheap, fast and accurate gene sequencing, there has been an explosion of interest in the development and usage of the laboratory-on-a-chip for such purposes as gene testing, high throughput drug screening, and infectious disease diagnostics. This workshop will focus on scientific and mathematical issues arising in production, storage, and mining of genomic data, and use of the knowledge in application. It will be an opportunity for the scientific community to see a snapshot of the state of the arts in this field. Invited participants will be mathematicians, chemists, medical researchers and engineers; in particular, members of the bioinformatics community. Among the topics considered will be

  1. Data Production - discovery, sequencing, detection

  2. Storage - format, data size, combining heterogeneous data bases

  3. Mining - data analysis and knowledge discovery

  4. Usage - domain experts, patterned search, interaction with mining

The purpose of the meeting is to assemble an interdisciplinary working group in this fast moving field, to assess the state of the art and, in particular, gaps that need filling, and to define a set of pre-competitive research problems to be worked on. This will be accomplished through a series of talks and panel discussions. We intend to hold follow-up meetings at regular intervals (involving many of the original participants) as the field progresses.

WORKSHOP SCHEDULE

All talks are in Lecture Hall EE/CS 3-180 unless otherwise noted.

Saturday Sunday Monday Tuesday

SATURDAY, APRIL 24
7:00-9:00 pm Reception and Registration Radisson Hotel, Metrodome
SUNDAY, APRIL 25
8:30-9:00 am Registration and Coffee Reception Room EE/CS 3-176
9:00 am IMA Directors Welcome
9:15 am Ronald C. McGlennen
University of Minnesota 		Genomics: Discovery to Delivery
10:15-10:30 am Coffee Break Reception Room EE/CS 3-176
10:30 am James W. Jacobson
Luminex 		Multi-Analyte Profiling with Suspension ArraysTM
11:15 am-12:00 pm Gregory Stephanopoulos
Massachusetts Institute of Technology 		Mining of DNA Microarray Data
1:30 pm Roland Somogyi
Incyte Pharmaceuticals, Inc. 		Inference of Functional Programs from Gene Expression Data
2:15 pm Ross Overbeek
Argonne National Laboratories 		Exploitation of Chromosomal Locations to Establish Functions of Genes
3:00-3:15 pm Coffee Break Reception Room EE/CS 3-176
3:15-4:00 pm Nikos Kyrpides
University of Illinois Urbana-Champaign 		Methanococcus Jannaschii Genome: Annotations, Evolution and Evolution of Annotations
MONDAY, APRIL 26
9:00-9:15 am Coffee Reception Room EE/CS 3-176
9:15 am Roger Brent
Molecular Science Institute 		Intellectual Fallout from Biology's Success: Can Mathematics Help Us Out?
10:15 am Coffee Break Reception Room EE/CS 3-176
10:30 am Anne R. Kopf-Sill
Caliper Technologies Corporation 		Lab-on-a-Chip Technology Including Tools for Genomics Applications
11:15 am Isidore Rigoutsos
IBM 		Pattern Discovery and Its (Numerous) Applications in Computational Biology
1:30 pm Gary Benson
Mount Sinai School of Medicine 		Algorithms for Detection and Analysis of Tandem Repeats in DNA Sequences
2:15 pm John V. Carlis
University of Minnesota 		Adapting and Applying Simplical Complex Q-Analysis to Studying Sequence Similarity Databases
3:00-3:15 pm Coffee Break Reception Room EE/CS 3-176
3:15-4:00 pm John R. Yates
University of Washington 		Mining Proteomes Using Mass Spectrometry: New Approaches to Help Define Function
4:00-4:45 am William Swope
Almaden/IBM 		An Annotation Capture/Query System For Genomic Data
4:45-6:00 pm Panel Members:
Sangtae Kim (Parke-Davis Pharmaceutical Research)
Ron McGlennan (University of Minnesota
David Misemer (3M
Isidore Rigoutsos (IBM TJ Watson Research Center) 		Panel Discussion

The panel will attempt to assess the state of the art in this field and define future promising research directions. There will be special attention on interesting mathematical issues that need resolution.
6:30-8:00 pm Pizza Party IMA East, 400 Lind Hall
TUESDAY, APRIL 27
9:00-9:15 am Coffee Reception Room EE/CS 3-176
9:15 am Larry Carson
3M Corporate Research 		An Assessment of Micro-Array Technologies for High Throughput Genetic Analysis
10:00 am Coffee Break Reception Room EE/CS 3-176
10:30 am Vipin Kumar
University of Minnesota 		Data Mining for Genomics
11:15--12:30 pm Panel Members:
Sangtae Kim (Parke-Davis Pharmaceutical Research)
Ron McGlennan (University of Minnesota
David Misemer (3M
Isidore Rigoutsos (IBM TJ Watson Research Center) 		Panel Discussion

The panel will further discuss the issues raised in the first panel on Tuesday.

Saturday Sunday Monday Tuesday

LIST OF CONFIRMED PARTICIPANTS

as of 4/23/99
Name Department Affiliation
Edgar Arriage Chemistry University of Minnesota
John S. Baras Electrical Engineering & Institute for Systems Research University of Maryland-College Park
Gary Benson Biomathematical Sciences Mount Sinai School of Medicine
Roger Brent Molecular Science Institute University of California-Berkeley
Kathryn Bretscher   3M Center
Daniel M. Burns Mathematics University of Michigan
Roxanne Burns   Kent State University
John Carlis Computer Science and Engineering University of Minnesota
Lockwood Carlson   3M Center
Larry Carson   3M Center
Yang Da Veterenary Pathobiology University of Minnesota
Lynda Ellis Laboratory Medicine and Pathology University of Minnesota
Aris Floratos T.J. Watson Research Center IBM Corporation
Patrick Fu Chemical Engineering & Materials Science University of Minnesota
Debra Sue Goldberg Center for Applied Mathematics Cornell University
Laurel Harmon Informatics Nonlinear Dynamics Incorporated
Paula Hicks Central Research Cargill, Inc.
James W. Jacobsen Molecular Biology Luminex
Sangtae Kim   Parke-Davis Pharmaceutical Research
Anne Kopf-Sill Microfluidics & Advanced Technology Caliper Technologies Corp.
Rashmi Korke Chemical Engineering and Materials Science University of Minnesota
Vipin Kumar Computer Science University of Minnesota
Nikos Kyrpides Chemical & Life Science University of Illinois - Urbana-Champaign
Yun Seung Kyung Chemical Engineering & Materials Science University of Minnesota
Jongchan Lee Chemical Engineering and Materials Science University of Minnesota
Larry Lok   Molecular Sciences Institute
David Mack   Parke-Davis
Ron McGlennan Laboratory Medicine and Pathology University of Minnesota
David Misemer   3M
R.A. Narayanan CEMS University of Minnesota
George Nelson Mathematics The University of Iowa
Ross Overbeek   Argonne National Labs
Dhiraj Pathak   Glaxo Wellcome Inc.
Dennis Polla Electrical & Computer Engr. University of Minnesota
Alex Pothen Computer Science Old Dominion University and ICASE
Marian Pour-El Mathematics University of Minnesota
Ron Pratt   3M Center
Isidore Rigoutsos   IBM TJ Watson Research Center
Michael J. Sadowsky Microbiology and Soil Water and Climate University of Minnesota
William Satzer   3M Center
Steve Schlosser   Nonlinear Dynamics Incorporated
Elizabeth Shoop Academic Health Center Academic Computing Computational Biology Centers
Roland Somogyi Neurobiology Incyte Pharmaceuticals, Inc.
Gregory Stephanopoulos Chemical Engineering Massachusetts Institute of Technology
Joey W. Storer Computing, Modeling and Information Sciences The Dow Chemical Company
William Swope   Almaden/IBM
Paul J. Wagner Computer and Information Sciences University of Minnesota
Pearse Ward Biophysical Sciences and Medical Physics University of Minnesota
John Yates Molecular Biotechnology University of Washington
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