Introduction to Computational Genomics

University of Toronto, Canada

Mark W. Perlin, PhD, MD, PhD. Senior Research Scientist, Computer Science Department, Carnegie Mellon University; Joint Faculty, Department of Human Genetics, University of Pittsburgh; and Chief Executive Officer, Cybergenetics, Inc.

Genomics underlies the ongoing genetics revolution, which will have far-reaching consequences for medicine, biology, and society. Genomics is part molecular biology, and part mathematics. This course teaches what every applied mathematician should know about the mathematical and computational half of genomics.

This course introduces and motivates the field of genomics and includes all necessary biological background material. The focus is on genetic and physical mapping methods and their applications. The major topics include genetic mapping, radiation hybrid mapping, clone mapping, and disease gene mapping. The emphasis is on the mathematical and computational aspects of these methods. We also describe how these methods enable highly optimized biomedical research technologies.

- Introductory 50%
- Intermediate 40%
- Advanced 10%

An attendee of this course will be introduced to key mathematical and computational aspects of genomics. Most importantly, the attendee will acquire a broad perspective on how mathematics and information enable efficient genome technologies. This perspective might be useful in their identifying important new research areas in the field.

Any scientist who is interested in learning about or contributing to the genomics revolution. As the attendee will learn, genomics transcends discipline, occupation, or sector.

The attendee should have a solid undergraduate background in mathematics. Some exposure to computer science or biology could be helpful.

Dr. Perlin has developed biomedical information and automation technologies since 1984, and has focused on the area of genetics since 1989. Dr. Perlin developed the inner product mapping (IPM) method, and in 1994 led the group that produced the first high-resolution chromosome 11 clone map. He also developed the TrueAllele (TM) fully automated genotyping technology.

Dr. Perlin received a B.A. in Chemistry from SUNY/Binghamton, a Ph.D. in Mathematics from CUNY/Graduate School, an M.D. from the University of Chicago Pritzker School of Medicine, a Ph.D. in Computer Science from Carnegie Mellon University, completed a one year residency at Mercy Hospital in Pittsburgh, and was a Fellow at IBM's Watson research facility in Yorktown Heights, NY.

8:00 Registration

9:00-10:00 Introduction

- What is genomics?
- Biology and biotechnology
- The mathematical perspective

10:00-10:30 Coffee - Wilson Hall Cafeteria

10:30-11:15 Genetic Mapping

- Associating traits to locations
- Survey of methods
- Examples

11:15-12:00 Radiation Hybrid Mapping

- Associating DNA markers to locations
- Mathematical methods
- Examples

12:00-2:00 Lunch - Wilson Hall Cafeteria

2:00-3:00 Clone Mapping

- Associating DNA fragments to locations
- Efficient strategies
- Examples

3:00-3:30 Coffee - Exhibit Hall, Wetmore

3:30-4:15 Disease Gene Mapping

- Putting it all together
- Finding genes by positional cloning
- Examples

4:15-5:00 Research Technologies

- Large-scale screening
- Gene expression
- The future of medicine

5:00 Short course adjourns

Seats are limited. We urge attendees to register in advance. To register for either short course, please complete the preregistration form. Upon completion, return the form with your payment to reach the SIAM office on or before June 23, 1998.

**Registration fee for the short course includes short course notes, coffee breaks, and lunch on Sunday, July 12.**

The short course on Genomics will be in Room 1017 Wilson Hall; the morning coffee break and lunch will be in the Cafeteria, Wilson Hall. The afternoon coffee break will be in the Exhibit Hall of Wetmore Hall, New College.

TJF Created: 1/20/98, MMD Updated: 5/27/98