Goals of the Course

Genome Sequence Information

Genomic Variations Genomic Circuits

Proteomics

DNA Microarrays

Genomics, Proteomics & Bioinformatics: A Lecture Course with Online Resources#507

A. Malcolm Campbell and Laurie J. Heyer Biology and Mathematics Departments, Davidson College, Davidson, NC 28035

Assessment

Value Added Features

Thought Questions

Math Minutes (examples from sequence section)

15 Second Biographies

Integrate Bioinformatics with Biology Understand Methods and Research Questions Analyze Real Data Incorporate Case-based Context for Every Section Utilize Online Databases Appreciate Complexity of Research Systems Integrate Different Types of Information Reconsider Cells as Intracellular Ecosystems Engage Students in Realistic Learning Environment

www.bio.davidson.edu/courses/genomics/genomics.html

Applied Research

Basic Research

Ethics

Human Variations

Ecology

Applied Research

Basic Research

Identification and Quantification

Protein-Protein Interactions

Cellular Roles

Integrated Circuits

Toggle Switches

Single Gene Circuit

Query Online Databases

Explore Beyond Presented Material

Fully Understand Data

Web Pages

Critique Papers

Tests

www.bio.davidson.edu/courses/genomics/seq.html

www.bio.davidson.edu/courses/genomics/SNP.html

www.bio.davidson.edu/courses/genomics/chip.html

www.bio.davidson.edu/courses/genomics/proteomics.html

www.bio.davidson.edu/courses/genomics/circuits.html

Genomic Medicine

www.bio.davidson.edu/people/macampbell/strategies/overview.html

www.bio.davidson.edu/people/macampbell/strategies/handson.html

www.bio.davidson.edu/courses/genomics/genomicsyllabus.html

www.bio.davidson.edu/courses/genomics/studentpages.html

www.bio.davidson.edu/courses/genomics/Exams/exams.html

www.bio.davidson.edu/courses/genomics/Labpageslist.html

•Acquiring Sequence•Human Genome Draft•Evolution

•Identification of Biological Unknowns•Biomedical Research

•Tracking Ivory Sales•Diatoms and Global Warming

•SNPs•Disease Analysis

•GMO’s•Genetic Testing

•Introduction to Method•Data Analysis

•Cancer •Pharmacogenomics

permission from Blair Hedges

permission from Andreas Manz and David Burke

permission from Gordon Lithgow

permission form Kenine Comstock

permission form Ginger Armbrust

permission from Pat Brown

permission from Jeff Friedmanpermission from John Weinstein

permission from Rosetta Inpharmatics, Inc.

permission from Marcel Behr

permission form Susan Lindquist permission form Mike Snyder

permission form Stan Fields

permission form Stan Fields

permission from Benno Schwikowski

permission from Ruedi Aebersoldhttp://expasy.cbr.nrc.ca/ch2dothergifs/publi/yeast-low.gif

permission form Eric Davidson

permission form Leroy Hood

permission from Stan Leibler

• What could you do to ensure that all cells maintained the same periodicity?• Predict what would happen to the repressilator inside a single bacterium

when

stationary cells were placed in fresh medium. Is your prediction testable?

Design this experiment.

• How can a biological clock outlive its host cell? • Why did they need to design proteins that are rapidly degraded by cells? What

would have happened if the proteins were all long-lived?

• Go to the MIPS site <http://mips.gsf.de/proj/yeast/search/code_search.htm> and

enter the names of the two deleted genes: Rnr1 and Rps24a. What do they have in

common?

• What is an E value?• Are the hit numbers significantly different?• How do you fit a line to data?• How do you know if the phylogenetic tree is correct?• How can you tell if base compositions are different?

• Begin the course with medical case studies to confront the misconception of “one gene, one phenotype.

• Provide photos and mpeg movies of people who conduct genomic research so students can observe their heterogeneity and “regular person” qualities.

permission from Laura Richman

permission from Ulf Gyllensten

permission from Kevin Campbell and Jim Ervasti

permission from Lee Hartwell, Ginger Armbrust, and Pat Brown

1) Describe a genomic method.2) Describe a known and unknown yeast gene.3) Describe gene expression profiles for same two genes.4) Describe proteomics for same two genes.

macampbell@davidson.edu Want to see the textbook (Cold Spring Harbor Press & Benjamin Cummings)? email Michele.Sordi@AWL.com