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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
Goals of the Course
DNA Microarrays
www.bio.davidson.edu/courses/genomics/genomics.html
Thought Questions
www.bio.davidson.edu/courses/genomics/chip.html
Basic Research
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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
• 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?
permission from Rosetta Inpharmatics, Inc.
Applied Research
•Cancer
•Pharmacogenomics
Query Online Databases
permission from Pat Brown
permission from John Weinstein
permission from Marcel Behr
• 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?
Proteomics
Value Added Features
www.bio.davidson.edu/courses/genomics/proteomics.html
Cellular Roles
•Acquiring Sequence
•Human Genome Draft
•Evolution
Explore Beyond Presented Material
• 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.
Genome Sequence Information
Basic Research
www.bio.davidson.edu/people/macampbell/strategies/handson.html
Fully Understand Data
•Introduction to Method
•Data Analysis
permission from Jeff Friedman
www.bio.davidson.edu/courses/genomics/seq.html
28035
www.bio.davidson.edu/people/macampbell/strategies/overview.html
Math Minutes (examples from sequence section)
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permission form Mike Snyder
permission form Susan Lindquist
Protein-Protein Interactions
Applied Research
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? permission from
permission from
Laura Richman
Ulf Gyllensten
Genomic Medicine
•Identification of Biological Unknowns
•Biomedical Research
permission from
Benno Schwikowski
• Begin the course with medical case studies to confront the
misconception of “one gene, one phenotype.
permission form Stan Fields
Identification and Quantification
15 Second Biographies
permission from Andreas
Manz and David Burke
permission from Blair Hedges
permission form Stan Fields
Genomic Variations
www.bio.davidson.edu/courses/genomics/SNP.html
http://expasy.cbr.nrc.ca/ch2dothergifs/publi/yeast-low.gif
Genomic Circuits
Assessment
www.bio.davidson.edu/courses/genomics/circuits.html
www.bio.davidson.edu/courses/genomics/genomicsyllabus.html
Single Gene Circuit
Ecology
permission from Ruedi Aebersold
permission from Kevin Campbell and Jim Ervasti
• Provide photos and mpeg movies of people who
conduct genomic research so students can observe
their heterogeneity and “regular person” qualities. permission from Lee Hartwell, Ginger Armbrust, and Pat Brown
Tests
www.bio.davidson.edu/courses/genomics/Exams/exams.html
•Tracking Ivory Sales
•Diatoms and Global Warming
permission form Ginger Armbrust
Human Variations
permission form
Kenine Comstock
Toggle Switches
permission form
Eric Davidson
•SNPs
•Disease Analysis
permission from
Gordon Lithgow
Ethics
permission from
Stan Leibler
Web Pages
1) Describe
2) Describe
3) Describe
4) Describe
www.bio.davidson.edu/courses/genomics/studentpages.html
a genomic method.
a known and unknown yeast gene.
gene expression profiles for same two genes.
proteomics for same two genes.
Critique Papers
Integrated Circuits
www.bio.davidson.edu/courses/genomics/Labpageslist.html
•GMO’s
•Genetic Testing
permission form
Leroy Hood
[email protected]
Want to see the textbook (Cold Spring Harbor Press & Benjamin Cummings)? email [email protected]