Goals of the Course

1
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
Goals of the Course
DNA Microarrays
Thought Questions
www.bio.davidson.edu/courses/genomics/genomics.htm
l
www.bio.davidson.edu/people/macampbell/strategies/
handson.html
www.bio.davidson.edu/courses/genomics/chip.html
Basic Research
Fully Understand Data

• Introduction to Method
• Data Analysis

• 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?

Explore Beyond Presented Material
permission from Rosetta Inpharmatics, Inc.

• 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.

Applied Research

• Cancer
• Pharmacogenomics

Query Online Databases
permission from Pat Brown

• Go to the MIPS site lthttp//mips.gsf.de/proj/ye
  ast/search/code_search.htmgt and enter the names
  of the two deleted genes Rnr1 and Rps24a. What
  do they have in common?

permission from John Weinstein
permission from Jeff Friedman
permission from Marcel Behr
Proteomics
Value Added Features
Genome Sequence Information
www.bio.davidson.edu/people/macampbell/strategies/
overview.html
www.bio.davidson.edu/courses/genomics/seq.html
www.bio.davidson.edu/courses/genomics/proteomics.h
tml
Cellular Roles
Basic Research
Math Minutes (examples from sequence section)

• Acquiring Sequence
• Human Genome Draft
• Evolution

• 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 form Mike Snyder
permission form Susan Lindquist
Protein-Protein Interactions
permission from Laura Richman
permission from Ulf Gyllensten
Applied Research
Genomic Medicine

• Identification of Biological Unknowns
• Biomedical Research

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

permission from Benno Schwikowski
permission form Stan Fields
Identification and Quantification
15 Second Biographies
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 Andreas Manz and David Burke
permission from Blair Hedges
permission form Stan Fields
http//expasy.cbr.nrc.ca/ch2dothergifs/publi/yeast
-low.gif
permission from Ruedi Aebersold
permission from Lee Hartwell, Ginger Armbrust,
and Pat Brown
Genomic Variations
Genomic Circuits
Assessment
www.bio.davidson.edu/courses/genomics/SNP.html
www.bio.davidson.edu/courses/genomics/circuits.htm
l
www.bio.davidson.edu/courses/genomics/genomicsylla
bus.html
Single Gene Circuit
Ecology
Tests
www.bio.davidson.edu/courses/genomics/Exams/exams.
html

• Tracking Ivory Sales
• Diatoms and Global Warming

permission form Kenine Comstock
permission form Ginger Armbrust
Human Variations
Web Pages
Toggle Switches
www.bio.davidson.edu/courses/genomics/studentpages
.html
permission form Eric Davidson
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.

• SNPs
• Disease Analysis

permission from Stan Leibler
permission from Gordon Lithgow
Ethics
Critique Papers
Integrated Circuits
www.bio.davidson.edu/courses/genomics/Labpageslist
.html

• GMOs
• Genetic Testing

permission form Leroy Hood
macampbell_at_davidson.edu
Want to see the textbook (Cold Spring Harbor
Press Benjamin Cummings)? email
Michele.Sordi_at_AWL.com