1. Goals of the Course Genome Sequence Information Genomic VariationsGenomic 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 Friedman permission 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 from Benno Schwikowski permission from Ruedi Aebersold http://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 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