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/people/macampbell/strategies/handson.html www.bio.davidson.edu/courses/genomics/genomics.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 <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? 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.html 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 Assessment Genomic Variations Genomic Circuits www.bio.davidson.edu/courses/genomics/SNP.html www.bio.davidson.edu/courses/genomics/circuits.html www.bio.davidson.edu/courses/genomics/genomicsyllabus.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 • GMO’s • Genetic Testing permission form Leroy Hood macampbell@davidson.edu Want to see the textbook (Cold Spring Harbor Press & Benjamin Cummings)? email Michele.Sordi@AWL.com