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Download MMG 232: Methods In Bioinformatics Spring 2016, 3 credits
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MMG 232: Methods In Bioinformatics Spring 2016, 3 credits Wednesdays 12:00-3:00, Ira Allen Lecture Hall/MLK Room Instructor: Julie Dragon, PhD Director, Bioinformatics Shared Resource (BSR) 4 Hills Building (ground floor) 802-656-7777; [email protected] Office hours by appointment “The course provides a methodological survey of bioinformatics techniques. Particular emphasis is given to popular bioinformatics applications. The final project of the course will be to demonstrate an understanding of bioinformatics approaches within the context of a biological scenario.” MMG232 Date Syllabus Topic 20-Jan Applied Bioinformatics 27-Jan Biological Databases Functional Domains & Sequence 3-Feb Similarity Sequence Alignment & Mapping: 10-Feb Microbiome 17-Feb Phylogenetics 24-Feb Metagenomics 2-Mar Mid-Term Projects 9-Mar Spring Break 16-Mar Structural Variation Gene Expression & Comparative 23-Mar Genomics 30-Mar Copy Number Variation 6-Apr Molecular Interactions 13-Apr Genomic variation 20-Apr Gene annotation 27-Apr Genome Wide Association Studies 4-May Presentations Discussion Survey bioinformatics applications & databases Database mining (continued) BLAST searches and Protein visualization Amplicon sequencing & OTU identification Inferring evolutionary history Metagenomics: the complete picture What have you learned so far? Structural changes & DNA integration: inversion/translocation & viral insertion The effects of differential gene expression Identification of copy number variations and their impact on disease Protein binding sites and chromosomal conformation Is a variant real: frequentist vs bayesian models Variant annotation and functional consequences The association of genotype and phenotype Wrapping the tools together! This course provides a methodological survey of bioinformatics techniques. Particular emphasis is given to popular bioinformatics applications. Classes will include about an hour of theory/background, followed by an hour of hands on bioinformatics tool application at your laptop. Lastly we will summarize what we did and review any confusing points. This is not a course for learning to program. Most activities will involve databases and freeware with web-interfaces, or limited commercial software. I cannot guarantee that you will learn to use your favorite bioinformatics tool or learn to analyze your own genomics data, though I can work with folks who have their own data to include those in their project. Your grade will be based on 1) attendance and participation (20%), 2) the mid-term project (40%), and 3) the final project (40%). The projects will require you to employee a set of bioinformatics tools to address a question. Your comprehension of bioinformatics methods will be assessed by the competency and depth at with which you apply appropriate bioinformatics tools.