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Functional Genomics

Functional Genomics. http://www.ruf.rice.edu/~metabol/images/genotype.jpg. Winter/Spring 2012. Carol Bult, Ph.D. Course coordinator carol.bult@jax.org The Jackson Laboratory. Keith Hutchison, Ph.D. Course co-coordinator keithh@maine.edu University of Maine. What is Functional Genomics?.

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Functional Genomics

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  1. Functional Genomics http://www.ruf.rice.edu/~metabol/images/genotype.jpg Winter/Spring 2012 Carol Bult, Ph.D. Course coordinator carol.bult@jax.org The Jackson Laboratory Keith Hutchison, Ph.D. Course co-coordinator keithh@maine.edu University of Maine

  2. What is Functional Genomics? • A field of molecular genetics that uses genome-wide, high-throughput measurement technologies to understanding the relationships between genotype and phenotype • Genomics, epigenomics, transcriptomics, proteomics • Computational genomics (data mining) • Transgenics, targeted mutations, etc. http://en.wikipedia.org/wiki/Functional_genomics

  3. What topics will this course cover? • Primary focus: • Transcriptional profiling using microarrays and high-throughput sequencing (RNA-Seq) • Data analysis • R statistical programming language/environment • Galaxy sequence analysis workflow system • Other topics: • Genome structure and sequence variation • Epigenomics • Bio-ontologies • Proteomics • Metabolomics

  4. How will this course be structured? • Lectures and readings assigned by instructors • Assignments and discussion (50% of grade) • Student project (50% of grade) • Choose a data set to analyze from several options • Do some background research on the data set • Perform an analysis of the data • Write up the analysis in the format of a scientific manuscript as if you were submitting the manuscript to PLOS Computational Biology • http://www.ploscompbiol.org/home.action • Oral presentation on the project • Preliminary results mid-course (15 minutes per student) • Final presentation at end of course (20 minutes per student)

  5. Who are the instructors? • Carol Bult (JAX), course coordinator • Microarrays, Using R, Galaxy • Keith Hutchison (UM), co-coordinator • Genome structure/variation • Gary Churchill (JAX) • experimental design • Doug Hinerfeld (JAX) • next generation sequencing and proteomics • Judith Blake (JAX) • bio-ontologies • Matt Hibbs (JAX) • mining expression data • Joel Graber (JAX) • RNA processing

  6. What resources will be used for this course? • Class Web Site • functionalgenomics.wordpress.com • R Project for Statistical Computing • http://www.r-project.org/ • Gene Expression Omnibus (GEO) @ NCBI • http://www.ncbi.nlm.nih.gov/geo/ • Gene Ontology web site • http://www.geneontology.org/ • Maine Innovation Cloud • http://www.cloud.target.maine.edu/

  7. For next time • Read about R • http://www.r-project.org/ • You might find the following link to Dr. Karl Broman’s into to R useful: • http://www.biostat.wisc.edu/~kbroman/Rintro/ • In the next week you will be given an account on the Maine Innovation Cloud which will give you access to R • You will need some basic Linux/Unix commands to use the Cloud • http://code.google.com/edu/tools101/linux/basics.html • http://www.reallylinux.com/docs/basic.shtml • Next time…Keith Hutchison will lecture on • Genome Structure/Sequence Variation

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