Course Description and Syllabus
Catalog Description: A data driven approach for the computational and statistical understanding and expertise needed to solve bioinformatics problems that you will likely encounter in your research. Topics will include: microarray data analysis, high-throughput sequence data analysis and SNP genotyping analysis as well as some additional specific advanced topics.
Class Meetings: Monday/Wednesday 1:00-2:30 in LSS 440 (IBEST Classroom)
Course Credits: 3 cr.
Prerequisites: One of CS 120 (Computer Science I), Stat 452 (Mathematical Statistics), Biology 456 (Computer Skills for Biologists), or with permission.
Instructor: Matt Settles
Office: LSS 441C; Phone:885-6051; Email:firstname.lastname@example.org
Teaching Assistant: Hannah Marx
Course Goals: Following this course the student will be capable of performing their own data analysis project, understanding the technical and statistical tools needed to conduct the analysis with the computational ability to do so, and critically review and implement techniques and methods in publications.
Course Format: The course will be divided into both lecture and lab/workshop sessions.
Topics will include:
- Expression microarray analysis
- CGH/CHiP-Chip microarray overview
- Phylogenetic methods and analysis
- High-throughput sequence assembly analysis
- High-throughput sequence mapping analysis
- RNA-seq overview
- Metagenomics overview
- Whole Genome Association Studies overview
Course Grading:A point system will be used for grading. Your semester grade will be based on a standard grading curve (90%, 80%, 70%,…) of the cumulative number of points you have earned by the last day of finals week. There will be 4 projects (each worth a 20 points), and 20 points for either publication reviews (each worth 2 points), or participation in Sequence Analysis Discussion (SAD) group on Fridays, for a total of 100 points.
Each project will be a report on the analysis of provided data (or your own data) using the techniques discussed in class. The reports must be written using Latex or markdown, with embedded R code when appropriate, of the complete analysis. A template with brief introduction is provided in the documents section below.
Publication reviews will be short 1/2 to full page comments on assigned methods papers. A Template is provided in the documents section below.
Most documents associated with this course are available here