BioE 594
-- Design and Implementation of Computational Methods in
Bioinformatics
11:00am-12:15pm Tuesdays and Thursdays
Room : 419 CMW (College of Medicine West)
Instructor: Yang Dai (yangdai@uic.edu)
Office Hours : 1:00pm -2:00pm, Tuesdays
Office Location :
Room W125
Medical Sciences Building
835 S. Wolcott Ave.
Tel : (312)413-1487
Share the entrance with
CLIMB Clinical Laboratory for Interfacial Molecular Bioengineering
Quick Links
Course Description
This semester we focus on study and implementation of methods that are useful in the analysis of
microarray gene expression data.
Course Requirements
Required background includes ability to program in a high-level language.
S-Plus(or R) or Matlab experience may also be helpful.
Homework assignments may include reading, mathematical analysis, programming, and the use of software tools.
Student will be asked to present papers from the literature. Students will also need to complete a term project, and produce both a written final report and a class presentation.
Grading Policy
Homework assignments (30%)
Term project (20%)
Two exams (40%)
Class participation and discussion (10%)
mid-term exam on February 25, final exam on April 29
final project presentation on April 17,22,24
Required Software (Base, upon which analysis tools will be used and built)
- Matlab (available from ACCC)
- R (download from here) and others.
Please make sure that you are familiar with them. Homework assignments are based on them.
Topics
- Primer on Molecular Genetics
- Microarray Technology
- Microarray experiments
- Preprocessing of Microarray data
- Resampling and bootstrap
- R and Bioconductor
- Multiple testing
- Distances and expression measures
- Feature selection techniques
- Cluster analysis in microarray experiments
- Classification in microarray experiments
- Experimental design
- Inferring genetic network
Schedule and materials presented
Reading
Reference Books
(1) Microarray for an Integrative Genomics, by Issac S, Kohane et al.,
The MIT Press, 2003. ISBN 0-262-11271-X.
(2) Biostatistics : a fundation for analysis in the health sciences, 7th edition, by W. Daniel,
John Wiley, 1999.
(3) Pattern Recognition, by S. Theodoridis and K. Koutroumbas, Academic Press, 1999.
Additional Online Reading Materials
- Statistics
- R References
- Molecular Biology
- DNA Chip Technology
-
Animation ( it's fun! )
-
Nature Genetics 21 (1) 1999 (In this issue you will find a series of state-of-the-art reviews of the technology
for production of DNA chips in various formats. Also it is published in 1999, many basic concepts
of the technology remains unchanged)
- Support Vector Machine
Major microarray databases
Stanford microarray database
Analysis tools for microarray data
SMD Microarray Links : Software & Tools
Bioconductor
Articles on Microarray Datamining:
Wentian Li of Rockefeller University maintains a list of papers on data analysis:
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