ECE-690-001: Genomic Signal Processing II (Spring, 2008)

CRN 33061
Course Number ECE-S690
Section Number 501
Credits 3.0
Time Mondays 6pm - 8:50pm
Office Hours upon request (email me)
Room Bossone 616
Instructor Gail Rosen
Restrictions signals and systems
Department Electrical and Computer Engineering


This course focuses on signal processing(SP) applied to analysis and design of biological systems. This is a growing area of interest with many topics ranging from gene prediction, genetic pathways, and microarray design.

References (put on reserve at the library)


Paper Reviews/Notes30%
Leading the discussion10%
Project Declaration (Due April 14th) and Progress Report (Due May 12th)) 30%
Final Project (Due June 11th)30%

Discussions include a 30 minute presentation about the topic followed by leading the discussion.
Everyone is expected to turn in a few pages of notes about the paper.

Proposed Timeline (subject to change):

Week 1 Guest Lecture by Prof. Bahrad Sokhansanj on the Challenges in Systems Biology Engineering Systems Biology (Lots of Questions....)
Week 2: Gail and Elaine (April 7th) Biology (pdf slides) and Database Primer for Genomics and Microarrays for Gene Expression
Week 3: Jack (April 14th) Braga-Neto, U. M., and Dougherty, E. R., "Is Cross-Validation Valid for Small-Sample Microarray Classification," Bioinformatics, Vol. 20, No. 3, 374-380, 2004
Week 3: Patrick A hybrid Bayesian network learning method for constructing gene networks
Week 4: Non (April 21th) Designing Compressive Sensing DNA Microarrays
Week 5: Wang (April 28th) DNA Microarray Analyses of the Long-Term Adaptive Response of Escherichia coli to Acetate and Propionate
Week 6: Elaine (May 5th) Dougherty, E. R., Hua, J., and M. L. Bittner, "Validation of Computational Methods in Genomics," Current Genomics, Vol. 8, No. 1, 1-19, March, 2007.
Week 7: Adheer (May 12th) $K$-SVD: An Algorithm for Designing Overcomplete Dictionaries for Sparse Representation
Week 8: Chidi (May 19th) Metagenomics: Application of Genomics to Uncultured Microorganisms
Week 8: Steve MEGAN analysis of metagenomic data
Week 9: Memorial Day Happy Holiday!
Week 10 (June 2nd): Four of the final presentations
Week 11: (June 11th or 12th) Four of the final presentations

Disability Information

Student with disabilities requesting accommodations and services at Drexel University need to present a current accommodation verification letter (AVL) to faculty before accommodations can be made. AVL's are issued by the Office of Disability Services (ODS). For additional information, contact ODS at, 3201 Arch St., Street, Suite 210, Philadelphia, PA 19104, 215.895.1401 (V), or 215.895.2299 (TTY).