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 |
Description
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)
- Introduction to Genomic Signal Processing with Control, Dhatta and Dougherty, 2006.
- Introduction to Computational Genomics: A Case Studies Approach, Cristianini and Hahn, 2007.
- Gene Expression Data Analysis and Modeling
Tutorial
- S. Marshall, L. Yu, Y.
Xiao, E. R. Dougherty, "Inference of a Probabilistic Boolean Network from
a Single Observed Temporal Sequence," EURASIP Journal on Bioinformatics
and Systems Biology., Vol. 2007, Article ID 32454, 15 pages, May, 2007.
Grading
Paper Reviews/Notes | 30%
|
Leading the discussion | 10% |
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 www.drexel.edu/edt/disability, 3201 Arch
St., Street, Suite 210, Philadelphia, PA 19104, 215.895.1401 (V), or
215.895.2299 (TTY).