ECE-690-503: Genomic Signal Processing (Spring, 2009)
| CRN |
33551 |
| Course Number |
ECE-S690 |
| Section Number |
503 |
| Credits |
3.0 |
| Time |
Tuesdays 6pm - 9pm |
| Office Hours |
upon request (email me) |
| Room |
Bossone 616 |
| Instructor |
Gail Rosen |
| Restrictions |
ECES-302 and Matlab knowledge |
| 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 DNA sequence analysis, to gene prediction, sequence alignment, and
metagenomics.
References (put on reserve at the library)
- Biological sequence analysis, Durbin et al., 8th edition, 1998.
- Introduction to Genomic Signal Processing with Control, Dhatta and Dougherty, 2006.
- Introduction to Computational Genomics, Cristianini and Hahn, 2006.
Grading
| Homework Assignments (Due TBA) | 40%
|
| Literature Review Topic Declared (emailed to me by April 10th) | 0% if sufficient OTHERWISE -5% (yes, that's a negative) if not declared on time. |
| Literature Review / Project Proposal(Due April 28th)) |
30% (20% for Report and 10% for Presentation) |
| Progress Report (Due May 19th) |
(0% if sufficient but -5% will be given if lack of preliminary results/progress) |
| Final Project (Due June 9th) | 30% (15%/15% for report and presentation)
|
Assignment descriptions
| Project Topic | Must relate to 1) genomics or 2) signal processing (SP)/algorithms |
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| Literature Review | Must be at least 15 pages single-spaced (12 pt. Times New Roman) , including figures and tables. Should Overview the area: 1) If a genomic topic, overview the genomic problem -- why is it a difficult problem, overview the state-of-the-art solutions in the area (example: novel gene prediction techniques, phylogenetic tree reconstruction, metagenomic taxa recognition, microarray organism detection, etc.) 2) If SP or algorithms, what problems do these algorithms attempt to solve, what are the challenges in these problems, and detailed workings of the signal processing method or algorithm. |
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| Project Proposal | Must be 1-2 pages (12 pt. Times New Roman) . State exactly what problem you will pursue and how will you pursue it (Goals/Solutions). Give the steps and timeline of what milestones you expect to complete on the project. The project proposal must be solving a genomic problem with an algorithm. |
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| Progress Report | Must be 1-2 pages (12 pt. Times New Roman) . Show preliminary work, data, results, and conclusions. State progress with respect to timeline. If restructuring of timeline is needed, please state. |
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| Final Project | Must be at least 10 pages single-spaced (12 pt. Times New Roman) , including figures and tables. Will give full details how Data was acquired for project, Method that was used, Extensive Results found, and Conclusions about Results. Results that were shown in the progress report can be repeated here. |
Proposed Timeline (subject to change)
| Week 1 | Introduction to Molecular Biology
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| Week 2 | Introduction, Tools, and Databases |
| Week 3 | DNA Representation, Analysis, and Bioinformatics Tools
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| Week 4 | Pairwise Alignment and BLAST |
| Week 5 | Literature Review and Project Proposals Presentations |
| Week 6 | Introduction to HMMs |
| Week 7 |
HMMs for Gene and CpG island prediction |
| Week 8 |
Information Theory for Motif-Finding, Autoregressive Analysis, and Compression of DNA sequences |
| Week 9 | Constructing Phylogeny |
| Week 10 | Machine Learning for Metagenomics |
| Week 11 | Final Project 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).
