ECE-690-501: Genomic Signal Processing (Winter, 2008)
Recommended Books (but not required)
Tozeren
and Byers. New
Biology for Engineers
Cristianini and
Hahn. Introduction to Computational Genomics.
Jones and Pevzner. An Introduction to Bioinformatics Algorithms.
Class Materials
Week 1
Vaidyanathan and Yoon. ``The role of signal-processing concepts in
genomics and proteomics," Journal of the Franklin Institute, Special Issue on Genomics, 2004.
E. R. Dougherty, A. Datta and C. Sima, "Research Issues in Genomic Signal
Processing," IEEE Signal Processing Magazine, Vol. 22, No. 6, 46-68,
November 2005.
Sequencing
Overview
of Systematic Sequencing Techniques
Week 2
-
Mahmood; Epps, Julien; Ambikairajah, Eliathamby. "On DNA Numerical
Representations for Period-3 Based Exon Prediction," IEEE GENSIPS
Workshop, 2007.
- Yin,
C. and Yau, S. S.-T. (2007) ``Prediction of Protein-Coding
Regions by the 3-Base Periodicity Analysis of a DNA Sequence," J. Theor.
Biol, 247, 687-694, 2007.
-
D. Sussillo, A. Kundaje, D. Anastassiou, "Spectrogram
Analysis of Genomes," EURASIP Journal of Applied Signal Processing
(2004) 29-42
This tool has been developed based on this
technique:
Spectrofish
-
Afef Elloumi Oueslati, Noureddine Ellouze, Zied Lachiri:
``3D Spectrum Analysis of DNA Sequence: Application to Caenorhabditis
elegans Genome," IEEE BIBE Conference,pp. 864-871, 2007.
Week 3
Week 4
Week 7
Week 8
Week 9
Homeworks
Links
Links from 2006 (may be out-of-date)