ECE-690-503: Genomic Signal Processing (Spring, 2009)

Class Materials

Week 1

• Fitch JP, Sokhansanj B. Genomic engineering: moving beyond DNA sequence to function. Proc. IEEE, 88(12): 1949-1971, Dec. 2000.


• Dimitris Anastassiou. "Genomic Signal Processing," IEEE Signal Processing Magazine, 2001.


• 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

• The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet


• Signal Processing for Metagenomics


• A Bioinformatician's Guide to Metagenomics


• Genbank

Week 3

• Mahmood; Epps, Julien; Ambikairajah, Eliathamby. "Signal Processing in Sequence Analysis: Advances in Eukaryotic Gene Prediction," IEEE Journal of Selected Topics in Signal Processing, 2008.


• 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 4

• Niranjan Chakravarthy, A. Spanias, L. D. Iasemidis, and K. Tsakalis. "Autoregressive Modeling and Feature Analysis of DNA Sequences," EURASIP Journal on Applied Signal Processing, Volume 2004 (2004), Issue 1, Pages 13-28.


• Blinowska et al. "Multivariate autoregressive model for a study of phylogenetic diversity," Gene, 2009.

Week 6

• Chapter 2 of Biological Sequence Analysis by Durbin et al.
• Chapter 3 in Cristianini and Hahn

Week 7

• Chapter 3 of Biological Sequence Analysis by Durbin et al.


• Chapter 4 in Cristianini and Hahn


• Lawrence Rabiner. "A Tutorial on Hidden Markov Models and Selected Applications in Speech Recognition," Proceedings of the IEEE, Vol. 77, No. 2, February 1989.


• A Quick Intro to HMMs for Computational Biology

Course Notes

• Class 1


• Introduction to Metagenomics


• Class 2
• Class 3
• Class 4
• Functional Genomics Lecture
• Class 5
• Class 6 (Sub matrices)
• Introduction to HMMs
• Mutations and Phylogeny

In-class Assignments

1. Databases


2. Continuation of Databases and FFT and Power Spectrum of a DNA Sequence
   • dinoDNA
   • mystery_sequence
3. Alignment in-class assignment
4. ORF-Finding and C+G Content Segmentation (DUE May 19th)

Homeworks