EE381V Genomic Signal Processing: Final Project

The University of Texas at Austin
Department of Electrical and Computer Engineering

EE381V Genomic Signal Processing: Final Project

A few IEEE special issues

IEEE Journal on Selected Topics in Signal Processing, Special Issue on Genomic and Proteomic Signal Processing, vol. 2, no. 3, June 2008.

IEEE Signal Processing Magazine, Special Issue on Signal Processing in Genomics , vol. 24, no. 1, January 2007.

IEEE Transaction on Signal Processing, Special Issue on Genomic Signal Processing, vol. 54, no. 6, part: 2, June 2006.

An incomplete list of potential projects, with some interesting papers:

Sequencing by synthesis: modeling and detection aspects

H. Eltoukhy and A. El Gamal, `` Modeling and base-calling for DNA sequencing-by-synthesis,'' IEEE ICASSP, 2006.

Combinatorial techniques for motif finding

E. Zaslavsky and M. Singh, ``A combinatorial optimization approach for diverse motif finding applications,'' Algorithms Mol Biol., 2006, pp: 1:13.

RNA secondary structure

B.-J. Yoon and P. P. Vaidyanathan, Structural Alignment of RNAs Using Profile-csHMMs and Its Application to RNA homology Search: Overview and New Results, IEEE Transactions on Automatic Control (Joint Special Issue on Systems Biology with IEEE Transactions on Circuits and Systems: Part-I), vol. 53, pp. 10-25, Jan. 2008.

Design of DNA microarrays

A. Ben-Dor et. al., "Universal DNA tag systems: a combinatorial design scheme", Proceedings of the fourth annual international conference on Computational Molecular Biology, Tokyo, 2000. [Also in: Journal of Computational Biology, August 2000, Vol. 7, No. 3-4, Pages 503-519.]

Methods for clustering of microarray data

S. C. Madeira and A. L. Oliveira, "Biclustering algorithms for biological data analysis: a survey", IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 1, Issue 1, Jan.-March 2004, Page(s): 24-45.
Z. Wang et. al., "Stochastic Dynamic Modeling of Short Gene Expression Time-Series Data", IEEE Transactions on NanoBioscience, Volume 7, Issue 1, March 2008, Page(s): 44 - 55.

Exploiting sparseness in genomic data

R. Pique-Regi et. al., "Sparse representation and Bayesian detection of genome copy number alterations from microarray data," Bioinformatics, 24(3), 2008, pp: 309-318. [Also in: "Wavelet footprints and sparse Bayesian learning for DNA copy number change analysis", IEEE ICASSP 2007.]

Stochastic simulations of genetic networks

Inference in genetic networks

W. Zhao et. al., "Inferring Connectivity of Genetic Regulatory Networks Using Information-Theoretic Criteria", IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 5, Issue 2, April-June 2008, Page(s): 262 - 274.
L. Qian et. al., "Inference of Noisy Nonlinear Differential Equation Models for Gene Regulatory Networks Using Genetic Programming and Kalman Filtering", IEEE Transactions on Signal Processing, Volume 56, Issue 7, Part 2, July 2008, Page(s):3327 - 3339.

Types of final projects:

Survey Paper: A paper in the format of a journal or a conference paper that provides a survey of a chosen topic. This project should have a detailed survey component and a simulation component for full credit. Survey papers should be unbiased and well written.

Research Paper: A paper in the format of a journal or a conference paper, containing some element of innovation, even if it is small or incremental.

Project Proposal (Due: on 10/30/08, in class)

Both individual projects and projects by groups of 2 are acceptable. Group projects are expected to be more refined/polished relative to a single student project.

The research paper proposal should state the problem that you are trying to solve, including setup, key assumptions, and methods to be used. For a survey project, the goal is a more detailed overview of the area.

Please include realistic plan of action proposed, including action items and a timeline. At least 2-3 papers that you have read should be cited. Proposal format: 1-2 pages in length (2 pages preferred) with 11pt or 12pt font, single spacing, and standard 1 inch margins.

The presentations (7-8 minutes long) are scheduled for Thursday, December 4, during the last class meeting.

Evaluating final reports (the reports are due 12/08/08, 11am, ACES 3.110):

Survey Article

(15 points) In the Introduction section, the article should provide background on the general area and motivate the survey.

(10 points) The references should be relevant to the topic of the survey. Journal papers are preferred (although conference papers are acceptable if there are no journal versions of the work). Including references which present different approaches to the solution of the same problem is desirable.

(65 points) The main part of the article -- survey of the area -- should provide details about the area/problem being surveyed; give a thorough description of the contributions in the cited papers; compare and contrast different contributions, including numerical/simulation illustrations; and give some insight and provide suggestions for future work.

(10 points) Since this is a report, please take care of clarity and style thereof. Please use 11pt or 12pt font (references may be 10pt), double spaced text, standard 1 inch margins. Preferred length (not including title, abstract, figures, and table-of-contents) is 8-10 pages (if necessary, the report may be longer than 10 pages but should not be shorter than 8; the maximum length -- not including title, abstract, figures, and table-of-contents -- is 14 pages).
Research Paper

(15 points) In the Introduction section, the article should provide background on the general area and motivate the research project.

(10 points) In the Introduction (or a Problem Statement) section, clearly describe the objectives of the project. (Ideally, they should be similar to the objectives outlined in the project proposal.)

(65 points) The main part of the paper should provide concise problem statement, setup, and key assumptions; description of methods (any derivations, algorithms employed, etc.); explanation of the project contributions illustrated with analytical and/or simulation results; and give some insight and provide suggestions for future work.

(10 points) Since this is a report, please take care of clarity and style thereof. Please use 11pt or 12pt font (references may be 10pt), double spaced text, standard 1 inch margins. Preferred length (not including title, abstract, figures, and table-of-contents) is 8-10 pages (if necessary, the report may be longer than 10 pages but should not be shorter than 8; the maximum length -- not including title, abstract, figures, and table-of-contents -- is 14 pages).