Spring 2007 CIS455 Home

CIS 455: Bioinformatics

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Term Project

You are required to do a term project in this class. Your project shall be an implementation of an algorithm in bioinformatics. The topics are not confined to the course syllabus. You should create and type in your own code, and any copying (electronic or otherwise) of another person's code or code fragments is a violation of the Academic Ethical Standards. You need to write a documentation for your project. The documentation should have the following components:

a cover page stating the title of the project, your name, the course name, the semester, the instructor's name, and the due date;
a description of your project that includes an introduction, major steps of the algorithm, and what is achieved;
a printout of your code or scripts that should be properly documented and indented.

You need to turn in one copy of this documentation as well as copies of the primary journal/conference articles that you used. You are also required to show a demo of your implementation to me before/when you turn in the above materials. Matlab is the recommended programming language for your project. If you want to use another language, it must be approved by the instructor.

Topic Proposal

As the class moves on, I will put a few potential project topics on this page. You can also select a different topic of your interest. However, all topics must be approved by the instructor. No matter whether you select a topic from here or by yourself, you are required to turn in a topic proposal that includes a title, a short abstract, and a bibliography. The bibliography must include at least the papers that describe the algorithm you want to implement.

If you are interested in any of the following topics, be sure to see me for a discussion and I will have more detailed information for you.

Potential topics
- Multifactor Dimensionality Reduction (MDR): MDR is a nonparametric and genetic model-free alternative to logistic regression for detecting and characterizing nonlinear interactions among discrete genetic and environmental attributes. The MDR method combines attribute selection, attribute construction, and classification with cross-validation and permutation testing to provide a comprehensive and powerful data mining approach to detecting nonlinear interactions. See more details about MDR at http://www.epistasis.org/mdr.html
  - Design a project in which you use MDR to solve some bioinformatics problem. (Ref1, Ref2)
- Microarray data analysis: Gene expression profiles from microarray data can be used to research the function of cells, compare the differences between healthy and diseased tissue, and observe changes with the application of drugs.
  - Design a project based on http://www.bioalgorithms.info/problems/05_asmt.htm
  - Design a project based on http://helix-web.stanford.edu/bmi214/files-2005/project2/proj2.htm
  - Design a project based on http://engr.smu.edu/~yuhangw/software.htm and a related paper
- Phylogenetic analysis: Phylogenetic analysis is the process you use to determine the evolutionary relationships between organisms. The results of an analysis can be drawn in a hierarchical diagram called a cladogram or phylogram (phylogenetic tree). The branches in a tree are based on the hypothesized evolutionary relationships (phylogeny) between organisms. Each member in a branch, also known as a monophyletic group, is assumed to be descended from a common ancestor. Originally, phylogenetic trees were created using morphology, but now, determining evolutionary relationships includes matching patterns in nucleic acid and protein sequences.
  - Design a project based on http://www.mathworks.com/access/helpdesk/help/toolbox/bioinfo/ug/a1075738729b2.html
- The project can also be studying a single paper, a book chapter or a web resource in depth and implementing/extending a related algorithm. The following includes several examples.
  - Hidden Markov Models: Chapter 11 of the textbook and http://www.bioalgorithms.info/problems/06_asmt.htm
  - Haplotype inference: Lusheng Wang and Ying Xu. Haplotype inference by maximum parsimony. Bioinformatics Vol. 19 no. 14 2003 Pages 1773-1780
  - Identification of functional sites in structures: http://helix-web.stanford.edu/bmi214/files-2005/project3/proj3.htm
  - RNA secondary structure prediction: http://www.nature.com/nbt/journal/v22/n11/pdf/nbt1104-1457.pdf
  - Protein docking: Some paper at http://www.cs.duke.edu/~edels/GeoBio/
  - SOM and microarrays:http://ieeexplore.ieee.org/iel5/8534/26965/01198159.pdf
  - Gibbs motif sampling: http://bayesweb.wadsworth.org/gibbs/

Potential resources to find your own topic
- Textbook Homepage: http://www.bioalgorithms.info/
- Bioinformatics Sequence and Genome Analysis: http://www.bioinformaticsonline.org/pr/index.html
- Ross Altman's Bioinformatics: http://www-helix.stanford.edu/people/altman/courses.html
- Chris Bailey-Kellogg's Bioinformatics: http://www.cs.dartmouth.edu/~cbk/bio/schedule.html
- CSB Lab at UGA: http://csbl.bmb.uga.edu/resources/
- Genbank: http://www.ncbi.nlm.nih.gov/Genbank/index.html
- Bioinformatics Web: http://www.geocities.com/bioinformaticsweb/index.html
- Introduction to Genetics: http://www.roche.com/home/science/sci_gengen/sci_gengen_cdrom/sci_gengen_cdrom_online.htm
- Primary Site at MIT: http://hrst.mit.edu/hrs/bioinformatics/public/PrimarySite.html
- Journals: Bioinformatics, Journal of Computational Biology, Briefings in Bioinformatics
- Conferences: RECOMB, CSB'04, CSB'03, CSB'02, PSB, ISBM

Presentation

You need to do a presentation on your term project. One goal is to introduce your work to other students in this class.

Grading

My evaluation of your project will, to some extent, be subjective. However, there are certain rules for the grading. You will receive a numerical score for your presentation and project. The maximum scores for them are as follows:

presentation: totally 10 points
term project: totally 15 points

You are required to use a spelling check tool to make sure that your spelling, punctuation, and grammar in your final term project documentation are correct, as well as the overall readability of your writeup.

Note that plagiarism will not be tolerated; if you feel the need to include portions of a textbook or article in your paper, remember to attribute them properly.

Late project will not be accepted.