Epistasis Blog

From the Computational Genetics Laboratory at Dartmouth Medical School (www.epistasis.org)

Tuesday, January 29, 2008

Odds Ratio MDR

A version of our Multifactor Dimesnionality Reduction (MDR) method that uses odds ratios to determine high-risk and low-risk genotype combinations prior to constructuve induction is available as a package for R called ORMDR. I haven't had time to try it. Let me know if you like it or find it useful.

Here is the paper that describes this approach:

Chung Y, Lee SY, Elston RC, Park T. Odds ratio based multifactor-dimensionality reduction method for detecting gene-gene interactions. Bioinformatics. 2007 Jan 1;23(1):71-6. [PubMed]

Monday, January 28, 2008

New Journal - BioData Mining

I am the Editor-in-Chief, along with Dr. Jesus Alguilar-Ruiz, of a new BioMed Central (BMC) journal called BioData Mining. The journal is open-access and features rapid reviews. The reviews are not anonymous which we hope will give authors more confidence that the comments are fair. BioData Mining has officially launched and is now accepting papers to be considered for review and publication. Please plan on submitting a paper. Details can be found here.

Sunday, January 27, 2008

Genetic Programming Theory and Practice (GPTP'08)

We have been invited for the third year in a row to attend and present at the 2008 Genetic Programming Theory and Practice (GPTP'08) workshop organized by the Center for the Study of Complex Systems at the University of Michigan. I will be presenting our work on a new computational evolution system for the genome-wide genetic analysis of epistasis. See my Dec. 23 (2007) post below for a brief description. We will be preparing soon a paper for the workshop proceedings that will be published as a book chapter by Springer. A preprint for this new paper will be available at the end of March. Feel free to email me for a pdf then.

Click here to find past GPTP workshop proceedings books on Amazon. You can find my previous posts about GPTP by clicking on the following links: GPTP'07, GPTP'06.

Saturday, January 26, 2008

New MDR Papers

There are a number of new papers on our MDR method reporting both theoretical and applied studies. Click here to find some of these using PubMed.

We are currently working on including interaction graphs in the next version of the MDR software. These will complement the interaction dendrograms that use information theory to help interpret MDR models. We hope to have this new version ready in the next few months.

Friday, January 11, 2008

BioText Search Engine

The BioText Search Engine allows you to search for keywords in full text documents and figure legends for example.

Click here to search full text from open access journals for 'multifactor dimensionality reduction'.

Friday, January 04, 2008

Pacific Symposium on Biocomputing

I am attending the Pacific Symposium on Biocomputing (PSB) this week in Hawaii and will be presenting our work on the MDR software. If you are also attending PSB please find me and introduce yourself. I personally think this is the best bioinformatics conference around. There is always a nice diversity of high quality work presented in a small intimate setting. If you have never been you should definitely consider attending next year.