Entropy-based Multilocus LD Measure & Haplotype Blocks
I am interested in two-loci and multilocus linkage disequilibrium (LD) measures and their application, for example, in the definition of (multilocus) haplotype LD blocks.
We developed a multi-marker measure for LD that is based on the concept of entropy. A Web calculator is available for this measure.
We used this measure to define haplotype blocks as regions
of elevated LD and evaluated this method on simulated and real-world data sets;
my Ph.D. thesis
and several talks and posters have resulted from this work
(see Publications).
However, I have become sceptical of the concept of haplotype blocks and opine that it is too simplistic to reliably describe the LD structure of the human genome.
[ Top of Page ]SNaP Simulation Software
I developed SNaP as a software to generate haplotype and genotype data of single nucleotide polymorphisms (SNP) that occur in blocks of high linkage disequilibrium (LD). It was first presented at the 52nd Annual Meeting of the American Society of Human Genetics, October 15-19 2002, Baltimore, U.S.A. (Abstract). Please see the SNaP web page for more details.
[ Top of Page ]SLM in Multilocus Association Analysis
Using simulation studies, I investigated the usefulness of some supervised learning methods in multi-locus association analysis using SNP. Preliminary results were presented at the ASHG Meeting 2002 in Baltimore, MD, U.S.A. (Abstract & Poster).
You can access detailed tables with classification results. (not yet in function)
[ Top of Page ]BibTeX Tools
Some perl tools to import medline entries into BibTeX libraries (last modification: 08/01/2003):
- med2bib.pl converts Medline query results into BibTeX format. It is based on the software developed by Dana Jacobson
- importbib.pl imports BibTeX files into a target BibTeX archive file, checking for doublettes