Research Overview
I develop statistical methods and software for various high-throughput technologies. For SNP arrays, I am an interested in improving measures of DNA copy number. For gene expression arrays, I am developing methods for cross-study analysis of expression data to identify concordant and discordant patterns of differential gene expression.
Software for copy number detection and gene expression arrays are freely available in the form of R packages under the GNU General Public Licence of the Free Software Foundation.
- crlmm : Locus-level estimation of copy number for Affymetrix whole genome genotyping arrays.
- VanillaICE: Hidden Markov model for identifying alterations in chromosomal copy number and/or loss of heterozygosity.
- A joint Hidden Markov model for identifying de-novo and inherited chromosomal alterations in trios.
- SNPchip : Visualization tools for high-throughput estimates of copy number and genotype.
- XDE : A Bayesian hierarchial model for identifying concordant and discordant differential gene expression in multiple studies.
- crlmmCompendium : Compendium for `Using the R package crlmm for genotyping and copy number estimation'