I am part of a bioinformatics and computational biology group embedded in the lab of Dr. Paul Meltzer. I am mainly interested in the application of high-throughput technologies to the study of cancer. I am heavily involved in the design, analysis, and interpretation of integrated genomics projects. In addition, I develop algorithms, software, and online tools to further research by others. I am also involved in open source projects such as the Bioconductor project and Biopython.

Bioconductor

The Bioconductor project is a large, open-source project devoted to the development of software tools and algorithms related to the analysis of high-throughput genomics technologies such as DNA microarrays and second-generation sequencing.

GEOquery

The NCBI Gene Expression Omnibus (GEO) is the largest repository of publicly available microarray data. GEOquery is a software package that allows access to that repository from R and Bioconductor. One can use it in small-scale projects to grab datasets of interest or in very large scale to parse and analyse all of NCBI GEO in an automated fashion.

ACME

The ACME (Algorithms for Calculating Microarray Enrichment) is a Bioconductor software package for finding regions of significance when using tiling arrays for ChIP-chip or DNAse-chip.