Cell Differentation

Genomic Tools

Development of new functional genomic techniques and analytical tools

We continue to develop new techniques for the analysis of sequencing data. The first project in the laboratory was the development of new computational tools for the analysis of RNA Editing in humans using RNA-seq and ChIP-seq data for ENCODE. We are now using an experimental method to validate inosine RNA editing genome-wide using inosine cyanoethylation (ICE-seq) that we applied to two Drosophila species to assess the conservation of RNA editing.

We continue to work on the integrative analysis of dozens of data sets using Self-Organizing Maps (SOM) as part of ENCODE and for a project in Xenopus development in collaboration with the Cho lab at UCI. Our laboratory is also funded by the European Union as the only American participant in STATegra, which is a consortium of 11 institutions that is developing new tools for the integrative analysis of next-generation sequencing data for the last two years and next. We are currently working within the STATegra consortium on a high-profile publication of our results on the changes in DNaseI footprints associated with the induction of Ikaros during a critical stage of B-cell development.