Past work includes
- Pathogenica, Inc, developing new methods for infection diagnosis
using high-throughput sequencing.
Genomics Group at
MIT CSAIL. My research
focused on the genetic regulatory networks of pancreatic development
as part of the SysCODE Project.
We used ChIP-Seq (detects protein-DNA interactions), gene expression data,
and proteomics data (protein-protein interactions and protein
abundance) to understand the steps in development as cells go from
stem cells to endoderm and hopefully to pancreatic beta cells.
- ReadDB, a custom
column store database system for short reads (eg, Illumina/Solexa,
ABI/SOLiD) that have been mapped to a genome. We currently store
several thousand lanes of sequencing data in this system to support
ChIP-Seq and RNA-Seq analysis and visualization.
Arrays, a novel method to detect structural variants between two
- GSE, a
database and codebase for genomic analysis. This is the shared Java
environment that our group uses.
- Joint Binding
method for analyzing ChIP-Chip data that improves the spatial accuracy
of the resulting protein-DNA interaction predictions and can detect
pairs of closely spaced interactions.
- Gene regulation
in yeast cell
chromatin modifiers, and