Slides at http://databio.org/slides/research_overview.html
Every cell in your body has the same genome*
Yet your cells are diverse...
How can a single set of instructions give rise to such a complex multicellular being?
The answer lies in the process of differentiation,
wherein cells assume individual functions and roles
By packaging DNA differently, each cell uses only a subset of instructions Rosa and Shaw 2013. Biology
If we can measure how DNA is packaged,
we can understand what a cell is doing
DNA sequencing technology is also useful for measuring quantitative cellular signals
But huge, diverse datasets lead to computational challenges.
My research is to develop and apply computational methods
to organize, analyze, and understand large epigenomic data.
How are genes regulated?
What DNA use makes two cell types different?
What DNA use makes a cancer cell proliferate?
How does DNA use change in a dynamic process, like cell division, differentiation, or response to environment?
Regulatory elements database
Use clustering algorithms to annotate regulatory DNA by cell-type specificity. We used this to identify cell-type patterns of regulatory elements specific to cancer cells.
LOLA (Locus Overlap Analysis)
A method to identify enrichment of regulatory DNA to give context to newly generated data
MIRA (Methylation-based Inference of Regulatory Activity)
Predict DNA binding from DNA methylation data. Used to predict cancer progression in Ewing sarcoma tumor samples
Looper and pypiper
A standardized way of annotating large datasets to make sharing and re-analyzing data easier.
Thanks for listening!