Currently I am developing Napistu - a Python framework for creating geneome-scale graphs of molecular biology and biochemistry and integrating them with high-dimensional data.
-
During my time at Calico, I developed:
- Open-CPR - A framework for aggregating different sources of molecular mechanisms into genome-scale graphs of cellular physiology.
- OpenCLaM - A robust ecosystem for working with mass spectrometry data, codeveloped with Phil Seitzer, which combines a configurable Dockerized pipeline and R packages supporting the pipeline and downstream analysis.
- Approaches using genome-scale systems biology to understand regulation. See Induction Dynamics Expression Atlas and Impulse.
- romic - Data structures and strategies for generalizing common analysis steps in genomics.
-
My side-projects and past work can be found on my personal website. Here is a brief rundown.