The work with Shirley Pepke on using CorEx to find patterns in gene expression data is finally published in BMC Medical Genomics.

Shirley wrote a blog post about it as well. She will present this work at the Harvard Precision Medicine conference and we’ll both present at Berkeley’s Data Edge conference.

The code we used for the paper is online. I’m excited to see what people discover with these techniques, but I also can see we have more to do. If speed is an issue (it took us two days to run on a dataset with 6000 genes… many datasets can have an order of magnitude more genes), please get in touch as we have some experimental versions that are faster. We are also working on making the entire analysis pipeline more automated (i.e. connecting discovered factors with known biology and visualizing predictive factors.)