Epistasis Blog

From the Computational Genetics Laboratory at the University of Pennsylvania (www.epistasis.org)

Tuesday, June 20, 2017

PennAI

In my role as Director of the Penn Institute for Biomedical Informatics I am leading a project to develop an accessible artificial intelligence system called PennAI. More info can be found on the PennAI website launched to provide updates and info about the method and software. We are looking forward to using this in my research lab for data science.

Sunday, June 18, 2017

Is GWAS a hoax?

There is a great new Cell paper out from Jonathan Pritchard's group making the point that nearly the entire genome is connected to genes that impact risk of common human diseases. The implication is that genome-wide association studies (GWAS) are mostly finding incidental variants that happen to be involved in gene regulation or other genomic processes that only indirectly impact disease and thus might not make good drug targets. The identification of drug targets was the 'new' reason for doing GWAS replacing the old reason that focused on predicting risk which we now know doesn't work so well. The Cell paper is important but the point that it is really making is that disease risk is about systems and pathways rather than individual variants. This has been the focus of systems biology and complex adaptive systems all along. Human geneticists are perhaps finally waking up to this. I have written extensively about  a complex systems approach to human genetics for 20 years as partially documented in this blog. Here is a piece in Nature about this Cell paper and a thoughtful blog post by Dr. Ken Weiss from Penn State. Hopefully this is an indication that the univiariate approach to human genetics is finally over.

Friday, June 02, 2017

Automated Machine Learning Competition

We launched today a Kaggle-based competition for our tree-based pipeline optimization tool (TPOT) method for automated machine learning (AutoML). More information can be found here. Please spread the word!