Algorithms for predicting drug response from proteomic measurements

This repository will serve as the primary base to develop tools to assess and predict drug response from proteomics measurements in cancer model systems. There are multiple projects that surround this problem including previously published work as part of the CPTAC PTRC group.

Benchmarking of deep learning algorithms on proteomics data

As part of the CANDLE project we have collated numerous cancer-related datasets. We can see how well proteomics data can be used compared to mRNA data, and where it works.

Predicting drug response from baseline proteomics and transcriptomics

This can build on the existing two papers, or apply more advanced approaches.

Predicting drug sensitivity from time series phosphoproteomics data

How do we infer the pathway changes?