Faye’s paper Deciphering the dark cancer phosphoproteome using machine-learned co-regulation of phosphosites...

Faye’s paper Deciphering the dark cancer phosphoproteome using machine-learned co-regulation of phosphosites has been published in Nature Communications. Congratulations! This study introduces CoPheeMap, a network built from phosphoproteomic data across 11 cancer types that maps how over 26,000 phosphorylation sites are co-regulated. Using this network, we further developed CoPheeKSA, a machine learning model that predicts which kinases modify which phosphosites. The model uncovered over 24,000 kinase–substrate relationships, including many involving poorly understood sites and kinases. Validated with experimental data, these tools help reveal cancer-related signaling changes and highlight potential new drug targets. The code for CoPheeMap and CoPheeKSA is available on GitHub at: https://github.com/bzhanglab/CoPheeMap.