Brian A. Joughin

The paper uses phosphoproteomic data and KMEA to identify tumor-specific kinase activity in GEP-NETs, revealing potential therapeutic targets.

scLEMBAS models signaling pathway activity at single-cell resolution using a context-aware neural network to predict perturbation responses and capture cell-type-specific interactions.

The paper identifies molecular determinants for phosphotyrosine recognition in tyrosine kinases and shows their roles in tumor promotion and suppression.

This study identifies FANCL and Ube2T as HR-promoting factors at DSBs and shows they regulate CtIP recruitment and end-resection for homologous recombination.

The paper uses phosphoproteomics to identify Siglec-F and Siglec-8 as upregulated in microglia during neurodegeneration, driving inflammatory responses in mouse and human models.

Transite identifies RNA-binding proteins modulating gene expression changes by analyzing RNA stability and degradation, validated with hnRNPC in chemotherapeutic resistance.

The paper benchmarks bulk functional genomics tools on scRNA-seq data, showing comparable performance to bulk data and suggesting their applicability over dedicated single-cell tools.