npj Digital Medicine, Published online: 02 May 2026; doi:10.1038/s41746-026-02630-5 OncoPT: long-context transformer models for in hospital tumor phenotype extraction from pathology reports

The Angiopoietin-Tie2 pathway is a key regulator of vascular stability, but therapeutic exploitation has been limited by the poor developability of Angiopoietin-1 (Ang1), and there are key unresolved mechanistic questions. Ang1 binds both Tie2 and 5beta1 integrin, and the role of the 5beta1 interaction in signaling has been unclear. We used RFdiffusion to design a […]

ATP-dependent chromatin remodeling enzymes play a central role in governing the essential functions of the genome, and deficiencies in their catalytic function often lead to developmental disorders or disease. While most remodelers use the energy of ATP hydrolysis to either mobilize nucleosomes or evict histone octamers, yeast SWR1C catalyzes the ATP-dependent replacement of nucleosomal H2A/H2B […]

Reversion mutations that restore BRCA2 function represent a major mechanism of resistance to poly(ADP-ribose) polymerase inhibitors (PARPi) in BRCA2-mutant cancers. Understanding and predicting these events could inform treatment strategies, identify patients at increased risk of acquiring PARPi resistance, and improve the clinical interpretation of secondary BRCA2 variants detected in resistant tumors. Here, we evaluated reversions […]

Emerging evidence suggest that gene expression is controlled though the modulation of transcriptional bursting across species. However, the underlying regulatory mechanisms remain largely uncertain. Recent live-imaging studies have reported that transcription factors (TFs) form a cluster at enhancers just prior to gene activation, thereby locally concentrating the active transcription machinery. This process is thought to […]