Beyond the gene: contextualizing novel isoforms through pathway analysis in long-read single-cell RNA sequencing

A new computational framework, Centroid-based Isoform Pathway Inference (CIPI), assigns biological context to the thousands of novel isoforms and genes uncovered by long-read single-cell RNA sequencing. Instead of relying on host-gene annotation or known protein domains, CIPI builds expression-based neighborhoods of reference genes and combines them with GO, KEGG, or Reactome pathway analyses to infer pathway-level roles for individual isoforms. The result is a hypothesis-generating method for prioritizing novel isoforms across the isonome.