Cell signaling pathways discovery from multi-modal data

Deciphering cell signaling pathways is key to understanding biology, disease mechanisms, and developing new therapies. Although advances in multi-omics technologies provide richer insight into signaling, the data remain high-dimensional, heterogeneous, and difficult to interpret, and current computational tools for inferring signaling pathways are limited. To address this, we developed Incytr, a method for efficient discovery of cell signaling pathways through integration of diverse data modalities, including transcriptomics, ATAC-seq, proteomics, phosphoproteomics, and kinomics. We demonstrate its application in COVID-19, Alzheimers disease, and cancer, where it successfully recovers known pathways and generates novel, cell-type-specific hypotheses supported by multiple data types. We further show how integrating Incytr-derived pathways with biomarker and drug databases can support target and drug discovery. Finally, we show that using Incytr-derived signaling pathways as training data for simple natural language processing models can deepen our understanding of cell-cell communication and immune cell dynamics, while helping identify new therapeutic targets.