Biological functions stem from coordinated interactions among proteins, nucleic acids and small molecules. Mass spectrometry technologies for reliable, high throughput single-cell proteomics will add a new modality to genomics and enable data-driven modeling of the molecular mechanisms coordinating proteins and nucleic acids at single-cell resolution. This promising potential requires estimating the reliability of measurements and computational analysis so that models can distinguish biological regulation from technical artifacts. We discuss approaches for developing both abstract and mechanistic models that aim to biologically interpret the measured differences across modalities. Mechanistic models of direct molecular interactions will provide generalizable and predictive representations of biological systems.
Leduc A,Harens H, Slavov N. Modeling and interpretation of single-cell proteogenomic data arXiv doi: 10.48550/arXiv.2308.07465 (2023) PDF