Logic-based modeling (e.g. Boolean networks) is a framework through which computational biology studies complex emergent biochemical processes. Traditionally, such models were constructed by hand with the help of domain experts. However, recent broad availability of detailed single-cell observation data makes research into automated inference of logic-based models extremely relevant. Here, we address the shortcomings of this emerging field while proposing a clear biological application in cell differentiation studies. Specifically, we challenge the 50 years of attractor-centric research in logic-based models by proposing a new formal characterization connecting differentiated and undifferentiated cell types. We then tie it to a novel inference workflow, which addresses the problem of identifiability (the ability to select a single ideal model) and co-development of gene regulatory networks together with the logic-based models. This project has great potential to revolutionize developmental biology and extract previously unrealized value from existing genomic datasets.

Sustainable Development Goals

Masaryk University is committed to the UN Sustainable Development Goals, which aim to improve the conditions and quality of life on our planet by 2030.