Samuel Pastva
Complete snapshot of gene expression (active cell "logic")
Logical Modelling
Logical Modelling
Qualitative approach is computationally less demanding than e.g. ODEs, but still powerful
White-box models: explainable, composable, generalisable to different organisms
Logical Modelling
State-space of a synchronous Boolean network
Logical Modelling
State-space of an asynchronous Boolean network
Cannot use single cell data (pre-dates single cell genomics)
Fits only synchronous Boolean networks
Only considers static properties (update function tables and their fixed-points)
Generates a single "correct" network instead of conservatively communicating uncertainty: How specific and sensitive is the result?
Workflow which accounts for different types of partial information (literature, data, assumptions):
Proper communication of uncertainty through gradual refinement of "partial" Boolean networks.
Partial Boolean Network
Refinement
Rejected Networks
Necessary and sufficient conditions for valid networks
prof. Thomas Henzinger
IST has multiple groups investigating gene regulation