This talk will outline a research program aimed to develop a formal foundation
for research on the concept of modularity that links structure and function of networks.
The program is based on an April 2026 workshop on this topic at the
National Institute for Theoretical and Mathematical Biology.
Elucidating the design principles of regulatory networks driving cellular decision-making is of fundamental importance in mapping and controlling cellular behaviour. Despite their size and complexity, large biological regulatory networks often lead to a limited number of cell-states/phenotypes. How this canalization is achieved remains largely elusive. Here, we investigated multiple different...
Strongly connected components (SCCs) are essential for identifying modular structures in directed networks. However, they are inherently fragile, as the removal of even a single node can fragment the component and compromise its functionality. To address this limitation and better capture structural stability, we study strongly bi-connected components (SBCs), subgraphs where every pair of...
Waddington’s epigenetic landscape has long served as a central metaphor for cellular differentiation, depicting mature cell types as stable valley floors. Boolean networks, introduced by Kauffman in 1969, provide a mathematical formalization in which attractors represent phenotypes and basins correspond to developmental valleys. Traditional stability measures assess robustness via...
Biological systems are thought to be hierarchically modular, such that small semi-autonomous modules work together to create larger modules, each responsible for function at a different scale of organization. We thus expect that understanding each module in isolation and putting them together tells us how the whole works. When it comes to cellular regulation, however, a registry of biological...
Nearly every physiological function declines with age, as risk of death, disability and chronic disease rises exponentially. Whereas many specific diseases have well-characterized biomarkers and diagnostic thresholds, age-related decline is difficult to quantify and often appears as small, ambiguous changes across many biomarkers. We hypothesized that these changes reflect collective,...
Across living systems, oscillations support coordination, information flow, and decision making, from neural rhythms to calcium signaling in single cells. The unicellular slime mold Physarum polycephalum is a striking example: despite lacking a nervous system, it exhibits decision-like behaviors including maze solving, network formation, and exploration–exploitation trade-offs. However,...
Understanding how the structure of a network constrains and drives its dynamics is a central challenge in complex biological systems. While network topology is known to influence phenomena such as multistability, robustness, synchronization, and spreading behavior, the precise mechanisms linking structure to dynamics remain only partially understood. Many real world networks display hallmark...
