For more than four decades, the nematode C. elegans has served as a key model organism in aging research, particularly at the cellular and molecular level. Recently single-cell time series studies have shown that different types of cells age at different rates and through distinct regulatory mechanisms. Using that published data, we identified transcription factors that are co-expressed in...
Boolean networks are a widely used modeling framework in systems biology for studying gene regulation, signal transduction, and cellular decision-making. Empirical studies indicate that biological Boolean networks exhibit a high degree of canalization, a structural property of Boolean update rules that stabilizes dynamics and constrains state transitions. Despite its central role, existing...
The complement system is a potent arm of the immune system, linking the adaptive and innate immune systems, and affecting many facets of human pathophysiology. Recent advances in the development of complement-specific drugs in several rare diseases have opened the gateways to apply complement interventions toward a broader array of pathologies. However, this goal remains elusive due to the...
Control of biological networks is often achieved by targeting a small number of regulatory nodes, but identifying optimal control strategies remains challenging. Existing control methods frequently yield multiple alternative control sets that satisfy the same objective, making it difficult to select among them. Optimality is typically defined by minimality or by minimizing a cost function....
In order to address the pervasive reproducibility crisis, we combine Docker containers (or Conda packages) with Jupyter electronic notebooks, in order to develop and document dynamical analyses of logical models of complex biological molecular networks. The resulting Common Logical Modelling Tools (CoLoMoTo) environment currently encompasses over 20 tools, written in multiple languages, making...
Discrete models are a natural framework for biological systems whose regulation is governed by switch-like interactions. In this talk, we will present a reverse-engineering approach to Boolean modeling of mammalian cell division through the regulation of the transcription factor E2F. Starting from partial biological knowledge about the roles of CycB, Rb, p27, and CycA, we will show how a...
A central challenge in systems biology is understanding how gene regulatory networks (GRNs) coordinate cellular decision-making within complex topological structures. This study introduces a framework to quantify the alignment of regulatory logic among interacting genes, a property defined here as structural coherence. By applying this metric, we identify "teamsโ, functionally coupled gene...
As biological data grows in both scale and complexity, discrete modeling methods are valuable complements to classical continuous frameworks as they connect diverse areas such as algebra and probability theory to discrete approaches. This minisymposium explores recent developments and challenges in discrete formalisms including Boolean networks, Petri nets, and polynomial dynamical systems,...
