The effective graph reveals redundancy, canalization, and control pathways in biochemical regulation and signaling

AJ Gates, R Brattig Correia, X Wang… - Proceedings of the …, 2021 - National Acad Sciences
The ability to map causal interactions underlying genetic control and cellular signaling has
led to increasingly accurate models of the complex biochemical networks that regulate …

A meta-analysis of Boolean network models reveals design principles of gene regulatory networks

C Kadelka, TM Butrie, E Hilton, J Kinseth, A Schmidt… - Science …, 2024 - science.org
Gene regulatory networks (GRNs) play a central role in cellular decision-making.
Understanding their structure and how it impacts their dynamics constitutes thus a …

Effective connectivity and bias entropy improve prediction of dynamical regime in automata networks

FX Costa, JC Rozum, AM Marcus, LM Rocha - Entropy, 2023 - mdpi.com
Biomolecular network dynamics are thought to operate near the critical boundary between
ordered and disordered regimes, where large perturbations to a small set of elements …

Canalization reduces the nonlinearity of regulation in biological networks

C Kadelka, D Murrugarra - npj Systems Biology and Applications, 2024 - nature.com
Biological networks, such as gene regulatory networks, possess desirable properties. They
are more robust and controllable than random networks. This motivates the search for …

Minimum complexity drives regulatory logic in Boolean models of living systems

A Subbaroyan, OC Martin, A Samal - PNAS nexus, 2022 - academic.oup.com
The properties of random Boolean networks have been investigated extensively as models
of regulation in biological systems. However, the Boolean functions (BFs) specifying the …

Effective connectivity determines the critical dynamics of biochemical networks

S Manicka, M Marques-Pita… - Journal of the Royal …, 2022 - royalsocietypublishing.org
Living systems comprise interacting biochemical components in very large networks. Given
their high connectivity, biochemical dynamics are surprisingly not chaotic but quite robust to …

Revealing the canalizing structure of Boolean functions: Algorithms and applications

E Dimitrova, B Stigler, C Kadelka, D Murrugarra - Automatica, 2022 - Elsevier
Boolean functions can be represented in many ways including logical forms, truth tables,
and polynomials. Additionally, Boolean functions have different canonical representations …

Diversified dynamic effects and their order origins in Boolean functions

Y Yao, ZG Huang, D Pei - Chaos, Solitons & Fractals, 2025 - Elsevier
Interaction relationships are fundamental to the behavior of complex systems. This study,
grounded in Boolean discrete systems, conducts a comprehensive investigation of ordered …

Stability of linear Boolean networks

K Chandrasekhar, C Kadelka, R Laubenbacher… - Physica D: Nonlinear …, 2023 - Elsevier
Stability is an important characteristic of network models that has implications for other
desirable aspects such as controllability. The stability of a Boolean network (BN) depends …

Decomposition of Boolean networks: An approach to modularity of biological systems

C Kadelka, R Laubenbacher, D Murrugarra… - arXiv preprint arXiv …, 2022 - arxiv.org
This paper presents the foundation for a decomposition theory for Boolean networks, a type
of discrete dynamical system that has found a wide range of applications in the life sciences …