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 …

Cancer mutationscape: revealing the link between modular restructuring and intervention efficacy among mutations

D Plaugher, D Murrugarra - NPJ Systems Biology and Applications, 2024 - nature.com
There is increasing evidence that biological systems are modular in both structure and
function. Complex biological signaling networks such as gene regulatory networks (GRNs) …

Integrative in silico approaches to analyse microRNA‐mediated responses in human diseases

M Agrawal, A Mani - The Journal of Gene Medicine, 2024 - Wiley Online Library
Advancements in sequencing technologies have facilitated omics level information
generation for various diseases in human. High‐throughput technologies have become a …

Life's building blocks: the modular path to multiscale complexity

S Huitzil, C Huepe - Frontiers in Systems Biology, 2024 - frontiersin.org
Modularity, the structuring of systems into discrete, interconnected units, is a fundamental
organizing principle in biology across multiple scales. Recent progress in understanding the …

Pancreatic cancer mutationscape: revealing the link between modular restructuring and intervention efficacy amidst common mutations

D Plaugher, D Murrugarra - bioRxiv, 2024 - pmc.ncbi.nlm.nih.gov
There is increasing evidence that biological systems are modular in both structure and
function. Complex biological signaling networks such as gene regulatory networks (GRNs) …

Beyond Boolean networks: new tools for the steady state analysis of multivalued networks

JG Galofre, MP Millán, AG Rial… - arxiv preprint arxiv …, 2024 - arxiv.org
Boolean networks can be viewed as functions on the set of binary strings of a given length,
described via logical rules. They were introduced as dynamic models into biology, in …

Modular construction of Boolean networks

M Wheeler, C Kadelka, A Veliz-Cuba… - Physica D: Nonlinear …, 2024 - Elsevier
Boolean networks have been used in a variety of settings, as models for general complex
systems as well as models of specific systems in diverse fields, such as biology …

Modular control of Boolean network models

D Murrugarra, A Veliz-Cuba, E Dimitrova, C Kadelka… - Ar**v, 2024 - pmc.ncbi.nlm.nih.gov
The concept of control is crucial for effectively understanding and applying biological
network models. Key structural features relate to control functions through gene regulation …

Learning dynamic representations of the functional connectome in neurobiological networks

L Dyballa, S Lang, A Haslund-Gourley, E Yemini… - Ar**v, 2024 - pmc.ncbi.nlm.nih.gov
The static synaptic connectivity of neuronal circuits stands in direct contrast to the dynamics
of their function. As in changing community interactions, different neurons can participate …

[PDF][PDF] Multiscale Information Processing in the Immune System

R Navarro-Quiroz, JV Camacho, EZ Peñata… - 2025 - preprints.org
The immune system is a dynamic network that processes information across multiple
biological scales, from molecular recognition of antigens to systemic coordination with the …