Cellular signaling pathways as plastic, proto-cognitive systems: Implications for biomedicine

J Mathews, AJ Chang, L Devlin, M Levin - Patterns, 2023 - cell.com
Many aspects of health and disease are modeled using the abstraction of a" pathway"—a
set of protein or other subcellular activities with specified functional linkages between them …

Behavior-related gene regulatory networks: A new level of organization in the brain

S Sinha, BM Jones, IM Traniello, SA Bukhari… - Proceedings of the …, 2020 - pnas.org
Neuronal networks are the standard heuristic model today for describing brain activity
associated with animal behavior. Recent studies have revealed an extensive role for a …

Integration of single-cell RNA-seq data into population models to characterize cancer metabolism

C Damiani, D Maspero, M Di Filippo… - PLoS computational …, 2019 - journals.plos.org
Metabolic reprogramming is a general feature of cancer cells. Regrettably, the
comprehensive quantification of metabolites in biological specimens does not promptly …

Dynamical criticality in gene regulatory networks

M Villani, L La Rocca, SA Kauffman, R Serra - Complexity, 2018 - Wiley Online Library
A well‐known hypothesis, with far‐reaching implications, is that biological evolution should
preferentially lead to states that are dynamically critical. In previous papers, we showed that …

A review of spatial computational models for multi-cellular systems, with regard to intestinal crypts and colorectal cancer development

G De Matteis, A Graudenzi, M Antoniotti - Journal of mathematical biology, 2013 - Springer
Colon rectal cancers (CRC) are the result of sequences of mutations which lead the
intestinal tissue to develop in a carcinoma following a “progression” of observable …

Angiogenic activity of breast cancer patients' monocytes reverted by combined use of systems modeling and experimental approaches

N Guex, I Crespo, S Bron… - PLoS computational …, 2015 - journals.plos.org
Angiogenesis plays a key role in tumor growth and cancer progression. TIE-2-expressing
monocytes (TEM) have been reported to critically account for tumor vascularization and …

Integration of Boolean models exemplified on hepatocyte signal transduction

R Schlatter, N Philippi, G Wangorsch… - Briefings in …, 2012 - academic.oup.com
The number of mathematical models for biological pathways is rapidly growing. In particular,
Boolean modelling proved to be suited to describe large cellular signalling networks …

Some control and observation issues in cellular automata

S El Yacoubi, T Plénet, S Dridi, F Bagnoli, L Lefèvre… - Complex …, 2021 - hal.science
This review article focuses on studying problems of observability and controllability of
cellular automata (CAs) considered in the context of control theory, an important feature of …

Investigating the relation between stochastic differentiation, homeostasis and clonal expansion in intestinal crypts via multiscale modeling

A Graudenzi, G Caravagna, G De Matteis… - PLoS One, 2014 - journals.plos.org
Colorectal tumors originate and develop within intestinal crypts. Even though some of the
essential phenomena that characterize crypt structure and dynamics have been effectively …

Control of cellular automata

F Bagnoli, R Rechtman, S El Yacoubi - Physical Review E—Statistical …, 2012 - APS
We study the problem of master-slave synchronization and control of totalistic cellular
automata. The synchronization mechanism is that of setting a fraction of sites of the slave …