Discrete logic modeling of cell signaling pathways

N Ikonomi, SD Werle, JD Schwab… - TGF-Beta Signaling …, 2022 - Springer
Cell signaling pathways often crosstalk generating complex biological behaviors observed
in different cellular contexts. Frequently, laboratory experiments focus on a few putative …

Boolean modeling: a logic‐based dynamic approach for understanding signaling and regulatory networks and for making useful predictions

R Albert, J Thakar - Wiley Interdisciplinary Reviews: Systems …, 2014 - Wiley Online Library
The biomolecules inside or near cells form a complex interacting system. Cellular
phenotypes and behaviors arise from the totality of interactions among the components of …

Signaling networks: Asynchronous boolean models

R Albert, R Robeva - Algebraic and discrete mathematical methods for …, 2015 - Elsevier
Signal transduction allows a cell to communicate with its surroundings. Many diseases such
as developmental disorders, autoimmunity, and cancer have been shown to arise from …

Discrete dynamic modeling of cellular signaling networks

R Albert, RS Wang - Methods in enzymology, 2009 - Elsevier
Understanding signal transduction in cellular systems is a central issue in systems biology.
Numerous experiments from different laboratories generate an abundance of individual …

Boolean modeling in systems biology: an overview of methodology and applications

RS Wang, A Saadatpour, R Albert - Physical biology, 2012 - iopscience.iop.org
Mathematical modeling of biological processes provides deep insights into complex cellular
systems. While quantitative and continuous models such as differential equations have been …

[HTML][HTML] Concepts in Boolean network modeling: What do they all mean?

JD Schwab, SD Kühlwein, N Ikonomi, M Kühl… - Computational and …, 2020 - Elsevier
Boolean network models are one of the simplest models to study complex dynamic behavior
in biological systems. They can be applied to unravel the mechanisms regulating the …

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 …

Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling

DM Wittmann, J Krumsiek, J Saez-Rodriguez… - BMC systems …, 2009 - Springer
Background The understanding of regulatory and signaling networks has long been a core
objective in Systems Biology. Knowledge about these networks is mainly of qualitative …

Boolean network simulations for life scientists

I Albert, J Thakar, S Li, R Zhang, R Albert - Source code for biology and …, 2008 - Springer
Modern life sciences research increasingly relies on computational solutions, from large
scale data analyses to theoretical modeling. Within the theoretical models Boolean networks …

[HTML][HTML] Boolean modelling as a logic-based dynamic approach in systems medicine

AA Hemedan, A Niarakis, R Schneider… - Computational and …, 2022 - Elsevier
Molecular mechanisms of health and disease are often represented as systems biology
diagrams, and the coverage of such representation constantly increases. These static …