Exosomal cargos-mediated metabolic reprogramming in tumor microenvironment

S Tan, Y Yang, W Yang, Y Han, L Huang… - Journal of Experimental …, 2023 - Springer
Metabolic reprogramming is one of the hallmarks of cancer. As nutrients are scarce in the
tumor microenvironment (TME), tumor cells adopt multiple metabolic adaptations to meet …

Systems biology of angiogenesis signaling: Computational models and omics

Y Zhang, H Wang, RHM Oliveira… - WIREs mechanisms …, 2022 - Wiley Online Library
Angiogenesis is a highly regulated multiscale process that involves a plethora of cells, their
cellular signal transduction, activation, proliferation, differentiation, as well as their …

Boolean modeling reveals that cyclic attractors in macrophage polarization serve as reservoirs of states to balance external perturbations from the tumor …

UAP de León, A Vázquez-Jiménez… - Frontiers in …, 2022 - frontiersin.org
Cyclic attractors generated from Boolean models may explain the adaptability of a cell in
response to a dynamical complex tumor microenvironment. In contrast to this idea, we …

Data integration in logic-based models of biological mechanisms

BA Hall, A Niarakis - Current Opinion in Systems Biology, 2021 - Elsevier
Discrete, logic-based models are increasingly used to describe biological mechanisms.
Initially introduced to study gene regulation, these models evolved to cover various …

Modeling signaling pathways in biology with MaBoSS: From one single cell to a dynamic population of heterogeneous interacting cells

L Calzone, V Noël, E Barillot, G Kroemer… - Computational and …, 2022 - Elsevier
As a result of the development of experimental technologies and the accumulation of data,
biological and molecular processes can be described as complex networks of signaling …

Uncoding the interdependency of tumor microenvironment and macrophage polarization: insights from a continuous network approach

U Avila-Ponce de León, A Vázquez-Jiménez… - Frontiers in …, 2023 - frontiersin.org
The balance between pro-and anti-inflammatory immune system responses is crucial to
preventing complex diseases like cancer. Macrophages are essential immune cells that …

Effective Reversal of Macrophage Polarization by Inhibitory Combinations Predicted by a Boolean Protein–Protein Interaction Model

G Szegvari, D Dora, Z Lohinai - Biology, 2023 - mdpi.com
Simple Summary Understanding the effects of the tumor microenvironment is an essential
step to advance treatments for cancer, but it is also one that is problematic to reproduce in …

Agent-based vs. equation-based multi-scale modeling for macrophage polarization

SB Minucci, RL Heise, AM Reynolds - Plos one, 2024 - journals.plos.org
Macrophages show high plasticity and result in heterogenic subpopulations or polarized
states identified by specific cellular markers. These immune cells are typically characterized …

An agent-based model of monocyte differentiation into tumour-associated macrophages in chronic lymphocytic leukemia

N Verstraete, M Marku, M Domagala, H Arduin… - Iscience, 2023 - cell.com
Monocyte-derived macrophages help maintain tissue homeostasis and defend the organism
against pathogens. In tumors, recent studies have uncovered complex macrophage …

[PDF][PDF] Dissecting Cellular Phenotypes in the Tumour Microenvironment through Gene Regulatory Networks: Inference, Analysis and Dynamical Modelling

M Marku, H Chenel, V Pancaldi - 2023 - researchgate.net
Gene regulatory networks (GRNs) and mathematical modelling are critical for understanding
the complex regulatory mechanisms that underlie tumour development and progression …