Logical modeling and dynamical analysis of cellular networks
W Abou-Jaoudé, P Traynard, PT Monteiro… - Frontiers in …, 2016 - frontiersin.org
The logical (or logic) formalism is increasingly used to model regulatory and signaling
networks. Complementing these applications, several groups contributed various methods …
networks. Complementing these applications, several groups contributed various methods …
[HTML][HTML] Mesenchymal stromal cell exosome–enhanced regulatory T-cell production through an antigen-presenting cell–mediated pathway
Background aims The immunomodulatory property of mesenchymal stromal cell (MSC)
exosomes is well documented. On the basis of our previous report that MSC exosomes …
exosomes is well documented. On the basis of our previous report that MSC exosomes …
Gene regulatory network modeling of macrophage differentiation corroborates the continuum hypothesis of polarization states
Macrophages derived from monocyte precursors undergo specific polarization processes
which are influenced by the local tissue environment: classically activated (M1) …
which are influenced by the local tissue environment: classically activated (M1) …
Reconciling qualitative, abstract, and scalable modeling of biological networks
Predicting biological systems' behaviors requires taking into account many molecular and
genetic elements for which limited information is available past a global knowledge of their …
genetic elements for which limited information is available past a global knowledge of their …
Logical modeling of lymphoid and myeloid cell specification and transdifferentiation
S Collombet, C Van Oevelen… - Proceedings of the …, 2017 - National Acad Sciences
Blood cells are derived from a common set of hematopoietic stem cells, which differentiate
into more specific progenitors of the myeloid and lymphoid lineages, ultimately leading to …
into more specific progenitors of the myeloid and lymphoid lineages, ultimately leading to …
Automated inference of Boolean models from molecular interaction maps using CaSQ
Motivation Molecular interaction maps have emerged as a meaningful way of representing
biological mechanisms in a comprehensive and systematic manner. However, their static …
biological mechanisms in a comprehensive and systematic manner. However, their static …
The CoLoMoTo interactive notebook: accessible and reproducible computational analyses for qualitative biological networks
Analysing models of biological networks typically relies on workflows in which different
software tools with sensitive parameters are chained together, many times with additional …
software tools with sensitive parameters are chained together, many times with additional …
Logical modeling and analysis of cellular regulatory networks with GINsim 3.0
The logical formalism is well adapted to model large cellular networks, in particular when
detailed kinetic data are scarce. This tutorial focuses on this well-established qualitative …
detailed kinetic data are scarce. This tutorial focuses on this well-established qualitative …
Role of cytokine combinations on CD4+ T cell differentiation, partial polarization, and plasticity: continuous network modeling approach
ME Martinez-Sanchez, L Huerta… - Frontiers in …, 2018 - frontiersin.org
Purpose: We put forward a theoretical and dynamical approach for the semi-quantitative
analysis of CD4+ T cell differentiation, the process by which cells with different functions are …
analysis of CD4+ T cell differentiation, the process by which cells with different functions are …
Modeling the Th17 and tregs paradigm: implications for cancer immunotherapy
KF Corral-Jara, G Rosas da Silva, NA Fierro… - Frontiers in Cell and …, 2021 - frontiersin.org
CD4+ T cell differentiation is governed by gene regulatory and metabolic networks, with both
networks being highly interconnected and able to adapt to external stimuli. Th17 and Tregs …
networks being highly interconnected and able to adapt to external stimuli. Th17 and Tregs …