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 …

Boolean network modeling in systems pharmacology

P Bloomingdale, VA Nguyen, J Niu… - … of pharmacokinetics and …, 2018 - Springer
Quantitative systems pharmacology (QSP) is an emerging discipline that aims to discover
how drugs modulate the dynamics of biological components in molecular and cellular …

Reconciling qualitative, abstract, and scalable modeling of biological networks

L Paulevé, J Kolčák, T Chatain, S Haar - Nature communications, 2020 - nature.com
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 …

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 …

Model checking to assess T-helper cell plasticity

W Abou-Jaoudé, PT Monteiro, A Naldi… - … in bioengineering and …, 2015 - frontiersin.org
Computational modeling constitutes a crucial step toward the functional understanding of
complex cellular networks. In particular, logical modeling has proven suitable for the …

A network model to describe the terminal differentiation of B cells

A Méndez, L Mendoza - PLoS computational biology, 2016 - journals.plos.org
Terminal differentiation of B cells is an essential process for the humoral immune response
in vertebrates and is achieved by the concerted action of several transcription factors in …

Modeling biology spanning different scales: an open challenge

F Castiglione, F Pappalardo, C Bianca… - BioMed research …, 2014 - Wiley Online Library
It is coming nowadays more clear that in order to obtain a unified description of the different
mechanisms governing the behavior and causality relations among the various parts of a …

Continuous modeling of T CD4 lymphocyte activation and function

D Martínez-Méndez, L Mendoza, C Villarreal… - Frontiers in …, 2021 - frontiersin.org
T CD4+ cells are central to the adaptive immune response against pathogens. Their
activation is induced by the engagement of the T-cell receptor by antigens, and of co …

Boolean networks: beyond generalized asynchronicity

T Chatain, S Haar, L Paulevé - … and Discrete Complex Systems: 24th IFIP …, 2018 - Springer
Boolean networks are commonly used in systems biology to model dynamics of biochemical
networks by abstracting away many (and often unknown) parameters related to speed and …

A Framework of Pinning Control for Non-periodical Stable Behaviors of Large-scale Asynchronous Boolean Networks

J Zhong, Q Pan, W Xu, B Chen - IEEE Transactions on …, 2024 - ieeexplore.ieee.org
In this paper, two pinning control (PC) schemes are proposed to achieve non-periodical
stable behaviors for asynchronous Boolean networks (BNs), from the aspects of state …