Boolean modeling in systems biology: an overview of methodology and applications
Mathematical modeling of biological processes provides deep insights into complex cellular
systems. While quantitative and continuous models such as differential equations have been …
systems. While quantitative and continuous models such as differential equations have been …
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 …
Hypergraphs and cellular networks
Background The understanding of biological networks is a fundamental issue in
computational biology. When analyzing topological properties of networks, one often tends …
computational biology. When analyzing topological properties of networks, one often tends …
Cancer systems biology: a network modeling perspective
PK Kreeger, DA Lauffenburger - Carcinogenesis, 2010 - academic.oup.com
Cancer is now appreciated as not only a highly heterogenous pathology with respect to cell
type and tissue origin but also as a disease involving dysregulation of multiple pathways …
type and tissue origin but also as a disease involving dysregulation of multiple pathways …
Logic-based models for the analysis of cell signaling networks
Computational models are increasingly used to analyze the operation of complex
biochemical networks, including those involved in cell signaling networks. Here we review …
biochemical networks, including those involved in cell signaling networks. Here we review …
Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction
J Saez‐Rodriguez, LG Alexopoulos… - Molecular systems …, 2009 - embopress.org
Large‐scale protein signalling networks are useful for exploring complex biochemical
pathways but do not reveal how pathways respond to specific stimuli. Such specificity is …
pathways but do not reveal how pathways respond to specific stimuli. Such specificity is …
Dynamical and structural analysis of a T cell survival network identifies novel candidate therapeutic targets for large granular lymphocyte leukemia
A Saadatpour, RS Wang, A Liao, X Liu… - PLoS computational …, 2011 - journals.plos.org
The blood cancer T cell large granular lymphocyte (T-LGL) leukemia is a chronic disease
characterized by a clonal proliferation of cytotoxic T cells. As no curative therapy is yet …
characterized by a clonal proliferation of cytotoxic T cells. As no curative therapy is yet …
Modeling formalisms in systems biology
Abstract Systems Biology has taken advantage of computational tools and high-throughput
experimental data to model several biological processes. These include signaling, gene …
experimental data to model several biological processes. These include signaling, gene …
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 …
objective in Systems Biology. Knowledge about these networks is mainly of qualitative …
[图书][B] Probabilistic Boolean networks: the modeling and control of gene regulatory networks
I Shmulevich, ER Dougherty - 2010 - SIAM
It was around the period of World War II that Arturo Rosenblueth and Norbert Wiener were
taking the first steps in the direction of systems medicine. They formed an interesting pair …
taking the first steps in the direction of systems medicine. They formed an interesting pair …