Boolean modeling: a logic-based dynamic approach for understanding signaling and regulatory networks and for making useful predictions (Q38255571)

1 September 2017

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title

Boolean modeling: a logic-based dynamic approach for understanding signaling and regulatory networks and for making useful predictions (English)

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1 September 2017

Réka Albert

1

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author name string

Juilee Thakar

series ordinal

2

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1 September 2017

1 September 2014

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Wiley interdisciplinary reviews. Systems biology and medicine

1 September 2017

17

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based on heuristic

inferred from page(s)

published in

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1 September 2017

6

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1 September 2017

353-369

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1 September 2017

5

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Reconstruction of cellular signalling networks and analysis of their properties

1 September 2017

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The edges of understanding

21 January 2018

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Statistical mechanics of complex networks

21 January 2018

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Network modeling of signal transduction: establishing the global view

21 January 2018

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Modelling and analysis of gene regulatory networks

21 January 2018

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Protein interaction networks

21 January 2018

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Metabolic stability and epigenesis in randomly constructed genetic nets

21 January 2018

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Boolean formalization of genetic control circuits.

21 January 2018

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Methods of robustness analysis for Boolean models of gene control networks.

21 January 2018

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A Boolean model of the gene regulatory network underlying Mammalian cortical area development

21 January 2018

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Exploring phospholipase C-coupled Ca(2+) signalling networks using Boolean modelling.

21 January 2018

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A logical model provides insights into T cell receptor signaling

21 January 2018

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Modeling systems-level regulation of host immune responses

21 January 2018

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Network model of immune responses reveals key effectors to single and co-infection dynamics by a respiratory bacterium and a gastrointestinal helminth.

21 January 2018

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Computational and experimental analysis reveals a requirement for eosinophil-derived IL-13 for the development of allergic airway responses in C57BL/6 mice.

21 January 2018

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A network model for plant-pollinator community assembly

21 January 2018

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Boolean network model predicts cell cycle sequence of fission yeast

21 January 2018

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The yeast cell-cycle network is robustly designed

21 January 2018

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Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae

21 January 2018

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Genetic regulation of root hair development in Arabidopsis thaliana: a network model.

21 January 2018

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Predicting essential components of signal transduction networks: a dynamic model of guard cell abscisic acid signaling

21 January 2018

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Digital clocks: simple Boolean models can quantitatively describe circadian systems

21 January 2018

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Studying the effect of cell division on expression patterns of the segment polarity genes

21 January 2018

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Network model of survival signaling in large granular lymphocyte leukemia

21 January 2018

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Dynamical and structural analysis of a T cell survival network identifies novel candidate therapeutic targets for large granular lymphocyte leukemia

21 January 2018

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Integration of Boolean models exemplified on hepatocyte signal transduction.

21 January 2018

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Attractor landscape analysis reveals feedback loops in the p53 network that control the cellular response to DNA damage

21 January 2018

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Systems biology--biomedical modeling

21 January 2018

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Physicochemical modelling of cell signalling pathways.

21 January 2018

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Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling

21 January 2018

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Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli

21 January 2018

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Petri net modelling of biological networks

21 January 2018

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The signaling petri net-based simulator: a non-parametric strategy for characterizing the dynamics of cell-specific signaling networks

21 January 2018

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The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data

21 January 2018

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ON/OFF and beyond--a boolean model of apoptosis

21 January 2018

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The transition from differential equations to Boolean networks: a case study in simplifying a regulatory network model

21 January 2018

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The segment polarity network is a robust developmental module

21 January 2018

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Attractor analysis of asynchronous Boolean models of signal transduction networks

21 January 2018

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Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell

21 January 2018

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The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster

21 January 2018

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A robust model to describe the differentiation of T-helper cells.

21 January 2018

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Molecular and functional profiling of memory CD8 T cell differentiation.

21 January 2018

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Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET

21 January 2018

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Discrete dynamic modeling with asynchronous update, or how to model complex systems in the absence of quantitative information

21 January 2018

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A novel method for signal transduction network inference from indirect experimental evidence.

21 January 2018

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Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles

21 January 2018

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Using Bayesian networks to analyze expression data

21 January 2018

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Inferring genetic networks and identifying compound mode of action via expression profiling

21 January 2018

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Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks.

21 January 2018

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Inferring gene networks from time series microarray data using dynamic Bayesian networks

21 January 2018

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NET-SYNTHESIS: a software for synthesis, inference and simplification of signal transduction networks.

21 January 2018

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Cytoscape: a software environment for integrated models of biomolecular interaction networks

21 January 2018

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Cytoscape 2.8: new features for data integration and network visualization

21 January 2018

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Structural and functional analysis of cellular networks with CellNetAnalyzer

21 January 2018

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A methodology for the structural and functional analysis of signaling and regulatory networks

21 January 2018

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Genomic analysis of regulatory network dynamics reveals large topological changes

21 January 2018

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Evidence for dynamically organized modularity in the yeast protein-protein interaction network

21 January 2018

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Relating three-dimensional structures to protein networks provides evolutionary insights

21 January 2018

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Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach

21 January 2018

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The transcriptional regulatory network of Mycobacterium tuberculosis

21 January 2018

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The connectivity structure, giant strong component and centrality of metabolic networks

21 January 2018

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Formation of regulatory patterns during signal propagation in a Mammalian cellular network

21 January 2018

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Network motifs: simple building blocks of complex networks

21 January 2018

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Network motifs in the transcriptional regulation network of Escherichia coli

21 January 2018

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The effect of negative feedback loops on the dynamics of boolean networks

21 January 2018

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Boolean network models of cellular regulation: prospects and limitations

21 January 2018

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An Evaluation of Methods for Inferring Boolean Networks from Time-Series Data

21 January 2018

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Autonomous Boolean modelling of developmental gene regulatory networks

21 January 2018

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Modeling stochasticity and variability in gene regulatory networks

21 January 2018

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Robustness and fragility of Boolean models for genetic regulatory networks.

21 January 2018

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Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle.

21 January 2018

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Uncovering operational interactions in genetic networks using asynchronous Boolean dynamics.

21 January 2018

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Synchronous versus asynchronous modeling of gene regulatory networks

21 January 2018

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Boolean network simulations for life scientists

21 January 2018

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BoolNet--an R package for generation, reconstruction and analysis of Boolean networks

21 January 2018

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A SAT-based algorithm for finding attractors in synchronous Boolean networks.

21 January 2018

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Dynamical modeling and analysis of large cellular regulatory networks.

21 January 2018

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Stability of the Kauffman model

21 January 2018

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Reduction of Boolean network models.

21 January 2018

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Cancer attractors: a systems view of tumors from a gene network dynamics and developmental perspective

21 January 2018

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Computing combinatorial intervention strategies and failure modes in signaling networks.

21 January 2018

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Elementary signaling modes predict the essentiality of signal transduction network components

21 January 2018

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An effective network reduction approach to find the dynamical repertoire of discrete dynamic networks

21 January 2018

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Qualitative simulation of genetic regulatory networks using piecewise-linear models.

21 January 2018

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Constraint-based network model of pathogen-immune system interactions

21 January 2018

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Genetic Network Analyzer: qualitative simulation of genetic regulatory networks.

21 January 2018

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Dynamic simulation of regulatory networks using SQUAD

21 January 2018

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Odefy--from discrete to continuous models.

21 January 2018

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Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology.

21 January 2018

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Logical modelling of regulatory networks with GINsim 2.3.

21 January 2018

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Polynomial algebra of discrete models in systems biology

21 January 2018

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ADAM: analysis of discrete models of biological systems using computer algebra

21 January 2018

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Constraint and contingency in multifunctional gene regulatory circuits

21 January 2018

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

21 January 2018

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Hierarchy of models: from qualitative to quantitative analysis of circadian rhythms in cyanobacteria.

21 January 2018

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Causal structure of oscillations in gene regulatory networks: Boolean analysis of ordinary differential equation attractors

21 January 2018

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Logic-based models for the analysis of cell signaling networks

21 January 2018

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Logic-based models in systems biology: a predictive and parameter-free network analysis method.

21 January 2018

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Boolean models of within-host immune interactions

21 January 2018

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Dynamically consistent reduction of logical regulatory graphs

21 January 2018

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21 January 2018

Identifiers

DOI

10.1002/WSBM.1273

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1 September 2017

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PubMed ID

25269159