(Q26745955)

Pedro T Monteiro

3

0 references

Claudine Chaouiya

Claudine Chaouiya

7

0 references

Denis Thieffry

Denis Thieffry

6

0 references

Julio Saez-Rodriguez

Julio Saez-Rodriguez

4

0 references

author name string

Wassim Abou-Jaoudé

1

0 references

Pauline Traynard

2

0 references

language of work or name

English

0 references

publication date

2016

0 references

published in

Frontiers in Genetics

1 reference

Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language

volume

7

0 references

page(s)

94

0 references

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Floral morphogenesis: stochastic explorations of a gene network epigenetic landscape

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Models in biology: lessons from modeling regulation of the eukaryotic cell cycle

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Quantitative and logic modelling of molecular and gene networks

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

A comprehensive, multi-scale dynamical model of ErbB receptor signal transduction in human mammary epithelial cells

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

A cell simulator platform: the cell collective

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Ergodic sets as cell phenotype of budding yeast cell cycle

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Minimum information requested in the annotation of biochemical models (MIRIAM)

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Genetic regulatory mechanisms in the synthesis of proteins

7 April 2017

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

7 April 2017

https://api.crossref.org/works/10.3389/FGENE.2016.00094

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

22 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Metabolic stability and epigenesis in randomly constructed genetic nets

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Coordinating Role of RXRα in Downregulating Hepatic Detoxification during Inflammation Revealed by Fuzzy-Logic Modeling

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

BioModels: ten-year anniversary

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Integrative modelling of the influence of MAPK network on cancer cell fate decision

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

The Cell Collective: toward an open and collaborative approach to systems biology.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

The yeast cell-cycle network is robustly designed

7 April 2017

1 reference

https://api.crossref.org/works/10.3389/FGENE.2016.00094

Systems Perturbation Analysis of a Large-Scale Signal Transduction Model Reveals Potentially Influential Candidates for Cancer Therapeutics.

22 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

A Modeling Approach to Explain Mutually Exclusive and Co-Occurring Genetic Alterations in Bladder Tumorigenesis

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

A Minimal Regulatory Network of Extrinsic and Intrinsic Factors Recovers Observed Patterns of CD4+ T Cell Differentiation and Plasticity.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Model checking to assess T-helper cell plasticity

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Modelling the onset of senescence at the G1/S cell cycle checkpoint

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Design, Assessment, and in vivo Evaluation of a Computational Model Illustrating the Role of CAV1 in CD4(+) T-lymphocytes.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

A discrete model of Drosophila eggshell patterning reveals cell-autonomous and juxtacrine effects

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Mapping differentiation under mixed culture conditions reveals a tunable continuum of T cell fates

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Continuous time Boolean modeling for biological signaling: application of Gillespie algorithm

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

State-time spectrum of signal transduction logic models

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Helper T cell diversity and plasticity

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

"Antelope": a hybrid-logic model checker for branching-time Boolean GRN analysis

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Modeling the cell cycle: why do certain circuits oscillate?

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Applications of a formal approach to decipher discrete genetic networks

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Logic-based models for the analysis of cell signaling networks

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Logical modelling of cell cycle control in eukaryotes: a comparative study

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Hypergraphs and cellular networks

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Network model of survival signaling in large granular lymphocyte leukemia

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Boolean network models of cellular regulation: prospects and limitations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

A logical model provides insights into T cell receptor signaling

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Dynamical roles of biological regulatory circuits

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Teleonomic mechanisms in cellular metabolism, growth, and differentiation

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

The duration of T cell stimulation is a critical determinant of cell fate and plasticity.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Predicting missing expression values in gene regulatory networks using a discrete logic modeling optimization guided by network stable states.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

A logical model of HIV-1 interactions with the T-cell activation signalling pathway

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Dynamical modeling and analysis of large cellular regulatory networks.

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Synchronous versus asynchronous modeling of gene regulatory networks

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

A method for the generation of standardized qualitative dynamical systems of regulatory networks

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

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

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Boolean formalization of genetic control circuits.

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

A complex control circuit. Regulation of immunity in temperate bacteriophages.

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Logical modelling of gene regulatory networks with GINsim

31 May 2018

1 reference

https://api.crossref.org/works/10.3389%2FFGENE.2016.00094

Robustness and fragility of Boolean models for genetic regulatory networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFGENE.2016.00094

Comparing Boolean and piecewise affine differential models for genetic networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFGENE.2016.00094

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFGENE.2016.00094

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFGENE.2016.00094

Modular logical modelling of the budding yeast cell cycle

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFGENE.2016.00094

Modeling stochasticity and robustness in gene regulatory networks

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFGENE.2016.00094

Logical analysis of the budding yeast cell cycle.

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFGENE.2016.00094

Computational modeling of ERBB2-amplified breast cancer identifies combined ErbB2/3 blockade as superior to the combination of MEK and AKT inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFGENE.2016.00094

Dynamics of influenza virus and human host interactions during infection and replication cycle

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFGENE.2016.00094

The regulatory network that controls the differentiation of T lymphocytes.

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFGENE.2016.00094

Cooperative development of logical modelling standards and tools with CoLoMoTo

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFGENE.2016.00094

A model for restriction point control of the mammalian cell cycle.

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFGENE.2016.00094

A description of dynamical graphs associated to elementary regulatory circuits

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFGENE.2016.00094

Segmenting the fly embryo: logical analysis of the role of the segment polarity cross-regulatory module

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFGENE.2016.00094

Functional analysis of chemical systems in vivo using a logical circuit equivalent. 3. Analysis using a digital circuit combined with an analogue computer

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFGENE.2016.00094

Learning Boolean logic models of signaling networks with ASP

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFGENE.2016.00094

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFGENE.2016.00094

Dynamical behaviour of biological regulatory networks--II. Immunity control in bacteriophage lambda.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4885885

Dynamically consistent reduction of logical regulatory graphs

28 November 2018

1 reference

https://api.crossref.org/works/10.3389%2FFGENE.2016.00094

A network model for the control of the differentiation process in Th cells

21 January 2018

1 reference

12 December 2020

Functional analysis of chemical systems in vivo using a logical circuit equivalent. II. The idea of a molecular automaton

1 reference

12 December 2020

The logical analysis of continuous, non-linear biochemical control networks

1 reference

12 December 2020

Logical analysis of systems comprising feedback loops

1 reference

12 December 2020

SBML Level 3 package: Qualitative Models, Version 1, Release 1.

1 reference

12 December 2020