Modeling regulatory networks to understand plant development: small is beautiful. (Q38056561)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23110896 AND SRC:MED&resulttype=core&format=json

16 February 2020

title

Modeling regulatory networks to understand plant development: small is beautiful (English)

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16 February 2020

1 reference

3

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16 February 2020

Teva Vernoux

series ordinal

4

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16 February 2020

author name string

Alistair M Middleton

series ordinal

1

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16 February 2020

Etienne Farcot

series ordinal

2

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16 February 2020

publication date

30 October 2012

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16 February 2020

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16 February 2020

volume

24

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16 February 2020

issue

10

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16 February 2020

page(s)

3876-3891

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23110896 AND SRC:MED&resulttype=core&format=json

Multiscale systems analysis of root growth and development: modeling beyond the network and cellular scales

16 February 2020

cites work

1 reference

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Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks

31 August 2018

1 reference

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Elucidating the in vivo phosphorylation dynamics of the ERK MAP kinase using quantitative proteomics data and Bayesian model selection.

31 August 2018

1 reference

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Growth-induced hormone dilution can explain the dynamics of plant root cell elongation.

31 August 2018

1 reference

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Mathematical modeling elucidates the role of transcriptional feedback in gibberellin signaling

31 August 2018

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Computational approaches for analyzing information flow in biological networks

31 August 2018

1 reference

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A combinatorial TIR1/AFB-Aux/IAA co-receptor system for differential sensing of auxin.

31 August 2018

1 reference

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Root gravitropism is regulated by a transient lateral auxin gradient controlled by a tipping-point mechanism

31 August 2018

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New technologies for 21st century plant science

31 August 2018

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Cytokinin signaling as a positional cue for patterning the apical-basal axis of the growing Arabidopsis shoot meristem

31 August 2018

1 reference

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A novel sensor to map auxin response and distribution at high spatio-temporal resolution

31 August 2018

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Understanding biological timing using mechanistic and black-box models.

31 August 2018

1 reference

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A data-driven integrative model of sepal primordium polarity in Arabidopsis

31 August 2018

1 reference

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Distinguishing possible mechanisms for auxin-mediated developmental control in Arabidopsis: Models with two Aux/IAA and ARF proteins, and two target gene-sets

31 August 2018

1 reference

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WUSCHEL protein movement mediates stem cell homeostasis in the Arabidopsis shoot apex

31 August 2018

1 reference

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Stochastic properties of the plant circadian clock

31 August 2018

1 reference

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The auxin signalling network translates dynamic input into robust patterning at the shoot apex

31 August 2018

1 reference

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Generation of diverse biological forms through combinatorial interactions between tissue polarity and growth

31 August 2018

1 reference

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The influence of cytokinin-auxin cross-regulation on cell-fate determination in Arabidopsis thaliana root development

31 August 2018

1 reference

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Context, Specificity, and Self-Organization in Auxin Response

31 August 2018

1 reference

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Data assimilation constrains new connections and components in a complex, eukaryotic circadian clock model

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

Parameter inference and model selection in signaling pathway models

31 August 2018

1 reference

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Functional roles for noise in genetic circuits

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

Oscillating gene expression determines competence for periodic Arabidopsis root branching

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

Advantages and limitations of current network inference methods

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

Modelling polar auxin transport in developmental patterning

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

Computer simulation: the imaginary friend of auxin transport biology

31 August 2018

1 reference

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Continuous-time modeling of cell fate determination in Arabidopsis flowers

31 August 2018

1 reference

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BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

31 August 2018

1 reference

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Imaging plant growth in 4D: robust tissue reconstruction and lineaging at cell resolution.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

The Arabidopsis thaliana flower organ specification gene regulatory network determines a robust differentiation process.

31 August 2018

1 reference

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A dynamic model for stem cell homeostasis and patterning in Arabidopsis meristems

31 August 2018

1 reference

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Mathematical modelling of the Aux/IAA negative feedback loop

31 August 2018

1 reference

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Bimodular auxin response controls organogenesis in Arabidopsis

31 August 2018

1 reference

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The Modular Organization of Protein Interactions in Escherichia coli

31 August 2018

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Multiple feedback loops through cytokinin signaling control stem cell number within the Arabidopsis shoot meristem

31 August 2018

1 reference

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Mechanism of auxin-regulated gene expression in plants

31 August 2018

1 reference

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Bistability in a model of mesoderm and anterior mesendoderm specification in Xenopus laevis.

31 August 2018

1 reference

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Systems biology: parameter estimation for biochemical models

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

Floral morphogenesis: stochastic explorations of a gene network epigenetic landscape

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

A quantitative and dynamic model for plant stem cell regulation

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

Nature, nurture, or chance: stochastic gene expression and its consequences

31 August 2018

1 reference

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A mutual support mechanism through intercellular movement of CAPRICE and GLABRA3 can pattern the Arabidopsis root epidermis

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

Quantitative approaches to the study of bistability in the lac operon of Escherichia coli

31 August 2018

1 reference

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Universally sloppy parameter sensitivities in systems biology models

31 August 2018

1 reference

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The circadian clock regulates auxin signaling and responses in Arabidopsis

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

Network motifs: theory and experimental approaches

31 August 2018

1 reference

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Regularizing capacity of metabolic networks

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

Auxin-dependent regulation of lateral root positioning in the basal meristem of Arabidopsis

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana

31 August 2018

1 reference

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A novel computational model of the circadian clock in Arabidopsis that incorporates PRR7 and PRR9.

31 August 2018

1 reference

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

31 August 2018

1 reference

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Extension of a genetic network model by iterative experimentation and mathematical analysis

31 August 2018

1 reference

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The Arabidopsis Aux/IAA protein family has diversified in degradation and auxin responsiveness

31 August 2018

1 reference

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Proteome survey reveals modularity of the yeast cell machinery

31 August 2018

1 reference

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Modeling the organization of the WUSCHEL expression domain in the shoot apical meristem

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

Transcriptional regulation by the numbers: applications

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

Transcriptional regulation by the numbers: models.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

Modelling genetic networks with noisy and varied experimental data: the circadian clock in Arabidopsis thaliana.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

A gene regulatory network model for cell-fate determination during Arabidopsis thaliana flower development that is robust and recovers experimental gene expression profiles

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

Bow ties, metabolism and disease

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

Why the lysogenic state of phage lambda is so stable: a mathematical modeling approach

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

Protein complexes and functional modules in molecular networks

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

A gene-coexpression network for global discovery of conserved genetic modules

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

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

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

Hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

Network motifs: simple building blocks of complex networks

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

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

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

How to make a biological switch

31 August 2018

1 reference

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Construction of a genetic toggle switch in Escherichia coli

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

From molecular to modular cell biology

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

An auxin-dependent distal organizer of pattern and polarity in the Arabidopsis root

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

ThePS-IAA4/5-like Family of Early Auxin-inducible mRNAs inArabidopsis thaliana

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3517225

The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation

31 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23110896

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Dynamics of the Genetic Regulatory Network forArabidopsis thalianaFlower Morphogenesis

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23110896

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Core genetic module: the mixed feedback loop

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23110896

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1105/TPC.112.101840

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23110896 AND SRC:MED&resulttype=core&format=json

16 February 2020

PMC publication ID

3517225

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23110896 AND SRC:MED&resulttype=core&format=json