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Quantitative and logic modelling of molecular and gene networks
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scholarly article
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review article
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Europe PubMed Central
title
Quantitative and logic modelling of molecular and gene networks
(English)
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PubMed
author
Nicolas Le Novère
series ordinal
1
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language of work or name
English
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PubMed
publication date
March 2015
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PubMed
published in
Nature Reviews Genetics
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PubMed
volume
16
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PubMed
issue
3
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PubMed
page(s)
146-58
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PubMed
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Characterization of the proneural gene regulatory network during mouse telencephalon development
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
retrieved
29 September 2017
Modeling the segmentation clock as a network of coupled oscillations in the Notch, Wnt and FGF signaling pathways
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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29 September 2017
Dynamics of a three-variable nonlinear model of vasomotion: comparison of theory and experiment.
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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29 September 2017
Rules for modeling signal-transduction systems
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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29 September 2017
Scaffolding protein Grb2-associated binder 1 sustains epidermal growth factor-induced mitogenic and survival signaling by multiple positive feedback loops
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
retrieved
29 September 2017
The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
1 reference
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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29 September 2017
Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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29 September 2017
Space in systems biology of signaling pathways--towards intracellular molecular crowding in silico
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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29 September 2017
Advances to Bayesian network inference for generating causal networks from observational biological data
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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29 September 2017
Integrating high-throughput and computational data elucidates bacterial networks
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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29 September 2017
Apoptosis defects and chemotherapy resistance: molecular interaction maps and networks
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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29 September 2017
Qualitative simulation of genetic regulatory networks using piecewise-linear models.
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
retrieved
29 September 2017
Parameter estimation in biochemical pathways: a comparison of global optimization methods
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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29 September 2017
Modeling and simulation of genetic regulatory systems: a literature review
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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29 September 2017
Molecular interaction map of the mammalian cell cycle control and DNA repair systems
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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29 September 2017
Computer simulation of the phosphorylation cascade controlling bacterial chemotaxis
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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29 September 2017
Circuitry and dynamics of human transcription factor regulatory networks
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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2 June 2018
An overview of existing modeling tools making use of model checking in the analysis of biochemical networks
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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2 June 2018
Synchronous versus asynchronous modeling of gene regulatory networks
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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2 June 2018
How to infer gene networks from expression profiles
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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2 June 2018
Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks.
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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2 June 2018
Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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2 June 2018
Boolean formalization of genetic control circuits.
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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2 June 2018
Metabolic dynamics in the human red cell. Part I--A comprehensive kinetic model.
1 reference
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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2 June 2018
A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models.
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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27 November 2018
Defining an essential transcription factor program for naïve pluripotency
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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27 November 2018
Integrated metabolic spatial-temporal model for the prediction of ammonia detoxification during liver damage and regeneration
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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27 November 2018
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.
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27 November 2018
Using chemical kinetics to model biochemical pathways.
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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27 November 2018
BoolNet--an R package for generation, reconstruction and analysis of Boolean networks
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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27 November 2018
Comparing different ODE modelling approaches for gene regulatory networks.
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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27 November 2018
iBioSim: a tool for the analysis and design of genetic circuits.
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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27 November 2018
A yeast synthetic network for in vivo assessment of reverse-engineering and modeling approaches
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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27 November 2018
Simulation of the regulation of EGFR endocytosis and EGFR-ERK signaling by endophilin-mediated RhoA-EGFR crosstalk.
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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27 November 2018
Computational methods for diffusion-influenced biochemical reactions
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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27 November 2018
A genome-scale computational study of the interplay between transcriptional regulation and metabolism
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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27 November 2018
BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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27 November 2018
Discrete time piecewise affine models of genetic regulatory networks.
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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27 November 2018
Dynamic control of positional information in the early Drosophila embryo.
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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27 November 2018
A multi-algorithm, multi-timescale method for cell simulation
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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27 November 2018
Genetic Network Analyzer: qualitative simulation of genetic regulatory networks.
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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27 November 2018
Control mechanism of JAK/STAT signal transduction pathway
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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27 November 2018
Establishment of the dorso-ventral pattern during embryonic development of drosophila melanogasater: a logical analysis
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604653
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27 November 2018
Circuit simulation of genetic networks.
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27 November 2018
The mechanism of catalase action. II. Electric analog computer studies
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31 March 2020
Biochemical systems analysis. 3. Dynamic solutions using a power-law approximation
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31 March 2020
Functional capabilities of molecular network components controlling the mammalian G1/S cell cycle phase transition
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https://api.crossref.org/works/10.1038%2FNRG3885
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31 March 2020
NAIL, a software toolset for inferring, analyzing and visualizing regulatory networks
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31 March 2020
Biochemical Systems Theory: A Review
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31 March 2020
The logical analysis of continuous, non-linear biochemical control networks
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31 March 2020
Sampling-rate-dependent probabilistic Boolean networks
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31 March 2020
Core genetic module: the mixed feedback loop
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31 March 2020
NAIL, a software toolset for inferring, analyzing and visualizing regulatory networks
1 reference
stated in
PubMed
reference URL
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12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Identifiers
DOI
10.1038/NRG3885
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
1193626
Dimensions Publication ID
1013591105
0 references
OpenCitations bibliographic resource ID
1193626
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
1193626
PMC publication ID
4604653
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
1193626
PubMed publication ID
25645874
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
1193626
ResearchGate publication ID
272083794
0 references
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