Logic-based models in systems biology: a predictive and parameter-free network analysis method. (Q38052663)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23072820%20AND%20SRC:MED&resulttype=core&format=json

15 February 2020

title

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

1 reference

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15 February 2020

1 reference

2

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15 February 2020

Santiago Schnell

series ordinal

4

1 reference

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15 February 2020

author name string

Michelle L Wynn

series ordinal

1

1 reference

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15 February 2020

Sofia D Merajver

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23072820%20AND%20SRC:MED&resulttype=core&format=json

15 February 2020

language of work or name

1 reference

1 November 2012

1 reference

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15 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23072820%20AND%20SRC:MED&resulttype=core&format=json

15 February 2020

volume

4

1 reference

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15 February 2020

issue

11

1 reference

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15 February 2020

page(s)

1323-1337

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23072820%20AND%20SRC:MED&resulttype=core&format=json

Kinase inhibitors can produce off-target effects and activate linked pathways by retroactivity

15 February 2020

cites work

1 reference

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Stimulus-dependent dynamics of p53 in single cells

6 September 2017

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A Boolean probabilistic model of metabolic adaptation to oxygen in relation to iron homeostasis and oxidative stress

6 September 2017

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Interactome networks and human disease

6 September 2017

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Modeling the cell cycle: why do certain circuits oscillate?

6 September 2017

1 reference

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Mutant onco-proteins as drug targets: successes, failures, and future prospects

6 September 2017

1 reference

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Simulation of cellular biochemical system kinetics

6 September 2017

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Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G-protein action

6 September 2017

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Logic-based models for the analysis of cell signaling networks

6 September 2017

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

6 September 2017

1 reference

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A dynamic analysis of IRS-PKR signaling in liver cells: a discrete modeling approach.

6 September 2017

1 reference

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

6 September 2017

1 reference

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

6 September 2017

1 reference

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Oscillations of the p53-Akt network: implications on cell survival and death

6 September 2017

1 reference

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Boolean network simulations for life scientists

6 September 2017

1 reference

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Network model of survival signaling in large granular lymphocyte leukemia

6 September 2017

1 reference

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Modelling reaction kinetics inside cells

6 September 2017

1 reference

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Molecular logic and computing

6 September 2017

1 reference

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Boolean network models of cellular regulation: prospects and limitations

6 September 2017

1 reference

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A hidden feedback in signaling cascades is revealed

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3612358

Boolean network model predicts cell cycle sequence of fission yeast

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3612358

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3612358

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

6 September 2017

1 reference

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Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae

6 September 2017

1 reference

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A multiscale mathematical model of cancer, and its use in analyzing irradiation therapies

6 September 2017

1 reference

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3612358

GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3612358

A multiscale model for avascular tumor growth

6 September 2017

1 reference

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The Akt-mTOR tango and its relevance to cancer

6 September 2017

1 reference

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Steady states and oscillations in the p53/Mdm2 network.

6 September 2017

1 reference

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6 September 2017

Biological robustness

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Mathematical and computational techniques to deduce complex biochemical reaction mechanisms

6 September 2017

1 reference

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Stochastic approaches for modelling in vivo reactions.

6 September 2017

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The yeast cell-cycle network is robustly designed

6 September 2017

1 reference

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Random Boolean network models and the yeast transcriptional network

6 September 2017

1 reference

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A natural class of robust networks

6 September 2017

1 reference

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

6 September 2017

1 reference

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

6 September 2017

1 reference

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New roles for p21 and p27 cell-cycle inhibitors: a function for each cell compartment?

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3612358

The p53-Mdm2 module and the ubiquitin system.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3612358

A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3612358

A genomic regulatory network for development

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3612358

Direct interaction of c-Myc with Smad2 and Smad3 to inhibit TGF-beta-mediated induction of the CDK inhibitor p15(Ink4B)

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3612358

The segment polarity network is a robust developmental module

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3612358

Cyclin D1 is a nuclear protein required for cell cycle progression in G1

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3612358

Metabolic stability and epigenesis in randomly constructed genetic nets

6 September 2017

1 reference

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Cancer. p53, guardian of the genome

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3612358

Dynamics of the p53-Mdm2 feedback loop in individual cells

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3612358

Digital clocks: simple Boolean models can quantitatively describe circadian systems

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3612358

APC is essential for targeting phosphorylated beta-catenin to the SCFbeta-TrCP ubiquitin ligase.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3612358

c-myc is a downstream target of the Smad pathway

14 September 2017

1 reference

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Unraveling the complex regulatory relationships between metabolism and signal transduction in cancer

14 September 2017

1 reference

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Synchronous versus asynchronous modeling of gene regulatory 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=3612358

Signal transduction through MAP kinase cascades

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3612358

Boolean formalization of genetic control circuits.

23 June 2018

1 reference

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Load-induced modulation of signal transduction networks.

23 June 2018

1 reference

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Attractor analysis of asynchronous Boolean models of signal transduction 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=3612358

NET-SYNTHESIS: a software for synthesis, inference and simplification of signal transduction 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=3612358

Robustness and state-space structure of Boolean gene regulatory 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=3612358

Methods of robustness analysis for Boolean models of gene control 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=3612358

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3612358

Circuit diagrams for biological 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=3612358

Two coupled enzymes perform in parallel the 'AND' and 'InhibAND' logic gate operations.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3612358

Elementary arithmetic operations by enzymes: a model for metabolic pathway based computing.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3612358

A remark on "scalar equations for synchronous Boolean networks with biological applications" by C. Farrow, J. Heidel, J. Maloney, and J. Rogers.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3612358

Robustness and fragility of Boolean models for genetic 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=3612358

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

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3612358

A regulatory gene network that directs micromere specification in the sea urchin embryo.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3612358

New computational approaches for analysis of cis-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=3612358

Repression of transcription of the p27(Kip1) cyclin-dependent kinase inhibitor gene by c-Myc.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3612358

The relationship between BcI2, Bax and p53: consequences for cell cycle progression and cell death.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3612358

Statistical mechanics of complex networks

31 August 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2IB20193C

Signaling Recognition Events with Fluorescent Sensors and Switches

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2IB20193C

A molecular photoionic AND gate based on fluorescent signalling

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2IB20193C

The Transitive Reduction of a Directed Graph

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2IB20193C

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

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23072820

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1039/C2IB20193C

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23072820%20AND%20SRC:MED&resulttype=core&format=json

15 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23072820%20AND%20SRC:MED&resulttype=core&format=json

15 February 2020

PubMed publication ID

23072820

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23072820%20AND%20SRC:MED&resulttype=core&format=json