(Q36045478)

11 August 2017

Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach (English)

1 reference

11 August 2017

Miguel Rocha

2

0 references

Julio Saez-Rodriguez

object named as

Julio Saez-Rodriguez

series ordinal

3

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Julio R. Banga

object named as

Julio R Banga

series ordinal

4

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author name string

David Henriques

series ordinal

1

1 reference

PMC publication ID

4565031

11 August 2017

language of work or name

English

0 references

publication date

21 May 2015

1 reference

11 August 2017

9

1 reference

based on heuristic

inferred from page(s)

published in

Bioinformatics

1 reference

11 August 2017

31

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11 August 2017

18

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11 August 2017

2999-3007

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Creative Commons Attribution 4.0 International

11 August 2017

start time

2 October 2016

1 reference

April 2023 Public Data File from Crossref

copyright status

copyrighted

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cites work

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

1 reference

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Data-derived modeling characterizes plasticity of MAPK signaling in melanoma

2 October 2017

1 reference

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Assessment of network inference methods: how to cope with an underdetermined problem

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

Reverse engineering and identification in systems biology: strategies, perspectives and challenges

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

Simultaneous model discrimination and parameter estimation in dynamic models of cellular systems

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

Logic modeling and the ridiculome under the rug.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

State-time spectrum of signal transduction logic models

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

Histidine kinases and response regulators in networks.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

Inference of complex biological networks: distinguishability issues and optimization-based solutions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

Networks inferred from biochemical data reveal profound differences in toll-like receptor and inflammatory signaling between normal and transformed hepatocytes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

Odefy--from discrete to continuous models.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

The complexity of the 'simple' two-component system KdpD/KdpE in Escherichia coli.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

Optimization in computational systems biology

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

Ensemble modeling for analysis of cell signaling dynamics.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

Parameter estimation in biochemical pathways: a comparison of global optimization methods

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

Modeling and simulation of genetic regulatory systems: a literature review

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

Metabolic stability and epigenesis in randomly constructed genetic nets

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

AMIGO, a toolbox for advanced model identification in systems biology using global optimization

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

Identification of genetic networks from a small number of gene expression patterns under the Boolean network model.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

Identification of regulatory structure and kinetic parameters of biochemical networks via mixed-integer dynamic optimization

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

The sensor kinase KdpD of Escherichia coli senses external K+.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

MORE: mixed optimization for reverse engineering--an application to modeling biological networks response via sparse systems of nonlinear differential equations.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

A hybrid approach for efficient and robust parameter estimation in biochemical pathways.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4565031

10.1093/BIOINFORMATICS/BTV314

23 September 2018

Identifiers

DOI

1 reference

journals/bioinformatics/HenriquesRSB15

11 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

PMC publication ID

4565031

11 August 2017

PubMed publication ID

26002881

1 reference

PMC publication ID

4565031