(Q37679239)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24709703%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

title

Reverse engineering cellular networks with information theoretic methods (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24709703%20AND%20SRC:MED&resulttype=core&format=json

Alejandro Fernández Villaverde

13 March 2020

author

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24709703%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

author name string

John Ross

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24709703%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

Julio R Banga

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24709703%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

language of work or name

English

0 references

publication date

10 May 2013

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24709703%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24709703%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

volume

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24709703%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

issue

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24709703%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

page(s)

306-329

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24709703%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

13 March 2020

copyright license

start time

10 May 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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23 August 2017

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23 August 2017

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Using distance correlation and SS-ANOVA to assess associations of familial relationships, lifestyle factors, diseases, and mortality

23 August 2017

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23 August 2017

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Inferring biochemical reaction pathways: the case of the gemcitabine pharmacokinetics

23 August 2017

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23 August 2017

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Influence of statistical estimators of mutual information and data heterogeneity on the inference of gene regulatory networks

23 August 2017

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23 August 2017

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Gene network inference and visualization tools for biologists: application to new human transcriptome datasets.

23 August 2017

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Crowdsourcing network inference: the DREAM predictive signaling network challenge

23 August 2017

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Inference of gene regulatory networks from time series by Tsallis entropy

23 August 2017

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Reconstruction of transcriptional network from microarray data using combined mutual information and network-assisted regression

23 August 2017

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DREAM4: Combining genetic and dynamic information to identify biological networks and dynamical models

23 August 2017

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Inferring the conservative causal core of gene regulatory networks

23 August 2017

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Algorithmic and analytical methods in network biology

23 August 2017

1 reference

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Advantages and limitations of current network inference methods

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

A novel gene network inference algorithm using predictive minimum description length approach

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Revealing strengths and weaknesses of methods for gene network inference

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Metabolic network discovery through reverse engineering of metabolome data

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Inference of regulatory gene interactions from expression data using three-way mutual information

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Gene regulatory network inference: data integration in dynamic models-a review

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

minet: A R/Bioconductor package for inferring large transcriptional networks using mutual information

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Inference of gene regulatory networks based on a universal minimum description length

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

From correlation to causation networks: a simple approximate learning algorithm and its application to high-dimensional plant gene expression data

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Reverse engineering of gene regulatory networks

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Comparing association network algorithms for reverse engineering of large-scale gene regulatory networks: synthetic versus real data

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Inferring gene regulatory networks from time series data using the minimum description length principle

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Asymptotically scale-invariant occupancy of phase space makes the entropy Sq extensive

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Minimum redundancy feature selection from microarray gene expression data

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Genetical genomics analysis of a yeast segregant population for transcription network inference

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Reverse engineering of regulatory networks in human B cells

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Discovery of meaningful associations in genomic data using partial correlation coefficients

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Mathematical and computational techniques to deduce complex biochemical reaction mechanisms

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

On the deduction of chemical reaction pathways from measurements of time series of concentrations

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

The mutual information: detecting and evaluating dependencies between variables.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Modeling and simulation of genetic regulatory systems: a literature review

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Using Bayesian networks to analyze expression data

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Genetic network inference: from co-expression clustering to reverse engineering

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Emergence of Scaling in Random Networks

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Cluster analysis and data visualization of large-scale gene expression data

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: an information theoretic analysis

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Transcriptional gene network inference from a massive dataset elucidates transcriptome organization and gene function.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Estimating the directed information to infer causal relationships in ensemble neural spike train recordings

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

On the impact of entropy estimation on transcriptional regulatory network inference based on mutual information.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Information-theoretic inference of large transcriptional 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=3972682

Reverse engineering cellular 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=3972682

Estimation of mutual information using kernel density estimators.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

How to infer gene networks from expression profiles

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Reveal, a general reverse engineering algorithm for inference of genetic network architectures.

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Determination of eukaryotic protein coding regions using neural networks and information theory

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Network news: innovations in 21st century systems biology

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Multivariate dependence and genetic networks inference.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Revealing differences in gene network inference algorithms on the network level by ensemble methods.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Measuring correlations in metabolomic networks with mutual information.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Lessons from the DREAM2 Challenges

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Using directed information to build biologically relevant influence networks

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Inferring connectivity of genetic regulatory networks using information-theoretic criteria

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Determination of complex reaction mechanisms. Analysis of chemical, biological and genetic networks.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

A predictive model for transcriptional control of physiology in a free living cell.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Unravelling the regulatory structure of biochemical networks using stimulus response experiments and large-scale model selection.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Statistical validation of mutual information calculations: comparison of alternative numerical algorithms.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Reconstructing biological networks using conditional correlation analysis.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

Application of the mutual information criterion for feature selection in computer-aided diagnosis.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3972682

A Mathematical Theory of Communication

1 September 2018

1 reference

https://api.crossref.org/works/10.3390%2FCELLS2020306

msmsEval: tandem mass spectral quality assignment for high-throughput proteomics.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCELLS2020306

Regression Towards Mediocrity in Hereditary Stature

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCELLS2020306

Francis Galton's Account of the Invention of Correlation

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCELLS2020306

Modeling by shortest data description

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCELLS2020306

Possible generalization of Boltzmann-Gibbs statistics

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCELLS2020306

Measuring and testing dependence by correlation of distances

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCELLS2020306

On Brownian Distance Covariance and High Dimensional Data

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCELLS2020306

Hubs of knowledge: using the functional link structure in Biozon to mine for biologically significant entities

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCELLS2020306

An introduction to causal inference.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCELLS2020306

Statistical Construction of Chemical Reaction Mechanisms from Measured Time-Series

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCELLS2020306

Scale-free networks: a decade and beyond

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24709703

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Independent coordinates for strange attractors from mutual information

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24709703

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.3390/CELLS2020306

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24709703%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24709703%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24709703%20AND%20SRC:MED&resulttype=core&format=json