(Q34191343)

31 July 2017

title

Statistical inference and reverse engineering of gene regulatory networks from observational expression data (English)

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31 July 2017

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Frank Emmert-Streib

1

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author name string

Galina V Glazko

series ordinal

2

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31 July 2017

Gökmen Altay

series ordinal

3

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31 July 2017

Ricardo de Matos Simoes

series ordinal

4

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31 July 2017

publication date

3 February 2012

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31 July 2017

published in

Frontiers in Genetics

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31 July 2017

volume

3

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31 July 2017

page(s)

8

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How to infer gene networks from expression profiles, revisited

31 July 2017

cites work

1 reference

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5 July 2018

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Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information

5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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Geometric interpretation of gene coexpression network analysis

5 July 2018

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Constructing disease-specific gene networks using pair-wise relevance metric: application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements

5 July 2018

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Inference of Boolean networks using sensitivity regularization

5 July 2018

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Gene regulatory network reconstruction using conditional mutual information

5 July 2018

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A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli

5 July 2018

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Information-theoretic inference of large transcriptional regulatory networks.

5 July 2018

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Variations in DNA elucidate molecular networks that cause disease

5 July 2018

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Rank-based edge reconstruction for scale-free genetic regulatory networks

5 July 2018

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RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.

5 July 2018

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5 July 2018

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Relative performance of mutual information estimation methods for quantifying the dependence among short and noisy data

5 July 2018

1 reference

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Theory and limitations of genetic network inference from microarray data

5 July 2018

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5 July 2018

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5 July 2018

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

5 July 2018

1 reference

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5 July 2018

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How to infer gene networks from expression profiles

5 July 2018

1 reference

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

5 July 2018

1 reference

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Methods for evaluating clustering algorithms for gene expression data using a reference set of functional classes

5 July 2018

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

5 July 2018

1 reference

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A general framework for weighted gene co-expression network analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

Reverse engineering of regulatory networks in human B cells

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

Estimating genomic coexpression networks using first-order conditional independence

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

Sparse graphical Gaussian modeling of the isoprenoid gene network in Arabidopsis thaliana

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

Estimating mutual information using B-spline functions--an improved similarity measure for analysing gene expression data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

Discovery of meaningful associations in genomic data using partial correlation coefficients

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

Estimating mutual information

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

Identification of genetic networks

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

Network biology: understanding the cell's functional organization

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

Statistical significance for genomewide studies

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

The mutual information: detecting and evaluating dependencies between variables.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

Transitive functional annotation by shortest-path analysis of gene expression data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

Modeling and simulation of genetic regulatory systems: a literature review

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

Relating whole-genome expression data with protein-protein interactions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

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5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

A relationship between gene expression and protein interactions on the proteome scale: analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

Using Bayesian networks to analyze expression data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

Gene ontology: tool for the unification of biology

5 July 2018

1 reference

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KEGG: kyoto encyclopedia of genes and genomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

Central Dogma of Molecular Biology

5 July 2018

1 reference

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Network biology: a direct approach to study biological function

5 July 2018

1 reference

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Local network-based measures to assess the inferability of different regulatory networks.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

Lessons from the DREAM2 Challenges

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

Resampling-based empirical Bayes multiple testing procedures for controlling generalized tail probability and expected value error rates: focus on the false discovery rate and simulation study

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

SIRENE: supervised inference of regulatory networks

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

Inferring connectivity of genetic regulatory networks using information-theoretic criteria

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

Low-order conditional independence graphs for inferring genetic networks.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

Gradient directed regularization for sparse Gaussian concentration graphs, with applications to inference of genetic networks.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

A causal inference approach for constructing transcriptional regulatory networks

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

An empirical Bayes approach to inferring large-scale gene association networks

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

Gene co-expression network topology provides a framework for molecular characterization of cellular state

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

Gene networks inference using dynamic Bayesian networks.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

Extreme self-organization in networks constructed from gene expression data.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271232

28 October 2018

Identifiers

DOI

10.3389/FGENE.2012.00008

1 reference

31 July 2017

1 reference

31 July 2017

1 reference