A comprehensive assessment of methods for de-novo reverse-engineering of genome-scale regulatory networks (Q30502335)

16 October 2017

A comprehensive assessment of methods for de-novo reverse-engineering of genome-scale regulatory networks (English)

1 reference

16 October 2017

Varun Narendra

1

1 reference

16 October 2017

Nikita I Lytkin

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2

1 reference

16 October 2017

Constantin F Aliferis

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3

1 reference

16 October 2017

Alexander Statnikov

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4

1 reference

16 October 2017

14 October 2010

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16 October 2017

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16 October 2017

97

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16 October 2017

1

1 reference

16 October 2017

7-18

1 reference

Analysis and computational dissection of molecular signature multiplicity

16 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

Revealing strengths and weaknesses of methods for gene network inference

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

Towards a rigorous assessment of systems biology models: the DREAM3 challenges

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

Towards the automated engineering of a synthetic genome.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

Reverse engineering of gene regulatory networks: a comparative study

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

Reverse engineering molecular regulatory networks from microarray data with qp-graphs.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

NCBI GEO: archive for high-throughput functional genomic data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

The public road to high-quality curated biological pathways

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

Sparse inverse covariance estimation with the graphical lasso

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

Dialogue on reverse-engineering assessment and methods: the DREAM of high-throughput pathway inference

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

How to infer gene networks from expression profiles

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

An improved map of conserved regulatory sites for Saccharomyces cerevisiae

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

Integrative analysis of the cancer transcriptome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

Reverse engineering of regulatory networks in human B cells

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

Transcriptional regulatory code of a eukaryotic genome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

A statistical problem for inference to regulatory structure from associations of gene expression measurements with microarrays

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

Transcriptional regulatory networks in Saccharomyces cerevisiae

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

The large-scale organization of metabolic networks

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

Cluster analysis and display of genome-wide expression patterns

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

Comparing the areas under two or more correlated receiver operating characteristic curves: a nonparametric approach

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

Lessons from the DREAM2 Challenges

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

Generating realistic in silico gene networks for performance assessment of reverse engineering methods

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

Fast calculation of pairwise mutual information for gene regulatory network reconstruction.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3132400

How to infer gene networks from expression profiles.

26 November 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2010.10.003

A Simple Generalisation of the Area Under the ROC Curve for Multiple Class Classification Problems

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2010.10.003

High-dimensional graphs and variable selection with the Lasso

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2010.10.003

7 January 2021

Markov logic networks

1 reference

https://api.crossref.org/works/10.1016%2FJ.YGENO.2010.10.003

10.1016/J.YGENO.2010.10.003

7 January 2021

Identifiers

DOI

1 reference

16 October 2017

1 reference

16 October 2017

PubMed publication ID

20951196

1 reference