(Q35860667)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22121215%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

title

Gene network inference and visualization tools for biologists: application to new human transcriptome datasets (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22121215%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

0 references

1 reference

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22121215%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

Yoshinori Tamada

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22121215%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

Stephen K. Smith

14

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22121215%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

Steve Charnock-Jone

17

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22121215%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

Cristin Print

19

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22121215%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

author name string

Hiromitsu Araki

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22121215%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

Ben Dunmore

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22121215%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

Deborah Sanders

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22121215%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

Sally Humphreys

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22121215%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

Muna Affara

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22121215%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

Seiya Imoto

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22121215%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

Kaori Yasuda

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22121215%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

Yuki Tomiyasu

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22121215%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

Kosuke Tashiro

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22121215%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

Christopher Savoie

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22121215%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

Vicky Cho

13

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22121215%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

Satoru Kuhara

15

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22121215%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

Satoru Miyano

16

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22121215%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

Edmund J Crampin

18

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22121215%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

language of work or name

English

0 references

publication date

24 November 2011

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22121215%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

published in

Nucleic Acids Research

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22121215%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

volume

40

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22121215%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

issue

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22121215%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

page(s)

2377-2398

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22121215%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution-NonCommercial 3.0 Unported

17 January 2020

copyright license

start time

11 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

How to infer gene networks from expression profiles, revisited

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

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

11 July 2018

1 reference

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Novel cross-talk within the IKK family controls innate immunity

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Tissue-specific disallowance of housekeeping genes: the other face of cell differentiation.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Regulating the regulators: modulators of transcription factor activity

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

geWorkbench: an open source platform for integrative genomics

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Revealing strengths and weaknesses of methods for gene network inference

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Mimosa: mixture model of co-expression to detect modulators of regulatory interaction

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

A roadmap of clustering algorithms: finding a match for a biomedical application

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Coordinated regulation of virulence during systemic infection of Salmonella enterica serovar Typhimurium

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Mistranslation of membrane proteins and two-component system activation trigger antibiotic-mediated cell death.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

PTM-Switchboard--a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Predicting gene targets of perturbations via network-based filtering of mRNA expression compendia

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Direct targets of the TRP63 transcription factor revealed by a combination of gene expression profiling and reverse engineering

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

The properties of high-dimensional data spaces: implications for exploring gene and protein expression data.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

The human disease network

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Reconstructing biochemical pathways from time course data

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

A network biology approach to prostate cancer

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Cross-talk between nuclear receptors and nuclear factor kappaB.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Post-translational modifications regulating the activity and function of the nuclear factor kappa B pathway

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Linear models and empirical bayes methods for assessing differential expression in microarray experiments

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Nucleolar sequestration of RelA (p65) regulates NF-kappaB-driven transcription and apoptosis

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Reverse engineering of regulatory networks in human B cells

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Phosphorylation of NF-kappaB and IkappaB proteins: implications in cancer and inflammation

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Advances to Bayesian network inference for generating causal networks from observational biological data

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Evidence for dynamically organized modularity in the yeast protein-protein interaction network

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Coexpression analysis of human genes across many microarray data sets

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

LSimpute: accurate estimation of missing values in microarray data with least squares methods

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Inferring genetic networks and identifying compound mode of action via expression profiling

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

A comparison of normalization methods for high density oligonucleotide array data based on variance and bias

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Network motifs in the transcriptional regulation network of Escherichia coli

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

A genomic regulatory network for development

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Estimating genome-wide gene networks using nonparametric Bayesian network models on massively parallel computers.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Inferring gene networks: dream or nightmare?

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

NIRest: a tool for gene network and mode of action inference.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Lessons from the DREAM2 Challenges

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Unraveling dynamic activities of autocrine pathways that control drug-response transcriptome networks.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

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

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

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

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Inference of gene networks from temporal gene expression profiles.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Computational strategy for discovering druggable gene networks from genome-wide RNA expression profiles.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Reconstructing gene regulatory networks: from random to scale-free connectivity.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

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

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Modulation of NF-kappaB activity by exchange of dimers.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Observing and interpreting correlations in metabolomic networks.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Estimation of genetic networks and functional structures between genes by using Bayesian networks and nonparametric regression.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Activation of NF-κB via the IκB Kinase Complex Is Both Essential and Sufficient for Proinflammatory Gene Expression in Primary Endothelial Cells

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315333

Master regulator unmasked

14 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22121215

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKR902

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22121215%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22121215%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

PubMed publication ID

22121215

1 reference