(Q35174713)

6 August 2017

title

Unraveling networks of co-regulated genes on the sole basis of genome sequences (English)

1 reference

6 August 2017

Jacques van Helden

6

0 references

author name string

Sylvain Brohée

1

1 reference

6 August 2017

Rekin's Janky

2

1 reference

6 August 2017

Fadi Abdel-Sater

3

1 reference

6 August 2017

Gilles Vanderstocken

4

1 reference

6 August 2017

Bruno André

5

1 reference

6 August 2017

language of work or name

English

0 references

publication date

13 May 2011

1 reference

6 August 2017

published in

Nucleic Acids Research

1 reference

6 August 2017

volume

39

1 reference

6 August 2017

issue

15

1 reference

6 August 2017

page(s)

6340-6358

1 reference

Creative Commons Attribution-NonCommercial 3.0 Unported

6 August 2017

copyright license

start time

4 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

The nuclear poly(A) polymerase and Exosome cofactor Trf5 is recruited cotranscriptionally to nucleolar surveillance

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

STRING 8--a global view on proteins and their functional interactions in 630 organisms

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

RSAT: regulatory sequence analysis tools

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

The role of DNA-binding specificity in the evolution of bacterial regulatory networks

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Theory and limitations of genetic network inference from microarray data

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

A phylogenetic Gibbs sampler that yields centroid solutions for cis-regulatory site prediction

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Effect of 21 different nitrogen sources on global gene expression in the yeast Saccharomyces cerevisiae

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

An arsenite-inducible 19S regulatory particle-associated protein adapts proteasomes to proteotoxicity

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Identification of direct and indirect targets of the Gln3 and Gat1 activators by transcriptional profiling in response to nitrogen availability in the short and long term

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

More robust detection of motifs in coexpressed genes by using phylogenetic information.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Identifying the conserved network of cis-regulatory sites of a eukaryotic genome

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Cell-cycle control of gene expression in budding and fission yeast

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Integrating phenotypic and expression profiles to map arsenic-response networks

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Transcriptional regulatory code of a eukaryotic genome

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Regulog analysis: detection of conserved regulatory networks across bacteria: application to Staphylococcus aureus

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

PredictRegulon: a web server for the prediction of the regulatory protein binding sites and operons in prokaryote genomes.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

PAINT: A Promoter Analysis and Interaction Network Generation Tool for Gene Regulatory Network Identification

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Transmitting the signal of excess nitrogen in Saccharomyces cerevisiae from the Tor proteins to the GATA factors: connecting the dots

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomics

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Discovery of regulatory elements by a computational method for phylogenetic footprinting

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Prediction of co-regulated genes in Bacillus subtilis on the basis of upstream elements conserved across three closely related species

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Upc2p and Ecm22p, dual regulators of sterol biosynthesis in Saccharomyces cerevisiae

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

RPN4 is a ligand, substrate, and transcriptional regulator of the 26S proteasome: a negative feedback circuit

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Gene ontology: tool for the unification of biology

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Discovering regulatory elements in non-coding sequences by analysis of spaced dyads

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

A nonameric core sequence is required upstream of the LYS genes of Saccharomyces cerevisiae for Lys14p-mediated activation and apparent repression by lysine

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Identification of regulatory regions which confer muscle-specific gene expression.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Comparative amino acid sequence analysis of the C6 zinc cluster family of transcriptional regulators.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

TRANSFAC: a database on transcription factors and their DNA binding sites

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

The value of prior knowledge in discovering motifs with MEME

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Identification of consensus patterns in unaligned DNA sequences known to be functionally related.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Preparation of high molecular weight RNA

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Computational discovery of gene modules and regulatory networks

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

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27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Combining pattern discovery and discriminant analysis to predict gene co-regulation

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3159452

Inferring the transcriptional network of Bacillus subtilis

8 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21572103

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Caveats and pitfalls of ROC analysis in clinical microarray research (and how to avoid them)

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21572103

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKR264

1 reference

release_dxguvn74qnblhojtorzluomsrq

6 August 2017

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/dxguvn74qnblhojtorzluomsrq

mapped directly with Wikidata item

24 November 2022

based on heuristic

PMC publication ID

3159452

1 reference

6 August 2017

1 reference