(Q31143553)

3 September 2017

COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia (English)

1 reference

3 September 2017

1

1 reference

3 September 2017

10

1 reference

3 September 2017

12

1 reference

3 September 2017

Daniela Ledezma-Tejeida

Daniela Ledezma-Tejeida

5

0 references

Paolo Sonego

Paolo Sonego

2

0 references

Luca Bianco

Luca Bianco

3

0 references

Kris Laukens

Kris Laukens

9

0 references

Julio Collado-Vides

Julio Collado-Vides

11

0 references

Jan Michiels

Jan Michiels

8

0 references

Socorro Gama-Castro

6

Socorro Gama-Castro

1 reference

3 September 2017

7

Veerle Liebens

1 reference

3 September 2017

Qiang Fu

4

1 reference

3 September 2017

language of work or name

English

0 references

publication date

8 November 2013

1 reference

3 September 2017

Nucleic Acids Research

1 reference

3 September 2017

42

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3 September 2017

Database issue

1 reference

3 September 2017

D649-53

1 reference

Creative Commons Attribution 3.0 Unported

3 September 2017

start time

4 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

The Mycobacterium tuberculosis regulatory network and hypoxia

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

Transcription factors in Escherichia coli prefer the holo conformation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

PheNetic: network-based interpretation of unstructured gene lists in E. coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

Evolutionary Genomics of Salmonella enterica Subspecies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

Expression divergence between Escherichia coli and Salmonella enterica serovar Typhimurium reflects their lifestyles

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

RNA-Seq vs dual- and single-channel microarray data: sensitivity analysis for differential expression and clustering

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

ArrayExpress update--trends in database growth and links to data analysis tools

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

NCBI GEO: archive for functional genomics data sets--update

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

GraphAlignment: Bayesian pairwise alignment of biological networks.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

Gene Ontology annotations and resources

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

EcoCyc: fusing model organism databases with systems biology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

Fast gapped-read alignment with Bowtie 2

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

The UniProt-GO Annotation database in 2011.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

Network-based functional modeling of genomics, transcriptomics and metabolism in bacteria

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

COLOMBOS: access port for cross-platform bacterial expression compendia

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

Microarrays, deep sequencing and the true measure of the transcriptome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

Query-based biclustering of gene expression data using Probabilistic Relational Models.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

COMODO: an adaptive coclustering strategy to identify conserved coexpression modules between organisms.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

Use of structural DNA properties for the prediction of transcription-factor binding sites in Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

Differential expression analysis for sequence count data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

Genome-wide detection of predicted non-coding RNAs in Rhizobium etli expressed during free-living and host-associated growth using a high-resolution tiling array

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

Model-based variance-stabilizing transformation for Illumina microarray data.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

A variance-stabilizing transformation for gene-expression microarray data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965013

An ensemble biclustering approach for querying gene expression compendia with experimental lists

21 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKT1086

Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKT1086

Systematic comparison of RNA-Seq normalization methods using measurement error models

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKT1086

Directed module detection in a large-scale expression compendium

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24214998

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKT1086

1 reference

journals/nar/MeysmanSBFLGLMLMCE14

3 September 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

3 September 2017

PubMed publication ID

24214998

1 reference