Comparative analysis of Lactobacillus plantarum WCFS1 transcriptomes by using DNA microarray and next-generation sequencing technologies (Q42119880)

16 October 2017

Comparative analysis of Lactobacillus plantarum WCFS1 transcriptomes by using DNA microarray and next-generation sequencing technologies (English)

1 reference

16 October 2017

0 references

Lactobacillus plantarum

object named as

Lactobacillus plantarum

1 reference

Milkha M Leimena

1

1 reference

16 October 2017

Michiel Wels

2

1 reference

16 October 2017

Roger S Bongers

3

1 reference

16 October 2017

Eddy J Smid

4

1 reference

16 October 2017

Erwin G Zoetendal

5

1 reference

16 October 2017

Michiel Kleerebezem

6

1 reference

16 October 2017

language of work or name

English

0 references

publication date

6 April 2012

1 reference

Applied and Environmental Microbiology

16 October 2017

1 reference

16 October 2017

78

1 reference

16 October 2017

12

1 reference

16 October 2017

4141-4148

1 reference

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

16 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Differential expression in RNA-seq: a matter of depth

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Transcript amplification from single bacterium for transcriptome analysis

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Prokaryotic whole-transcriptome analysis: deep sequencing and tiling arrays

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

From RNA-seq reads to differential expression results

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Differential expression analysis for sequence count data

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

baySeq: empirical Bayesian methods for identifying differential expression in sequence count data

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Identification of genetic loci in Lactobacillus plantarum that modulate the immune response of dendritic cells using comparative genome hybridization

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

RNA-Seq gene expression estimation with read mapping uncertainty

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

sigma54-Mediated control of the mannose phosphotransferase sytem in Lactobacillus plantarum impacts on carbohydrate metabolism

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

A single-base resolution map of an archaeal transcriptome

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Quantitative miRNA expression analysis: comparing microarrays with next-generation sequencing.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Next generation sequencing of microbial transcriptomes: challenges and opportunities.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Applications of new sequencing technologies for transcriptome analysis.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

A perspective: metatranscriptomics as a tool for the discovery of novel biocatalysts.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Structure and complexity of a bacterial transcriptome.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

RNA-Seq: a revolutionary tool for transcriptomics

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Stem cell transcriptome profiling via massive-scale mRNA sequencing

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Mapping and quantifying mammalian transcriptomes by RNA-Seq

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

The transcriptional landscape of the yeast genome defined by RNA sequencing

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Microbial community gene expression in ocean surface waters

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Transcript profiling by 3'-untranslated region sequencing resolves expression of gene families

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Thioredoxin reductase is a key factor in the oxidative stress response of Lactobacillus plantarum WCFS1.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Saturation and quantization reduction in microarray experiments using two scans at different sensitivities

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Degradation of RNA in bacteria: comparison of mRNA and stable RNA

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

In silico reconstruction of the metabolic pathways of Lactobacillus plantarum: comparing predictions of nutrient requirements with those from growth experiments.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Prediction of transcriptional terminators in Bacillus subtilis and related species

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Applications of DNA microarrays in biology

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Nucleotide metabolism and its control in lactic acid bacteria

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

MicroPreP: a cDNA microarray data pre-processing framework.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Complete genome sequence of Lactobacillus plantarum WCFS1

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Genesis: cluster analysis of microarray data

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Comparison of initiation of protein synthesis in procaryotes, eucaryotes, and organelles

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Isolation of RNA from bacterial samples of the human gastrointestinal tract.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Multiple-laboratory comparison of microarray platforms

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3370542

Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity

1 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22492454

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Challenges in applying microarrays to environmental studies

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22492454

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1128/AEM.00470-12

1 reference

16 October 2017

1 reference

16 October 2017

1 reference