(Q34658911)

3 August 2017

title

Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro (English)

1 reference

3 August 2017

0 references

0 references

1 reference

1 reference

Mycobacterium bovis

1 reference

Amanda J Lohan

10

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Kévin Rue-Albrecht

Kévin Rue-Albrecht

7

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Karsten Hokamp

Karsten Hokamp

9

0 references

Brendan Loftus

Brendan J Loftus

11

0 references

Eamonn Gormley

Eamonn Gormley

12

0 references

David E. MacHugh

David E MacHugh

14

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Stephen V. Gordon

Stephen V Gordon

13

0 references

Kate Killick

8

Kate E Killick

1 reference

3 August 2017

Nicolas C Nalpas

1

1 reference

3 August 2017

Stephen D E Park

2

1 reference

3 August 2017

David A Magee

3

1 reference

3 August 2017

Maria Taraktsoglou

4

1 reference

3 August 2017

John A Browne

5

1 reference

3 August 2017

Kevin M Conlon

6

1 reference

3 August 2017

language of work or name

English

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publication date

8 April 2013

1 reference

3 August 2017

1 reference

3 August 2017

volume

14

1 reference

3 August 2017

page(s)

230

1 reference

describes a project that uses

3 August 2017

limma

LIMMA

2 references

22 June 2022

https://europepmc.org/article/PMC/3640917

based on heuristic

inferred from PubMed Central ID database lookup

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

edgeR

edgeR

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

exact match

https://scigraph.springernature.com/pub.10.1186/1471-2164-14-230

0 references

cites work

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1 reference

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Statistical methods for identifying differentially expressed genes in RNA-Seq experiments

7 July 2018

1 reference

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Transcriptional response of peripheral blood mononuclear cells from cattle infected with Mycobacterium bovis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Estimating RNA-quality using GeneChip microarrays

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Can the battle against tuberculosis gain from epigenetic research?

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Pan-genomic analysis of bovine monocyte-derived macrophage gene expression in response to in vitro infection with Mycobacterium avium subspecies paratuberculosis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Global gene expression and systems biology analysis of bovine monocyte-derived macrophages in response to in vitro challenge with Mycobacterium bovis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Deep-sequencing analysis of the mouse transcriptome response to infection with Brucella melitensis strains of differing virulence

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Genome-wide transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis reveals suppression of host immune genes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Genome-wide antisense transcription drives mRNA processing in bacteria

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

An association between TRP64ARG polymorphism of the B3 adrenoreceptor gene and some metabolic disturbances

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Immunodiagnosis of tuberculosis: a dynamic view of biomarker discovery

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Differential expression in RNA-seq: a matter of depth

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Genome-Wide Gene Expression Profiling of Nucleus Accumbens Neurons Projecting to Ventral Pallidum Using both Microarray and Transcriptome Sequencing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Comparing next-generation sequencing and microarray technologies in a toxicological study of the effects of aristolochic acid on rat kidneys

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Palaeogenomics of Mycobacterium tuberculosis: epidemic bursts with a degrading genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Computational methods for transcriptome annotation and quantification using RNA-seq

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Full-length transcriptome assembly from RNA-Seq data without a reference genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

RNA-sequence analysis of human B-cells

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Immunological biomarkers of tuberculosis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

A comparison of analog and Next-Generation transcriptomic tools for mammalian studies.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Apoptosis is an innate defense function of macrophages against Mycobacterium tuberculosis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Tuberculosis immunity: opportunities from studies with cattle

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

RNA sequencing: advances, challenges and opportunities

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

SH3TC2, a protein mutant in Charcot-Marie-Tooth neuropathy, links peripheral nerve myelination to endosomal recycling

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

What are natural antisense transcripts good for?

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Survival mechanisms of pathogenic Mycobacterium tuberculosis H37Rv

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

A large-scale study of differential gene expression in monocyte-derived macrophages infected with several strains of Mycobacterium avium subspecies paratuberculosis.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Regulation of antigen presentation by Mycobacterium tuberculosis: a role for Toll-like receptors

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

A scaling normalization method for differential expression analysis of RNA-seq data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Intracellular Mycobacterium avium intersect transferrin in the Rab11(+) recycling endocytic pathway and avoid lipocalin 2 trafficking to the lysosomal pathway

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Mistargeting of SH3TC2 away from the recycling endosome causes Charcot-Marie-Tooth disease type 4C

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Regulatory roles of natural antisense transcripts

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Identification of differentially expressed sense and antisense transcript pairs in breast epithelial tissues

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Naturally occurring antisense RNA: function and mechanisms of action

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Gene expression profiling of the host response to Mycobacterium bovis infection in cattle

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

TopHat: discovering splice junctions with RNA-Seq

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

What do natural antisense transcripts regulate?

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Origin, spread and demography of the Mycobacterium tuberculosis complex

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Mapping and quantifying mammalian transcriptomes by RNA-Seq

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Interactions of pathogenic mycobacteria with host macrophages

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Interleukin-17: a novel inflammatory cytokine that bridges innate and adaptive immunity

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Innate gene repression associated with Mycobacterium bovis infection in cattle: toward a gene signature of disease

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Sense-antisense pairs in mammals: functional and evolutionary considerations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Cadherins in development: cell adhesion, sorting, and tissue morphogenesis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Genome-wide natural antisense transcription: coupling its regulation to its different regulatory mechanisms

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Bottlenecks and broomsticks: the molecular evolution of Mycobacterium bovis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

A new summarization method for Affymetrix probe level data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

The tuberculosis eradication programme in Ireland: a review of scientific and policy advances since 1988.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Immune responses in bovine tuberculosis: towards new strategies for the diagnosis and control of disease

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Antisense transcription in the mammalian transcriptome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Molecular structure and physiological functions of GABA(B) receptors

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Widespread occurrence of antisense transcription in the human genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Mycobacterium bovis infection and tuberculosis in cattle

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

A new evolutionary scenario for the Mycobacterium tuberculosis complex

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

LFG: an anti-apoptotic gene that provides protection from Fas-mediated cell death

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

GABAB receptors in the lung

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Early response of bovine alveolar macrophages to infection with live and heat-killed Mycobacterium bovis

7 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-14-230

ADRB3 adrenergic receptor is a key regulator of human myometrial apoptosis and inflammation during chorioamnionitis

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-14-230

The acute-phase protein serum amyloid A3 is expressed in the bovine mammary gland and plays a role in host defence.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-14-230

Polymorphisms of the SLC11A1 gene and resistance to bovine tuberculosis in African Zebu cattle.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-14-230

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-14-230

Transcriptional responses of host peripheral blood cells to tuberculosis infection.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640917

Inhibition of capsaicin-induced cough by the gamma-aminobutyric acid agonist baclofen

26 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23565803

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Macrophages exposed to Mycobacterium tuberculosis release chemokines able to recruit selected leucocyte subpopulations: focus on gammadelta cells

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23565803

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2164-14-230

1 reference

Dimensions Publication ID

3 August 2017

0 references

1 reference

3 August 2017

1 reference