Resolving host-pathogen interactions by dual RNA-seq (Q36282833)

13 August 2017

5 references

20 June 2019

19 September 2019

27 July 2020

28 January 2021

22 August 2022

Resolving host-pathogen interactions by dual RNA-seq (English)

1 reference

biomedical investigative technique

13 August 2017

1 reference

28 January 2021

1 reference

PubMed

host microbial interaction

19 September 2019

1 reference

27 July 2020

1 reference

3

1 reference

13 August 2017

Lars Barquist

2

0 references

author name string

Alexander J Westermann

series ordinal

1

1 reference

13 August 2017

16 February 2017

1 reference

PMCID

5313147

13 August 2017

1 February 2017

5 references

20 June 2019

19 September 2019

27 July 2020

28 January 2021

22 August 2022

6 references

13 August 2017

20 June 2019

19 September 2019

27 July 2020

28 January 2021

22 August 2022

13

1 reference

13 August 2017

e1006033

1 reference

13 August 2017

2

1 reference

Creative Commons Attribution 4.0 International

13 August 2017

5 references

20 June 2019

19 September 2019

27 July 2020

28 January 2021

describes a project that uses

22 August 2022

copyright status

copyrighted

0 references

limma

1 reference

22 June 2022

https://europepmc.org/article/PMC/5313147

based on heuristic

inferred from PubMed Central ID database lookup

edgeR

object named as

edgeR

1 reference

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

DESeq2

object named as

DESeq2

DESeq

1 reference

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

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30 September 2017

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30 September 2017

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30 September 2017

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Co-transcriptomic Analysis by RNA Sequencing to Simultaneously Measure Regulated Gene Expression in Host and Bacterial Pathogen

30 September 2017

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Dual RNA-seq unveils noncoding RNA functions in host–pathogen interactions

30 September 2017

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Simultaneous transcriptional profiling of Leishmania major and its murine macrophage host cell reveals insights into host-pathogen interactions

30 September 2017

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The Overlooked Fact: Fundamental Need for Spike-In Control for Virtually All Genome-Wide Analyses

30 September 2017

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Dual RNA-seq of Nontypeable Haemophilus influenzae and Host Cell Transcriptomes Reveals Novel Insights into Host-Pathogen Cross Talk

30 September 2017

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RNA-seq Brings New Insights to the Intra-Macrophage Transcriptome of Salmonella Typhimurium

30 September 2017

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High-throughput sequencing of human plasma RNA by using thermostable group II intron reverse transcriptases.

30 September 2017

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Practical impacts of genomic data "cleaning" on biological discovery using surrogate variable analysis

30 September 2017

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

30 September 2017

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KEGG as a reference resource for gene and protein annotation

30 September 2017

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Robust bioengineered 3D functional human intestinal epithelium

30 September 2017

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Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses

30 September 2017

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Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline

30 September 2017

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How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets

30 September 2017

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A functional perspective on phenotypic heterogeneity in microorganisms

30 September 2017

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Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma

30 September 2017

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Single prokaryotic cell isolation and total transcript amplification protocol for transcriptomic analysis

30 September 2017

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Dual 3'Seq using deepSuperSAGE uncovers transcriptomes of interacting Salmonella enterica Typhimurium and human host cells

30 September 2017

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Ballgown bridges the gap between transcriptome assembly and expression analysis

30 September 2017

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Computational prediction of molecular pathogen-host interactions based on dual transcriptome data

30 September 2017

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Comprehensive insights into transcriptional adaptation of intracellular mycobacteria by microbe-enriched dual RNA sequencing

30 September 2017

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Orchestrating high-throughput genomic analysis with Bioconductor

30 September 2017

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Reprogramming of Yersinia from virulent to persistent mode revealed by complex in vivo RNA-seq analysis

30 September 2017

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High-resolution transcriptomic analysis of the adaptive response of Staphylococcus aureus during acute and chronic phases of osteomyelitis.

30 September 2017

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Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

30 September 2017

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Gene Ontology Consortium: going forward

30 September 2017

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The co-transcriptome of uropathogenic Escherichia coli-infected mouse macrophages reveals new insights into host-pathogen interactions

30 September 2017

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svaseq: removing batch effects and other unwanted noise from sequencing data

30 September 2017

1 reference

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Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures

30 September 2017

1 reference

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Power analysis and sample size estimation for RNA-Seq differential expression

30 September 2017

1 reference

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Dual transcriptional profiling of mice and Toxoplasma gondii during acute and chronic infection

30 September 2017

1 reference

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A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

30 September 2017

1 reference

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Normalization of RNA-seq data using factor analysis of control genes or samples

30 September 2017

1 reference

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READemption-a tool for the computational analysis of deep-sequencing-based transcriptome data

30 September 2017

1 reference

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Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing

30 September 2017

1 reference

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Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

30 September 2017

1 reference

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Dual RNA-seq of parasite and host reveals gene expression dynamics during filarial worm-mosquito interactions

30 September 2017

1 reference

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MARIS: method for analyzing RNA following intracellular sorting

30 September 2017

1 reference

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Tissue fixation and the effect of molecular fixatives on downstream staining procedures

30 September 2017

1 reference

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voom: Precision weights unlock linear model analysis tools for RNA-seq read counts

30 September 2017

1 reference

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Sequencing depth and coverage: key considerations in genomic analyses

30 September 2017

1 reference

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Simultaneous transcriptional profiling of bacteria and their host cells

30 September 2017

1 reference

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RNA-seq differential expression studies: more sequence or more replication?

30 September 2017

1 reference

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Viral-bacterial interactions-therapeutic implications

30 September 2017

1 reference

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Systematic evaluation of spliced alignment programs for RNA-seq data

30 September 2017

1 reference

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Host-Mycobacterium avium subsp. paratuberculosis interactome reveals a novel iron assimilation mechanism linked to nitric oxide stress during early infection

30 September 2017

1 reference

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Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Laser microdissection coupled with RNA-seq analysis of porcine enterocytes infected with an obligate intracellular pathogen (Lawsonia intracellularis).

30 September 2017

1 reference

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Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Differences in gastric carcinoma microenvironment stratify according to EBV infection intensity: implications for possible immune adjuvant therapy

30 September 2017

1 reference

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Comprehensive assignment of roles for Salmonella typhimurium genes in intestinal colonization of food-producing animals

30 September 2017

1 reference

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Chlamydia trachomatis infection induces replication of latent HHV-6

30 September 2017

1 reference

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A comparison of methods for differential expression analysis of RNA-seq data

30 September 2017

1 reference

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Heterogeneity of intracellular replication of bacterial pathogens

30 September 2017

1 reference

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Alternative splicing: a pivotal step between eukaryotic transcription and translation

30 September 2017

1 reference

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Bacterial coinfection in influenza: a grand rounds review

30 September 2017

1 reference

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How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?

30 September 2017

1 reference

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InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation

30 September 2017

1 reference

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Revisiting global gene expression analysis

30 September 2017

1 reference

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Imbalanced oxidative stress causes chlamydial persistence during non-productive human herpes virus co-infection

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Dual RNA-seq of pathogen and host

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Non-genetic diversity shapes infectious capacity and host resistance

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Wisdom of crowds for robust gene network inference

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

RNA-Seq-based monitoring of infection-linked changes in Vibrio cholerae gene expression.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Synthetic spike-in standards for RNA-seq experiments

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Computational methods for transcriptome annotation and quantification using RNA-seq

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Molecular signatures database (MSigDB) 3.0.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Transcript amplification from single bacterium for transcriptome analysis

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

The effect of formaldehyde fixation on RNA: optimization of formaldehyde adduct removal.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Phenotypic landscape of a bacterial cell

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Differential expression analysis for sequence count data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Tackling the widespread and critical impact of batch effects in high-throughput data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Advantages and limitations of current network inference methods

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Gene ontology analysis for RNA-seq: accounting for selection bias

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Fast mapping of short sequences with mismatches, insertions and deletions using index structures

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Identifying genetic determinants needed to establish a human gut symbiont in its habitat

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Digital transcriptome profiling using selective hexamer priming for cDNA synthesis

30 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Investigating fixative-induced changes in RNA quality and utility by microarray analysis

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Elucidation of gene interaction networks through time-lagged correlation analysis of transcriptional data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

The extracellular matrix protein mindin is a pattern-recognition molecule for microbial pathogens

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Chlamydia trachomatis infection alters host cell transcription in diverse cellular pathways

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Spliced synthetic genes as internal controls in RNA sequencing experiments

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

An infection-relevant transcriptomic compendium for Salmonella enterica Serovar Typhimurium

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Comparison of software packages for detecting differential expression in RNA-seq studies

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

An Interspecies Regulatory Network Inferred from Simultaneous RNA-seq of Candida albicans Invading Innate Immune Cells

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Transcriptome sequencing, microarray, and proteomic analyses reveal cellular and metabolic impact of hepatitis C virus infection in vitro

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

RNA-Seq gene expression estimation with read mapping uncertainty

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Three-dimensional intestinal villi epithelium enhances protection of human intestinal cells from bacterial infection by inducing mucin expression

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Molecular mechanisms underlying bacterial persisters.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Assessment of fixatives, fixation, and tissue processing on morphology and RNA integrity

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Dynamics of bacterial growth and distribution within the liver during Salmonella infection.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

RNA recovery and detection of mRNA by RT-PCR from preserved prokaryotic samples

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5313147

Points of significance: Analysis of variance and blocking

22 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28207848

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PPAT.1006033

1 reference

release_2cnhyuecdrh77it7onweuyzt5i

13 August 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/2cnhyuecdrh77it7onweuyzt5i

mapped directly with Wikidata item

24 November 2022

based on heuristic

PMCID

5313147

1 reference

13 August 2017

1 reference

PMCID

5313147