(Q34388505)

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Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling

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scholarly article

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Europe PubMed Central

PubMed publication ID

1 August 2017

Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling (English)

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Europe PubMed Central

PubMed publication ID

1 August 2017

Klebsiella pneumoniae

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Escherichia coli

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Bernhard Palsson

8

object named as

Bernhard Ø Palsson

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Europe PubMed Central

PubMed publication ID

1 August 2017

author name string

Donghyuk Kim

1

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Europe PubMed Central

PubMed publication ID

1 August 2017

Jay Sung-Joong Hong

2

1 reference

Europe PubMed Central

PubMed publication ID

1 August 2017

Yu Qiu

3

1 reference

Europe PubMed Central

PubMed publication ID

1 August 2017

Harish Nagarajan

4

1 reference

Europe PubMed Central

PubMed publication ID

1 August 2017

Joo-Hyun Seo

5

1 reference

Europe PubMed Central

PubMed publication ID

1 August 2017

Byung-Kwan Cho

6

1 reference

Europe PubMed Central

PubMed publication ID

1 August 2017

Shih-Feng Tsai

7

1 reference

Europe PubMed Central

PubMed publication ID

1 August 2017

publication date

9 August 2012

1 reference

Europe PubMed Central

PubMed publication ID

1 August 2017

1 reference

Europe PubMed Central

PubMed publication ID

1 August 2017

8

1 reference

Europe PubMed Central

PubMed publication ID

1 August 2017

8

1 reference

Europe PubMed Central

PubMed publication ID

1 August 2017

e1002867

1 reference

Europe PubMed Central

PubMed publication ID

1 August 2017

copyright license

Creative Commons Attribution 4.0 International

9 August 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

0 references

Evolutionary dynamics of small RNAs in 27 Escherichia coli and Shigella genomes

1 reference

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6 July 2018

MrkH, a novel c-di-GMP-dependent transcriptional activator, controls Klebsiella pneumoniae biofilm formation by regulating type 3 fimbriae expression

1 reference

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6 July 2018

Impact of Hfq on global gene expression and virulence in Klebsiella pneumoniae

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Small RNAs endow a transcriptional activator with essential repressor functions for single-tier control of a global stress regulon

1 reference

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6 July 2018

Assessing computational tools for the discovery of small RNA genes in bacteria

1 reference

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6 July 2018

Genome-wide detection of novel regulatory RNAs in E. coli

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6 July 2018

Genetic regulation of the ramA locus and its expression in clinical isolates of Klebsiella pneumoniae.

1 reference

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6 July 2018

Accessibility and evolutionary conservation mark bacterial small-rna target-binding regions

1 reference

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6 July 2018

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)

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6 July 2018

A Bacterial mRNA Leader that Employs Different Mechanisms to Sense Disparate Intracellular Signals

1 reference

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6 July 2018

Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNA

1 reference

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6 July 2018

Structural and operational complexity of the Geobacter sulfurreducens genome.

1 reference

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6 July 2018

Positive regulation by small RNAs and the role of Hfq

1 reference

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6 July 2018

The primary transcriptome of the major human pathogen Helicobacter pylori

1 reference

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6 July 2018

Deep sequencing analysis of the Methanosarcina mazei Gö1 transcriptome in response to nitrogen availability.

1 reference

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6 July 2018

The transcription unit architecture of the Escherichia coli genome

1 reference

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6 July 2018

Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA

1 reference

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6 July 2018

Homologs of the small RNA SgrS are broadly distributed in enteric bacteria but have diverged in size and sequence

1 reference

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6 July 2018

Genome sequencing and comparative analysis of Klebsiella pneumoniae NTUH-K2044, a strain causing liver abscess and meningitis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Infernal 1.0: inference of RNA alignments

1 reference

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6 July 2018

EcoCyc: a comprehensive view of Escherichia coli biology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

The hpx genetic system for hypoxanthine assimilation as a nitrogen source in Klebsiella pneumoniae: gene organization and transcriptional regulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

The ArgP protein stimulates the Klebsiella pneumoniae gdhA promoter in a lysine-sensitive manner

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Complex regulation of urease formation from the two promoters of the ure operon of Klebsiella pneumoniae

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Dynamic usage of transcription start sites within core promoters

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Translation initiation and the fate of bacterial mRNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Base-pairing requirement for RNA silencing by a bacterial small RNA and acceleration of duplex formation by Hfq

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Genome-wide analysis of mammalian promoter architecture and evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

A high-resolution map of transcription in the yeast genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

The role of RNAs in the regulation of virulence-gene expression.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

LEGER: knowledge database and visualization tool for comparative genomics of pathogenic and non-pathogenic Listeria species

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Importance of tetramer formation by the nitrogen assimilation control protein for strong repression of glutamate dehydrogenase formation in Klebsiella pneumoniae

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

The bacterial Sm-like protein Hfq: a key player in RNA transactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

DBTSS, DataBase of Transcriptional Start Sites: progress report 2004.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Exploration, normalization, and summaries of high density oligonucleotide array probe level data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Multiple sequence alignment with the Clustal series of programs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

CORG: a database for COmparative Regulatory Genomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Regulation and mode of action of the second small RNA activator of RpoS translation, RprA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

ColE1-like plasmid pIP843 of Klebsiella pneumoniae encoding extended-spectrum beta-lactamase CTX-M-17.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Comparative genomics of closely related salmonellae

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Hfq: a bacterial Sm-like protein that mediates RNA-RNA interaction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Lysergic acid diethylamide- and mescaline-induced attenuation of the effect of punishment in the rat

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Novel small RNA-encoding genes in the intergenic regions of Escherichia coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

How sigma docks to RNA polymerase and what sigma does

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Comparison of the Escherichia coli K-12 genome with sampled genomes of a Klebsiella pneumoniae and three salmonella enterica serovars, Typhimurium, Typhi and Paratyphi

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

High-level expression of chromosomally encoded SHV-1 beta-lactamase and an outer membrane protein change confer resistance to ceftazidime and piperacillin-tazobactam in a clinical isolate of Klebsiella pneumoniae

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Prediction of transcription regulatory sites in Archaea by a comparative genomic approach

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

A- and T-tract-mediated intrinsic curvature in native DNA between the binding site of the upstream activator NtrC and the nifLA promoter of Klebsiella pneumoniae facilitates transcription.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Transcriptional regulation of a second flavodoxin gene from Klebsiella pneumoniae

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

The fur gene from Klebsiella pneumoniae: characterization, genomic organization and phylogenetic analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Escherichia coli promoter sequences: analysis and prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Redox-dependent shift of OxyR-DNA contacts along an extended DNA-binding site: a mechanism for differential promoter selection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

The value of prior knowledge in discovering motifs with MEME

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Compilation and analysis ofEscherichia colipromoter DNA sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Regulation of the rpsU-dnaG-rpoD macromolecular synthesis operon and the initiation of DNA replication in Escherichia coli K-12

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Codon--anticodon pairing: the wobble hypothesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Analysis of E. coli promoter sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Mutations in the RNA polymerase recognition sequence of the Klebsiella pneumoniae nifH promoter permitting transcriptional activation in the absence of NifA binding to upstream activator sequences.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Control of primer formation for ColE1 plasmid replication: conformational change of the primer transcript

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Arginine regulon of Escherichia coli K-12. A study of repressor-operator interactions and of in vitro binding affinities versus in vivo repression

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

6 July 2018

Competition between NarL-dependent activation and Fis-dependent repression controls expression from the Escherichia coli yeaR and ogt promoters.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

27 October 2018

The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

27 October 2018

Multidrug resistance in Klebsiella pneumoniae MGH78578 and cloning of genes responsible for the resistance

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

27 October 2018

Nitrate and nitrite-mediated transcription antitermination control of nasF (nitrate assimilation) operon expression in Klebsiella pheumoniae M5al

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

27 October 2018

Identification of a nitrogen-regulated promoter controlling expression of Klebsiella pneumoniae urease genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

27 October 2018

The operon that encodes the sigma subunit of RNA polymerase also encodes ribosomal protein S21 and DNA primase in E. coli K12.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3415461

27 October 2018

Regulation of the homologous two-component systems KvgAS and KvhAS in Klebsiella pneumoniae CG43

1 reference

https://pubmed.ncbi.nlm.nih.gov/22912590

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Regulation of the Klebsiella pneumoniae Kpc fimbriae by the site-specific recombinase KpcI

1 reference

https://pubmed.ncbi.nlm.nih.gov/22912590

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

An aminoacyl tRNA synthetase binds to a specific DNA sequence and regulates its gene transcription

1 reference

https://pubmed.ncbi.nlm.nih.gov/22912590

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Fur-dependent MrkHI regulation of type 3 fimbriae in Klebsiella pneumoniae CG43

1 reference

https://pubmed.ncbi.nlm.nih.gov/22912590

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Suppression analysis of positive control mutants of NifA reveals two overlapping promoters for Klebsiella pneumoniae rpoN

1 reference

https://pubmed.ncbi.nlm.nih.gov/22912590

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Novel mode of transcription regulation by SdiA, an Escherichia coli homologue of the quorum-sensing regulator

1 reference

https://pubmed.ncbi.nlm.nih.gov/22912590

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Interaction of Escherichia coli RNA polymerase holoenzyme containing sigma 32 with heat shock promoters. DNase I footprinting and methylation protection

1 reference

https://pubmed.ncbi.nlm.nih.gov/22912590

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The Klebsiella pneumoniae nifJ promoter: analysis of promoter elements regulating activation by the NifA promoter

1 reference

https://pubmed.ncbi.nlm.nih.gov/22912590

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1371/JOURNAL.PGEN.1002867

1 reference

Europe PubMed Central

PubMed publication ID

1 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

1 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

1 August 2017

ResearchGate publication ID

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