(Q33530403)

27 July 2017

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title

Integration of 'omics' data: does it lead to new insights into host-microbe interactions? (English)

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27 July 2017

Kathleen Marchal

3

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author name string

Gwendoline Kint

1

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27 July 2017

Carolina Fierro

2

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27 July 2017

Jos Vanderleyden

4

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27 July 2017

Sigrid C J De Keersmaecker

5

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27 July 2017

1 February 2010

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27 July 2017

16

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based on heuristic

inferred from page(s)

published in

Future Microbiology

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27 July 2017

5

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27 July 2017

2

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27 July 2017

313-328

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Integration of omics data: how well does it work for bacteria?

27 July 2017

1 reference

Interactions of the intestinal epithelium with the pathogen and the indigenous microbiota: a three-way crosstalk

21 January 2018

1 reference

Examination of post-transcriptional regulations in prokaryotes by integrative biology.

21 January 2018

1 reference

Micros for microbes: non-coding regulatory RNAs in bacteria

21 January 2018

1 reference

Regulatory RNAs in bacteria

21 January 2018

1 reference

Host-microbe interaction systems biology: lifecycle transcriptomics and comparative genomics

21 January 2018

1 reference

Proteomics as a probe of microbial pathogenesis and its molecular boundaries

21 January 2018

1 reference

Defining the humoral immune response to infectious agents using high-density protein microarrays

21 January 2018

1 reference

Uncovering the interplay between CD8, CD4 and antibody responses to complex pathogens.

21 January 2018

1 reference

Custom design and analysis of high-density oligonucleotide bacterial tiling microarrays

21 January 2018

1 reference

The Listeria transcriptional landscape from saprophytism to virulence.

21 January 2018

1 reference

Comprehensive identification of Salmonella enterica serovar typhimurium genes required for infection of BALB/c mice

21 January 2018

1 reference

Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH)

21 January 2018

1 reference

Analysis of pools of targeted Salmonella deletion mutants identifies novel genes affecting fitness during competitive infection in mice

21 January 2018

1 reference

Signature-tagged mutagenesis: barcoding mutants for genome-wide screens

21 January 2018

1 reference

Deletion of tolA in Salmonella Typhimurium generates an attenuated strain with vaccine potential.

21 January 2018

1 reference

Applications of DNA tiling arrays for whole-genome analysis

21 January 2018

1 reference

ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments

21 January 2018

1 reference

DNA sampling: a method for probing protein binding at specific loci on bacterial chromosomes

21 January 2018

1 reference

Dissecting regulatory networks in host-pathogen interaction using chIP-on-chip technology

21 January 2018

1 reference

Extraction of transcription regulatory signals from genome-wide DNA-protein interaction data

21 January 2018

1 reference

RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.

21 January 2018

1 reference

DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics

21 January 2018

1 reference

A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli

21 January 2018

1 reference

Computational discovery of gene modules and regulatory networks

21 January 2018

1 reference

Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data

21 January 2018

1 reference

Inferring transcriptional modules from ChIP-chip, motif and microarray data

21 January 2018

1 reference

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

21 January 2018

1 reference

H-NS mediates the silencing of laterally acquired genes in bacteria

21 January 2018

1 reference

Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella

21 January 2018

1 reference

A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi

21 January 2018

1 reference

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

21 January 2018

1 reference

Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants

21 January 2018

1 reference

Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung

21 January 2018

1 reference

Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms

21 January 2018

1 reference

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

21 January 2018

1 reference

Detection of small RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatic tools

21 January 2018

1 reference

Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq

21 January 2018

1 reference

Deep sequencing of Salmonella RNA associated with heterologous Hfq proteins in vivo reveals small RNAs as a major target class and identifies RNA processing phenotypes

21 January 2018

1 reference

Computational approaches for the discovery of bacterial small RNAs

21 January 2018

1 reference

Small RNA gene identification and mRNA target predictions in bacteria

21 January 2018

1 reference

Identification of differentially expressed small non-coding RNAs in the legume endosymbiont Sinorhizobium meliloti by comparative genomics

21 January 2018

1 reference

High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs

21 January 2018

1 reference

sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes

21 January 2018

1 reference

A genetic approach for finding small RNAs regulators of genes of interest identifies RybC as regulating the DpiA/DpiB two-component system

21 January 2018

1 reference

The E. coli signal recognition particle is required for the insertion of a subset of inner membrane proteins

21 January 2018

1 reference

SOS response induction by beta-lactams and bacterial defense against antibiotic lethality

21 January 2018

1 reference

Phosphoproteomics in bacteria: towards a systemic understanding of bacterial phosphorylation networks

21 January 2018

1 reference

Insights from site-specific phosphoproteomics in bacteria

21 January 2018

1 reference

Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation

21 January 2018

1 reference

The Ser/Thr/Tyr phosphoproteome of Lactococcus lactis IL1403 reveals multiply phosphorylated proteins

21 January 2018

1 reference

Interactome data and databases: different types of protein interaction

21 January 2018

1 reference

A method for investigating protein-protein interactions related to salmonella typhimurium pathogenesis

21 January 2018

1 reference

Reconstruction of biochemical networks in microorganisms

21 January 2018

1 reference

Metabolic modeling of microbial strains in silico.

21 January 2018

1 reference

Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1

21 January 2018

1 reference

Genome-scale reconstruction of the metabolic network in Yersinia pestis, strain 91001.

21 January 2018

1 reference

GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism

21 January 2018

1 reference

Novel biological insights through metabolomics and 13C-flux analysis.

21 January 2018

1 reference

Mass spectrometry based metabolomics and enzymatic assays for functional genomics

21 January 2018

1 reference

Genome-scale models of bacterial metabolism: reconstruction and applications

21 January 2018

1 reference

Prediction of missing enzyme genes in a bacterial metabolic network. Reconstruction of the lysine-degradation pathway of Pseudomonas aeruginosa

21 January 2018

1 reference

Metabolic pathway alignment between species using a comprehensive and flexible similarity measure

21 January 2018

1 reference

Robust Salmonella metabolism limits possibilities for new antimicrobials.

21 January 2018

1 reference

System-level analysis of Salmonella metabolism during infection

21 January 2018

1 reference

Symbiotic gut microbes modulate human metabolic phenotypes

21 January 2018

1 reference

Systemic multicompartmental effects of the gut microbiome on mouse metabolic phenotypes.

21 January 2018

1 reference

Global phenotypic characterization of bacteria

21 January 2018

1 reference

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

21 January 2018

1 reference

The proteome of Salmonella Typhimurium grown under in vivo-mimicking conditions.

21 January 2018

1 reference

Global systems-level analysis of Hfq and SmpB deletion mutants in Salmonella: implications for virulence and global protein translation

21 January 2018

1 reference

Global analysis of small RNA and mRNA targets of Hfq

21 January 2018

1 reference

Genomic and metabolic studies of the impact of probiotics on a model gut symbiont and host

21 January 2018

1 reference

The protein network of bacterial motility

21 January 2018

1 reference

Regulation of gene expression by small non-coding RNAs: a quantitative view

21 January 2018

1 reference

Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation

21 January 2018

1 reference

Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target

21 January 2018

1 reference

Hydrophobic peptides: novel regulators within bacterial membrane

21 January 2018

1 reference

H-NS, the genome sentinel.

21 January 2018

1 reference

Roles of DNA adenine methylation in host-pathogen interactions: mismatch repair, transcriptional regulation, and more.

21 January 2018

1 reference

eSGA: E. coli synthetic genetic array analysis

21 January 2018

1 reference

Global and site-specific quantitative phosphoproteomics: principles and applications

21 January 2018

1 reference

Novel genetic tools for studying food-borne Salmonella

21 January 2018

1 reference

Proteomic investigation of the time course responses of RAW 264.7 macrophages to infection with Salmonella enterica

21 January 2018

1 reference

Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut

21 January 2018

1 reference

Identification of Lactobacillus plantarum genes that are induced in the gastrointestinal tract of mice

21 January 2018

1 reference

Identification of Mycobacterium tuberculosis RNAs synthesized in response to phagocytosis by human macrophages by selective capture of transcribed sequences (SCOTS)

21 January 2018

1 reference

Benefits and pitfalls of using microarrays to monitor bacterial gene expression during infection

21 January 2018

1 reference

Self-destructive cooperation mediated by phenotypic noise.

21 January 2018

1 reference

Systems biology: Functional analysis of natural microbial consortia using community proteomics

21 January 2018

1 reference

Gastrointestinal microbiology enters the metagenomics era.

21 January 2018

1 reference

Viruses manipulate the marine environment

21 January 2018

1 reference

CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaea

21 January 2018

1 reference

Multiple high-throughput analyses monitor the response of E. coli to perturbations

21 January 2018

1 reference

NCBI GEO: mining tens of millions of expression profiles--database and tools update

21 January 2018

1 reference

ArrayExpress--a public database of microarray experiments and gene expression profiles

21 January 2018

1 reference

Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles

21 January 2018

1 reference

The condition-dependent transcriptional network in Escherichia coli

21 January 2018

1 reference

The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo

21 January 2018

1 reference

Module networks revisited: computational assessment and prioritization of model predictions.

21 January 2018

1 reference

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

21 January 2018

1 reference

Bottlenecks and hubs in inferred networks are important for virulence in Salmonella typhimurium

21 January 2018

1 reference

Coordinated regulation of virulence during systemic infection of Salmonella enterica serovar Typhimurium

21 January 2018

1 reference

The model organism as a system: integrating 'omics' data sets

21 January 2018

1 reference

The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest.

21 January 2018

1 reference

Principles of transcriptional regulation and evolution of the metabolic system in E. coli

21 January 2018

1 reference

Gut microorganisms, mammalian metabolism and personalized health care

21 January 2018

1 reference

Synthetic biology: promises and challenges

21 January 2018

1 reference

Engineering the Salmonella type III secretion system to export spider silk monomers

21 January 2018

1 reference

The impact of synthetic biology on drug discovery

21 January 2018

1 reference

Synthetic biology: new engineering rules for an emerging discipline

21 January 2018

1 reference

Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period

21 January 2018

1 reference

An interactive regulatory network controls stress response in Bifidobacterium breve UCC2003.

21 January 2018

1 reference

Synergistic contribution of the Legionella pneumophila lqs genes to pathogen-host interactions

21 January 2018

1 reference

Genomic and proteomic analysis of the Alkali-Tolerance Response (AlTR) in Listeria monocytogenes 10403S

21 January 2018

1 reference

Insight into the core and variant exoproteomes of Listeria monocytogenes species by comparative subproteomic analysis.

21 January 2018

1 reference

Comparative proteome analysis of secretory proteins from pathogenic and nonpathogenic Listeria species

21 January 2018

1 reference

The GacS/GacA signal transduction system of Pseudomonas aeruginosa acts exclusively through its control over the transcription of the RsmY and RsmZ regulatory small RNAs

21 January 2018

1 reference

Delineation of the Salmonella enterica serovar Typhimurium HilA regulon through genome-wide location and transcript analysis

21 January 2018

1 reference

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

21 January 2018

1 reference

Analysis of the Salmonella typhimurium proteome through environmental response toward infectious conditions

21 January 2018

1 reference

From proteomics to systems biology of bacterial pathogens: Approaches, tools, and applications

21 January 2018

1 reference

The Serine/Threonine/Tyrosine Phosphoproteome of the Model BacteriumBacillus subtilis

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.2217/FMB.10.1

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27 July 2017

1 reference