Detecting unknown sequences with DNA microarrays: explorative probe design strategies (Q37927182)

25 August 2017

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title

Detecting unknown sequences with DNA microarrays: explorative probe design strategies (English)

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25 August 2017

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Eric Dugat-Bony

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25 August 2017

Eric Peyretaillade

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25 August 2017

Nicolas Parisot

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25 August 2017

Corinne Biderre-Petit

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25 August 2017

Faouzi Jaziri

5

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25 August 2017

David Hill

6

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25 August 2017

Sébastien Rimour

7

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25 August 2017

Pierre Peyret

8

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25 August 2017

5 September 2011

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Environmental Microbiology

25 August 2017

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14

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2

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25 August 2017

356-371

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describes a project that uses

25 August 2017

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Direct selection of human genomic loci by microarray hybridization

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PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database

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Homogeneous versus heterogeneous probes for microbial ecological microarrays

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Thermodynamic parameters for DNA sequences with dangling ends

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Design of long oligonucleotide probes for functional gene detection in a microbial community.

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Selective progressive response of soil microbial community to wild oat roots

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High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment

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Fabrication of high quality microarrays

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HiSpOD: probe design for functional DNA microarrays.

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DNA microarray technology for the microbiologist: an overview

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PROBEmer: A web-based software tool for selecting optimal DNA oligos

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A fast and flexible approach to oligonucleotide probe design for genomes and gene families

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Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa

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Design and development of the ANAEROCHIP microarray for investigation of methanogenic communities.

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In an early branching metazoan, bacterial colonization of the embryo is controlled by maternal antimicrobial peptides

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Computational improvements reveal great bacterial diversity and high metal toxicity in soil

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Microarray applications in microbial ecology research

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Prokaryotic community structure and sulfate reducer activity in water from high-temperature oil reservoirs with and without nitrate treatment

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Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer

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Novel microarray design strategy to study complex bacterial communities

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Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays

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Dysbiosis of fecal microbiota in Crohn's disease patients as revealed by a custom phylogenetic microarray

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DNA microarray detection of nitrifying bacterial 16S rRNA in wastewater treatment plant samples

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Bacterial diversity of weathered terrestrial Icelandic volcanic glasses.

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Evidence of multiple Treponema phylotypes involved in bovine digital dermatitis as shown by 16S rRNA gene analysis and fluorescence in situ hybridization.

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Specificity of DNA microarray hybridization: characterization, effectors and approaches for data correction

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Development of a 16S rRNA gene-based prototype microarray for the detection of selected actinomycetes genera.

21 January 2018

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Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations

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The European Nucleotide Archive

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An evaluation of custom microarray applications: the oligonucleotide design challenge.

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Model-based probe set optimization for high-performance microarrays

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Designing better probes: effect of probe size, mismatch position and number on hybridization in DNA oligonucleotide microarrays

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Selection of optimal DNA oligos for gene expression arrays

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Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation.

21 January 2018

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Improvement of oligonucleotide probe design criteria for functional gene microarrays in environmental applications

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High density synthetic oligonucleotide arrays

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Highly parallel microbial diagnostics using oligonucleotide microarrays.

21 January 2018

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Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment

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16S rRNA gene-based oligonucleotide microarray for environmental monitoring of the betaproteobacterial order "Rhodocyclales"

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ARB: a software environment for sequence data

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Accurately quantifying low-abundant targets amid similar sequences by revealing hidden correlations in oligonucleotide microarray data

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1 reference

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PhylArray: phylogenetic probe design algorithm for microarray

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Improved group-specific PCR primers for denaturing gradient gel electrophoresis analysis of the genetic diversity of complex microbial communities

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Composition of microbial communities in hexachlorocyclohexane (HCH) contaminated soils from Spain revealed with a habitat-specific microarray

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YODA: selecting signature oligonucleotides

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A molecular view of microbial diversity and the biosphere

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High-throughput quantitative analysis of the human intestinal microbiota with a phylogenetic microarray

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Rapid quantitative profiling of complex microbial populations

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Application and validation of DNA microarrays for the 16S rRNA-based analysis of marine bacterioplankton.

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Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted

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Oligonucleotide microarrays: widely applied--poorly understood.

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The rational exploration of microbial diversity

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Microbial and mineralogical characterizations of soils collected from the deep biosphere of the former Homestake gold mine, South Dakota

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Investigation of microbial populations in the extremely metal-contaminated Coeur d'Alene River sediments

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Optimization of oligonucleotide-based DNA microarrays.

21 January 2018

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Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays

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GoArrays: highly dynamic and efficient microarray probe design.

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Comparing microarrays and next-generation sequencing technologies for microbial ecology research.

21 January 2018

1 reference

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Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences

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1 reference

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CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design

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OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach

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Order-specific 16S rRNA-targeted oligonucleotide probes for (hyper)thermophilic archaea and bacteria.

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Bacterial diversity analysis of Huanglongbing pathogen-infected citrus, using PhyloChip arrays and 16S rRNA gene clone library sequencing

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1 reference

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Rhizosphere bacterial communities associated with disease suppressiveness stages of take-all decline in wheat monoculture

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Computational solutions to large-scale data management and analysis

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Decoding non-unique oligonucleotide hybridization experiments of targets related by a phylogenetic tree

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ORMA: a tool for identification of species-specific variations in 16S rRNA gene and oligonucleotides design

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Avian incubation inhibits growth and diversification of bacterial assemblages on eggs

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Microbial diversity and function in soil: from genes to ecosystems

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Nucleic acid amplification strategies for DNA microarray-based pathogen detection

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Unravelling microbial communities with DNA-microarrays: challenges and future directions

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Selection of oligonucleotide probes for protein coding sequences

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PhyloChip hybridization uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa

21 January 2018

1 reference

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OligoWiz 2.0--integrating sequence feature annotation into the design of microarray probes.

21 January 2018

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Prokaryotes: the unseen majority

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High-density microarray of small-subunit ribosomal DNA probes

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Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya

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Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances

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Environmental microarray analyses of Antarctic soil microbial communities

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1 reference

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Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction.

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Microarrays for bacterial detection and microbial community analysis

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Mfold web server for nucleic acid folding and hybridization prediction

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1 reference

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Taking arrays from the lab to the field: trying to make sense of the unknown

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1 reference

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Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities

21 January 2018

1 reference

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16S rRNA gene-based phylogenetic microarray for simultaneous identification of members of the genusBurkholderia

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1 reference

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Oligonucleotide microarray for identification ofEnterococcusspecies

21 January 2018

1 reference

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10.1111/J.1462-2920.2011.02559.X

21 January 2018

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25 August 2017

1 reference