4.6 Review

Detecting unknown sequences with DNA microarrays: explorative probe design strategies

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biotechnology & Applied Microbiology

Accessing the Soil Metagenome for Studies of Microbial Diversity

Tom O. Delmont et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2011)

Article Biotechnology & Applied Microbiology

Microarray Analysis and Barcoded Pyrosequencing Provide Consistent Microbial Profiles Depending on the Source of Human Intestinal Samples

Bartholomeus van den Bogert et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2011)

Article Biochemical Research Methods

HiSpOD: probe design for functional DNA microarrays

Eric Dugat-Bony et al.

BIOINFORMATICS (2011)

Article Biochemistry & Molecular Biology

DDBJ progress report

Eli Kaminuma et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biochemistry & Molecular Biology

The European Nucleotide Archive

Rasko Leinonen et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biochemistry & Molecular Biology

GenBank

Dennis A. Benson et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Gastroenterology & Hepatology

Dysbiosis of Fecal Microbiota in Crohn's Disease Patients as Revealed by a Custom Phylogenetic Microarray

Seungha Kang et al.

INFLAMMATORY BOWEL DISEASES (2010)

Review Genetics & Heredity

Computational solutions to large-scale data management and analysis

Eric E. Schadt et al.

NATURE REVIEWS GENETICS (2010)

Article Ecology

Bacterial Diversity of Weathered Terrestrial Icelandic Volcanic Glasses

Laura C. Kelly et al.

MICROBIAL ECOLOGY (2010)

Article Multidisciplinary Sciences

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

Sebastian Fraune et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Review Biotechnology & Applied Microbiology

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

Seong Woon Roh et al.

TRENDS IN BIOTECHNOLOGY (2010)

Article Biotechnology & Applied Microbiology

High-Throughput Quantitative Analysis of the Human Intestinal Microbiota with a Phylogenetic Microarray

Oleg Paliy et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2009)

Article Biotechnology & Applied Microbiology

Bacterial Diversity Analysis of Huanglongbing Pathogen-Infected Citrus, Using PhyloChip Arrays and 16S rRNA Gene Clone Library Sequencing

Uma Shankar Sagaram et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2009)

Article Biotechnology & Applied Microbiology

Prokaryotic Community Structure and Sulfate Reducer Activity in Water from High-Temperature Oil Reservoirs with and without Nitrate Treatment

Antje Gittel et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2009)

Review Biotechnology & Applied Microbiology

Achievements and new knowledge unraveled by metagenomic approaches

Carola Simon et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2009)

Article Ecology

Selective progressive response of soil microbial community to wild oat roots

Kristen M. DeAngelis et al.

ISME JOURNAL (2009)

Article Biochemical Research Methods

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

Ingrid H. Franke-Whittle et al.

JOURNAL OF MICROBIOLOGICAL METHODS (2009)

Article Biochemistry & Molecular Biology

Model-based probe set optimization for high-performance microarrays

German Gaston Leparc et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Biochemistry & Molecular Biology

Petabyte-scale innovations at the European Nucleotide Archive

Guy Cochrane et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Biochemistry & Molecular Biology

An evaluation of custom microarray applications: the oligonucleotide design challenge

Sophie Lemoine et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Biochemistry & Molecular Biology

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

Marco Severgnini et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Biochemistry & Molecular Biology

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

J. R. Cole et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Multidisciplinary Sciences

Avian Incubation Inhibits Growth and Diversification of Bacterial Assemblages on Eggs

Matthew D. Shawkey et al.

PLOS ONE (2009)

Article Microbiology

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

Martina Kyselkova et al.

ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY (2008)

Article Biotechnology & Applied Microbiology

Novel Microarray design strategy to study complex bacterial communities

Antoine Huyghe et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2008)

Article Biotechnology & Applied Microbiology

Accumulation of trans C18:1 Fatty Acids in the Rumen after Dietary Algal Supplementation Is Associated with Changes in the Butyrivibrio Community

Charlotte Boeckaert et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2008)

Article Ecology

The rational exploration of microbial diversity

Christopher Quince et al.

ISME JOURNAL (2008)

Article Biochemistry & Molecular Biology

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

Hinanit Koltai et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Metallurgy & Metallurgical Engineering

Development and application of functional gene arrays for microbial community analysis

Z. L. He et al.

TRANSACTIONS OF NONFERROUS METALS SOCIETY OF CHINA (2008)

Article Biochemistry & Molecular Biology

SILVA:: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

Elmar Pruesse et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biochemical Research Methods

Direct selection of human genomic loci by microarray hybridization

Thomas J. Albert et al.

NATURE METHODS (2007)

Article Biochemical Research Methods

PhylArray: phylogenetic probe design algorithm for microarray

Cecile Militon et al.

BIOINFORMATICS (2007)

Article Biochemical Research Methods

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

Shengzhong Feng et al.

BIOINFORMATICS (2007)

Article Multidisciplinary Sciences

Urban aerosols harbor diverse and dynamic bacterial populations

Eoin L. Brodie et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Review Biotechnology & Applied Microbiology

DNA microarray technology for the microbiologist: an overview

Armin Ehrenreich

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2006)

Article Multidisciplinary Sciences

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

Luisa A. Marcelino et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Biotechnology & Applied Microbiology

Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation

Eoin L. Brodie et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2006)

Review Ecology

Microarray applications in microbial ecology research

T. J. Gentry et al.

MICROBIAL ECOLOGY (2006)

Article Biochemical Research Methods

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

Alexander Schliep et al.

BIOINFORMATICS (2006)

Review Biotechnology & Applied Microbiology

Homogeneous versus heterogeneous probes for microbial ecological microarrays

Jin-Woo Bae et al.

TRENDS IN BIOTECHNOLOGY (2006)

Article Biotechnology & Applied Microbiology

Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB

T. Z. DeSantis et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2006)

Article Biotechnology & Applied Microbiology

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

J Liebich et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2006)

Review Biochemistry & Molecular Biology

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

Jianping Xu

MOLECULAR ECOLOGY (2006)

Review Medical Laboratory Technology

Highly parallel microbial diagnostics using oligonucleotide microarrays

A Loy et al.

CLINICA CHIMICA ACTA (2006)

Article Biochemistry & Molecular Biology

Rapid quantitative profiling of complex microbial populations

C Palmer et al.

NUCLEIC ACIDS RESEARCH (2006)

Review Biochemical Research Methods

Fabrication of high quality microarrays

M Dufva

BIOMOLECULAR ENGINEERING (2005)

Article Biochemical Research Methods

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

WH Chung et al.

BIOINFORMATICS (2005)

Article Biochemistry & Molecular Biology

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

R Wernersson et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Microbiology

Oligonucleotide microarray for identification of Enterococcus species

A Lehner et al.

FEMS MICROBIOLOGY LETTERS (2005)

Article Biochemical Research Methods

YODA: selecting signature oligonucleotides

EK Nordberg

BIOINFORMATICS (2005)

Article Biochemical Research Methods

GoArrays: highly dynamic and efficient microarray probe design

S Rimour et al.

BIOINFORMATICS (2005)

Article Biochemical Research Methods

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

DP Chandler et al.

BIOTECHNIQUES (2005)

Article Biotechnology & Applied Microbiology

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

Y Yu et al.

BIOTECHNOLOGY AND BIOENGINEERING (2005)

Article Biotechnology & Applied Microbiology

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

A Loy et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2005)

Article Microbiology

Oligo-chip based detection of tick-borne bacteria

D Blaskovic et al.

FEMS MICROBIOLOGY LETTERS (2005)

Article Biochemical Research Methods

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

J Letowski et al.

JOURNAL OF MICROBIOLOGICAL METHODS (2004)

Article Biochemistry & Molecular Biology

ARB:: a software environment for sequence data

W Ludwig et al.

NUCLEIC ACIDS RESEARCH (2004)

Article Biochemical Research Methods

ROSO: optimizing oligonucleotide probes for microarrays

N Reymond et al.

BIOINFORMATICS (2004)

Article Biotechnology & Applied Microbiology

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

SK Rhee et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2004)

Article Biotechnology & Applied Microbiology

Development of a universal microarray based on the ligation detection reaction and 16S rRNA gene polymorphism to target diversity of cyanobacteria

B Castiglioni et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2004)

Article Biotechnology & Applied Microbiology

Nucleic acid amplification strategies for DNA microarray-based pathogen detection

GJ Vora et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2004)

Article Biochemistry & Molecular Biology

Mfold web server for nucleic acid folding and hybridization prediction

M Zuker

NUCLEIC ACIDS RESEARCH (2003)

Article Microbiology

Development and validation of a diagnostic microbial microarray for methanotrophs

L Bodrossy et al.

ENVIRONMENTAL MICROBIOLOGY (2003)

Article Biochemistry & Molecular Biology

CODEHOP (COnsensus-DEgenerate hybrid oligonucleotide primer) PCR primer design

TM Rose et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Biochemistry & Molecular Biology

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

SJ Emrich et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Biochemistry & Molecular Biology

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

JM Rouillard et al.

NUCLEIC ACIDS RESEARCH (2003)

Review Microbiology

Microarrays for bacterial detection and microbial community analysis

JH Zhou

CURRENT OPINION IN MICROBIOLOGY (2003)

Article Biochemical Research Methods

Selection of oligonucleotide probes for protein coding sequences

XW Wang et al.

BIOINFORMATICS (2003)

Article Biotechnology & Applied Microbiology

Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment

G Taroncher-Oldenburg et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2003)

Article Multidisciplinary Sciences

Estimating prokaryotic diversity and its limits

TP Curtis et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Review Microbiology

Microbial diversity and function in soil:: from genes to ecosystems

V Torsvik et al.

CURRENT OPINION IN MICROBIOLOGY (2002)

Article Biochemistry & Molecular Biology

Optimization of oligonucleotide-based DNA microarrays -: art. no. e51

A Relógio et al.

NUCLEIC ACIDS RESEARCH (2002)

Article Biotechnology & Applied Microbiology

High-density microarray of small-subunit ribosomal DNA probes

KH Wilson et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2002)

Article Biochemical Research Methods

Selection of optimal DNA oligos for gene expression arrays

FG Li et al.

BIOINFORMATICS (2001)

Article Biotechnology & Applied Microbiology

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

TR Hughes et al.

NATURE BIOTECHNOLOGY (2001)

Article Biochemistry & Molecular Biology

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

MD Kane et al.

NUCLEIC ACIDS RESEARCH (2000)

Article Multidisciplinary Sciences

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

MLT Lee et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2000)

Article Biochemistry & Molecular Biology

Thermodynamic parameters for DNA sequences with dangling ends

S Bommarito et al.

NUCLEIC ACIDS RESEARCH (2000)