Published in Nucleic Acids Res on October 24, 2005
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Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach. J Bacteriol (2006) 1.68
Microarray applications in microbial ecology research. Microb Ecol (2006) 1.64
The signature of maternal rearing in the methylome in rhesus macaque prefrontal cortex and T cells. J Neurosci (2012) 1.51
Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics (2007) 1.45
Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: a genome and transcriptome approach. BMC Genomics (2008) 1.43
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A high-throughput pipeline for designing microarray-based pathogen diagnostic assays. BMC Bioinformatics (2008) 1.20
An evaluation of custom microarray applications: the oligonucleotide design challenge. Nucleic Acids Res (2009) 1.19
Optimization and clinical validation of a pathogen detection microarray. Genome Biol (2007) 1.18
Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough. J Bacteriol (2007) 1.14
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Model-based probe set optimization for high-performance microarrays. Nucleic Acids Res (2008) 1.08
Development of a common oligonucleotide reference standard for microarray data normalization and comparison across different microbial communities. Appl Environ Microbiol (2009) 1.02
In silico microarray probe design for diagnosis of multiple pathogens. BMC Genomics (2008) 0.99
A general framework for designing and validating oligomer-based DNA microarrays and its application to Clostridium acetobutylicum. Appl Environ Microbiol (2007) 0.96
Correlation of genomic and physiological traits of thermoanaerobacter species with biofuel yields. Appl Environ Microbiol (2011) 0.96
Expectations, validity, and reality in gene expression profiling. J Clin Epidemiol (2010) 0.93
Profile of secreted hydrolases, associated proteins, and SlpA in Thermoanaerobacterium saccharolyticum during the degradation of hemicellulose. Appl Environ Microbiol (2014) 0.90
chipD: a web tool to design oligonucleotide probes for high-density tiling arrays. Nucleic Acids Res (2010) 0.88
The unique probe selector: a comprehensive web service for probe design and oligonucleotide arrays. BMC Bioinformatics (2008) 0.88
Analysis of endocrine disruption in Southern California coastal fish using an aquatic multispecies microarray. Environ Health Perspect (2008) 0.87
Custom design and analysis of high-density oligonucleotide bacterial tiling microarrays. PLoS One (2009) 0.86
The Thermoanaerobacter glycobiome reveals mechanisms of pentose and hexose co-utilization in bacteria. PLoS Genet (2011) 0.86
New model for electron flow for sulfate reduction in Desulfovibrio alaskensis G20. Appl Environ Microbiol (2013) 0.85
Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarrays. BMC Genomics (2008) 0.83
Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays. BMC Bioinformatics (2010) 0.83
Design and analysis of mismatch probes for long oligonucleotide microarrays. BMC Genomics (2008) 0.82
The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities. ISME J (2013) 0.81
UPS 2.0: unique probe selector for probe design and oligonucleotide microarrays at the pangenomic/genomic level. BMC Genomics (2010) 0.81
Development and application of bovine and porcine oligonucleotide arrays with protein-based annotation. J Biomed Biotechnol (2010) 0.81
Molecular analysis of endocrine disruption in hornyhead turbot at wastewater outfalls in southern california using a second generation multi-species microarray. PLoS One (2013) 0.80
Multipurpose instantaneous microarray detection of acute encephalitis causing viruses and their expression profiles. Curr Microbiol (2012) 0.80
Genome-scale resources for Thermoanaerobacterium saccharolyticum. BMC Syst Biol (2015) 0.79
BOND: Basic OligoNucleotide Design. BMC Bioinformatics (2013) 0.78
Development of HuMiChip for functional profiling of human microbiomes. PLoS One (2014) 0.78
Strain/species-specific probe design for microbial identification microarrays. Appl Environ Microbiol (2013) 0.77
Isolation and characterization of four gram-positive nickel-tolerant microorganisms from contaminated sediments. Microb Ecol (2007) 0.77
An in vitro selection scheme for oligonucleotide probes to discriminate between closely related DNA sequences. Nucleic Acids Res (2007) 0.76
Use of functional gene arrays for elucidating in situ biodegradation. Front Microbiol (2012) 0.75
Diagnostic microarray for 14 water and foodborne pathogens using a flatbed scanner. J Microbiol Methods (2017) 0.75
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PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis. Bioinformatics (2002) 2.65
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Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. ISME J (2012) 2.45
Current production and metal oxide reduction by Shewanella oneidensis MR-1 wild type and mutants. Appl Environ Microbiol (2007) 2.34
Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification. Appl Environ Microbiol (2006) 2.31
Global transcriptome analysis of the heat shock response of Shewanella oneidensis. J Bacteriol (2004) 2.28
Transcriptomic and proteomic characterization of the Fur modulon in the metal-reducing bacterium Shewanella oneidensis. J Bacteriol (2004) 2.23
GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity. ISME J (2010) 2.21
Transcriptional and proteomic analysis of a ferric uptake regulator (fur) mutant of Shewanella oneidensis: possible involvement of fur in energy metabolism, transcriptional regulation, and oxidative stress. Appl Environ Microbiol (2002) 2.14
Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl Environ Microbiol (2004) 2.11
Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume. ISME J (2011) 2.10
Metagenomic analysis reveals a marked divergence in the structure of belowground microbial communities at elevated CO2. Ecol Lett (2010) 1.95
Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. Proc Natl Acad Sci U S A (2005) 1.93
Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. Biotechniques (2004) 1.74
Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community. ISME J (2010) 1.71
Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach. J Bacteriol (2006) 1.68
Constructing gene co-expression networks and predicting functions of unknown genes by random matrix theory. BMC Bioinformatics (2007) 1.57
GeoChip 4: a functional gene-array-based high-throughput environmental technology for microbial community analysis. Mol Ecol Resour (2014) 1.52
Isolation and characterization of metal-reducing thermoanaerobacter strains from deep subsurface environments of the Piceance Basin, Colorado. Appl Environ Microbiol (2002) 1.52
Molecular diversity and characterization of nitrite reductase gene fragments (nirK and nirS) from nitrate- and uranium-contaminated groundwater. Environ Microbiol (2003) 1.49
Microarray-based analysis of microbial community RNAs by whole-community RNA amplification. Appl Environ Microbiol (2006) 1.49
Functional genomic analysis of three nitrogenase isozymes in the photosynthetic bacterium Rhodopseudomonas palustris. J Bacteriol (2005) 1.49
Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect. ISME J (2007) 1.48
Alkaline anaerobic respiration: isolation and characterization of a novel alkaliphilic and metal-reducing bacterium. Appl Environ Microbiol (2004) 1.48
Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: a genome and transcriptome approach. BMC Genomics (2008) 1.43
Molecular diversity of denitrifying genes in continental margin sediments within the oxygen-deficient zone off the Pacific coast of Mexico. Appl Environ Microbiol (2003) 1.43
Shifts in soil microorganisms in response to warming are consistent across a range of Antarctic environments. ISME J (2011) 1.42
Responses of the functional structure of soil microbial community to livestock grazing in the Tibetan alpine grassland. Glob Chang Biol (2012) 1.42
Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs). ISME J (2007) 1.41
Global transcriptome analysis of the cold shock response of Shewanella oneidensis MR-1 and mutational analysis of its classical cold shock proteins. J Bacteriol (2006) 1.40
GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent. Proc Natl Acad Sci U S A (2009) 1.38
Microarray transcription profiling of a Shewanella oneidensis etrA mutant. J Bacteriol (2002) 1.38
Probing regulon of ArcA in Shewanella oneidensis MR-1 by integrated genomic analyses. BMC Genomics (2008) 1.38
Pilot-scale in situ bioremedation of uranium in a highly contaminated aquifer. 2. Reduction of u(VI) and geochemical control of u(VI) bioavailability. Environ Sci Technol (2006) 1.38
Functional molecular ecological networks. MBio (2010) 1.37
Molecular dynamics of the Shewanella oneidensis response to chromate stress. Mol Cell Proteomics (2006) 1.35
The electron transfer system of syntrophically grown Desulfovibrio vulgaris. J Bacteriol (2009) 1.35
Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough, inferred from global transcriptional analysis. Appl Environ Microbiol (2006) 1.35
Global transcriptional profiling of Shewanella oneidensis MR-1 during Cr(VI) and U(VI) reduction. Appl Environ Microbiol (2005) 1.33
First investigation of the microbiology of the deepest layer of ocean crust. PLoS One (2010) 1.33
Microbial community analysis of a coastal salt marsh affected by the Deepwater Horizon oil spill. PLoS One (2012) 1.32
Stochasticity, succession, and environmental perturbations in a fluidic ecosystem. Proc Natl Acad Sci U S A (2014) 1.31
Transcriptome analysis of Shewanella oneidensis MR-1 in response to elevated salt conditions. J Bacteriol (2005) 1.31
Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris Hildenborough. Appl Environ Microbiol (2007) 1.31
Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes. BMC Evol Biol (2004) 1.30
Impacts on microbial communities and cultivable isolates from groundwater contaminated with high levels of nitric acid-uranium waste. FEMS Microbiol Ecol (2005) 1.29
Improvement of oligonucleotide probe design criteria for functional gene microarrays in environmental applications. Appl Environ Microbiol (2006) 1.28
Functional gene diversity of soil microbial communities from five oil-contaminated fields in China. ISME J (2010) 1.28
In situ bioreduction of uranium (VI) to submicromolar levels and reoxidation by dissolved oxygen. Environ Sci Technol (2007) 1.27
Empirical evaluation of a new method for calculating signal-to-noise ratio for microarray data analysis. Appl Environ Microbiol (2008) 1.27
Microbial functional structure of Montastraea faveolata, an important Caribbean reef-building coral, differs between healthy and yellow-band diseased colonies. Environ Microbiol (2009) 1.26
Sequencing of multiple clostridial genomes related to biomass conversion and biofuel production. J Bacteriol (2010) 1.25
Microarray-based characterization of microbial community functional structure and heterogeneity in marine sediments from the Gulf of Mexico. Appl Environ Microbiol (2008) 1.25
Microbial communities in contaminated sediments, associated with bioremediation of uranium to submicromolar levels. Appl Environ Microbiol (2008) 1.24
Prokaryotic diversity, distribution, and insights into their role in biogeochemical cycling in marine basalts. ISME J (2008) 1.23
Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere. ISME J (2011) 1.23
Field and laboratory studies on the bioconversion of coal to methane in the San Juan Basin. FEMS Microbiol Ecol (2012) 1.22
Transcriptome profiling of Shewanella oneidensis gene expression following exposure to acidic and alkaline pH. J Bacteriol (2006) 1.22
Bacterial community succession during in situ uranium bioremediation: spatial similarities along controlled flow paths. ISME J (2008) 1.21
Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation. ISME J (2010) 1.19
Molecular ecological network analyses. BMC Bioinformatics (2012) 1.19
Phylogenetic molecular ecological network of soil microbial communities in response to elevated CO2. MBio (2011) 1.18
Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site. BMC Genomics (2007) 1.18
Shewanella loihica sp. nov., isolated from iron-rich microbial mats in the Pacific Ocean. Int J Syst Evol Microbiol (2006) 1.18
Function of periplasmic hydrogenases in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. J Bacteriol (2007) 1.18
Stochastic assembly leads to alternative communities with distinct functions in a bioreactor microbial community. MBio (2013) 1.17
How sulphate-reducing microorganisms cope with stress: lessons from systems biology. Nat Rev Microbiol (2011) 1.16
Applications of functional gene microarrays for profiling microbial communities. Curr Opin Biotechnol (2012) 1.15
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Characterization of the central metabolic pathways in Thermoanaerobacter sp. strain X514 via isotopomer-assisted metabolite analysis. Appl Environ Microbiol (2009) 1.14
Development and evaluation of microarray-based whole-genome hybridization for detection of microorganisms within the context of environmental applications. Environ Sci Technol (2004) 1.14
Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough. J Bacteriol (2007) 1.14
Fruit and soil quality of organic and conventional strawberry agroecosystems. PLoS One (2010) 1.13
Energy metabolism in Desulfovibrio vulgaris Hildenborough: insights from transcriptome analysis. Antonie Van Leeuwenhoek (2007) 1.13
Physiological roles of ArcA, Crp, and EtrA and their interactive control on aerobic and anaerobic respiration in Shewanella oneidensis. PLoS One (2010) 1.13