Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities
暂无分享,去创建一个
Ye Deng | Zhili He | Jizhong Zhou | Jizhong Zhou | Zhili He | Ye Deng | J. V. Nostrand | Joy D. Van Nostrand
[1] Jizhong Zhou,et al. Functional gene diversity of soil microbial communities from five oil-contaminated fields in China , 2011, The ISME Journal.
[2] Jizhong Zhou,et al. GeoChip-Based Analysis of the Functional Gene Diversity and Metabolic Potential of Microbial Communities in Acid Mine Drainage , 2010, Applied and Environmental Microbiology.
[3] P. D’haeseleer,et al. Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria , 2010, Science.
[4] Jizhong Zhou,et al. Functional Biogeography as Evidence of Gene Transfer in Hypersaline Microbial Communities , 2010, PloS one.
[5] Jizhong Zhou,et al. Metagenomic analysis reveals a marked divergence in the structure of belowground microbial communities at elevated CO2. , 2010, Ecology letters.
[6] Christopher L. Hemme,et al. GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity , 2010, The ISME Journal.
[7] P. Bork,et al. A human gut microbial gene catalogue established by metagenomic sequencing , 2010, Nature.
[8] Jizhong Zhou,et al. Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation , 2010, The ISME Journal.
[9] Jizhong Zhou,et al. Applying GeoChip analysis to disparate microbial communities , 2010 .
[10] Jizhong Zhou,et al. Microbial functional structure of Montastraea faveolata, an important Caribbean reef-building coral, differs between healthy and yellow-band diseased colonies. , 2010, Environmental microbiology.
[11] James R. Cole,et al. Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment , 2009, The ISME Journal.
[12] Jizhong,et al. Microbial Communities and Functional Genes Associated , 2010 .
[13] E. E. L O G A N,et al. Geochip-Based Functional Gene Analysis of Anodophilic Communities in Microbial Electrolysis Cells under Different Operational Modes , 2010 .
[14] Jizhong Zhou,et al. Development of a Common Oligonucleotide Reference Standard for Microarray Data Normalization and Comparison across Different Microbial Communities , 2009, Applied and Environmental Microbiology.
[15] Ye Deng,et al. Microarray-based analysis of microbial functional diversity along an oil contamination gradient in oil field. , 2009, FEMS microbiology ecology.
[16] Ye Deng,et al. GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer. , 2009, Environmental microbiology.
[17] Jizhong Zhou,et al. Tracking Functional Guilds: “Dehalococcoides” spp. in European River Basins Contaminated with Hexachlorobenzene , 2009, Applied and Environmental Microbiology.
[18] Zhili He,et al. Functional gene array-based analysis of microbial community structure in groundwaters with a gradient of contaminant levels. , 2009, Environmental science & technology.
[19] Jizhong Zhou,et al. Microarray-based functional gene analysis of soil microbial communities during ozonation and biodegradation of crude oil. , 2009, Chemosphere.
[20] Jizhong Zhou,et al. GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent , 2009, Proceedings of the National Academy of Sciences.
[21] Jizhong Zhou,et al. Different influences of DNA purity indices and quantity on PCR-based DGGE and functional gene microarray in soil microbial community study , 2009, Applied Microbiology and Biotechnology.
[22] Jizhong Zhou,et al. Prokaryotic diversity, distribution, and insights into their role in biogeochemical cycling in marine basalts , 2008, The ISME Journal.
[23] Xue-duan Liu,et al. Micro-array based whole-genome hybridization for detection of microorganisms in acid mine drainage and bioleaching systems , 2009 .
[24] Ludwig Eichinger,et al. Large scale multiplex PCR improves pathogen detection by DNA microarrays , 2009, BMC Microbiology.
[25] Jizhong Zhou,et al. Development and application of functional gene arrays for microbial community analysis , 2008 .
[26] Jizhong Zhou,et al. Design and analysis of mismatch probes for long oligonucleotide microarrays , 2008, BMC Genomics.
[27] P. Schenk,et al. Isolation and analysis of mRNA from environmental microbial communities. , 2008, Journal of microbiological methods.
[28] Martin Dufva,et al. An inexpensive and simple method for thermally stable immobilization of DNA on an unmodified glass surface: UV linking of poly(T)10-poly(C)10-tagged DNA probes. , 2008, BioTechniques.
[29] Charles T. Garten,et al. Spatial scaling of functional gene diversity across various microbial taxa , 2008, Proceedings of the National Academy of Sciences.
[30] Jizhong Zhou,et al. Microarray-Based Characterization of Microbial Community Functional Structure and Heterogeneity in Marine Sediments from the Gulf of Mexico , 2008, Applied and Environmental Microbiology.
[31] Zhili He,et al. Empirical Evaluation of a New Method for Calculating Signal-to-Noise Ratio for Microarray Data Analysis , 2008, Applied and Environmental Microbiology.
[32] R. Knight,et al. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex , 2008, Nature Methods.
[33] Amanda B. Herzog,et al. In Situ-Synthesized Virulence and Marker Gene Biochip for Detection of Bacterial Pathogens in Water , 2008, Applied and Environmental Microbiology.
[34] Jizhong Zhou,et al. In situ bioreduction of uranium (VI) to submicromolar levels and reoxidation by dissolved oxygen. , 2007, Environmental science & technology.
[35] G. Casella,et al. Pyrosequencing enumerates and contrasts soil microbial diversity , 2007, The ISME Journal.
[36] Jizhong Zhou,et al. Development and evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in Acid Mine Drainages and bioleaching systems. , 2007, Journal of microbiological methods.
[37] Jizhong Zhou,et al. Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs) , 2007, The ISME Journal.
[38] Jizhong Zhou,et al. Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect , 2007, The ISME Journal.
[39] Baohua Gu,et al. GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes , 2007, The ISME Journal.
[40] James M Tiedje,et al. Multiscale responses of microbial life to spatial distance and environmental heterogeneity in a patchy ecosystem , 2007, Proceedings of the National Academy of Sciences.
[41] Jonathan P. Bollback,et al. The Use of Coded PCR Primers Enables High-Throughput Sequencing of Multiple Homolog Amplification Products by 454 Parallel Sequencing , 2007, PloS one.
[42] J. Fuscoe,et al. Elimination of laboratory ozone leads to a dramatic improvement in the reproducibility of microarray gene expression measurements , 2007, BMC biotechnology.
[43] Jizhong Zhou,et al. Microarray-based analysis of changes in diversity of microbial genes involved in organic carbon decomposition following land use/cover changes. , 2007, FEMS microbiology letters.
[44] T. Hurek,et al. A nifH-based Oligonucleotide Microarray for Functional Diagnostics of Nitrogen-fixing Microorganisms , 2007, Microbial Ecology.
[45] Gary L. Andersen,et al. High-Density Universal 16S rRNA Microarray Analysis Reveals Broader Diversity than Typical Clone Library When Sampling the Environment , 2007, Microbial Ecology.
[46] Terry J. Gentry,et al. Microarray-Based Analysis of Microbial Community RNAs by Whole-Community RNA Amplification , 2006, Applied and Environmental Microbiology.
[47] Jizhong Zhou,et al. Microbial Diversity and Bioremediation of a Hydrocarbon-Contaminated Aquifer (Vega Baja, Puerto Rico) , 2006, International journal of environmental research and public health.
[48] Eoin L Brodie,et al. Application of a High-Density Oligonucleotide Microarray Approach To Study Bacterial Population Dynamics during Uranium Reduction and Reoxidation , 2006, Applied and Environmental Microbiology.
[49] Murray Wolinsky,et al. Response to Comment by Volkov et al. on "Computational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil" , 2006, Science.
[50] Jizhong Zhou,et al. Microarray Applications in Microbial Ecology Research , 2006, Microbial Ecology.
[51] Christopher W. Schadt,et al. Microarray-Based Analysis of Subnanogram Quantities of Microbial Community DNAs by Using Whole-Community Genome Amplification , 2006, Applied and Environmental Microbiology.
[52] Berit E E Cleven,et al. Identification and Characterization of Bacterial Pathogens Causing Bloodstream Infections by DNA Microarray , 2006, Journal of Clinical Microbiology.
[53] Jo Handelsman,et al. Toward a Census of Bacteria in Soil , 2006, PLoS Comput. Biol..
[54] Jizhong Zhou,et al. Pilot-scale in situ bioremedation of uranium in a highly contaminated aquifer. 2. Reduction of u(VI) and geochemical control of u(VI) bioavailability. , 2006, Environmental science & technology.
[55] Levente Bodrossy,et al. mRNA-Based Parallel Detection of Active Methanotroph Populations by Use of a Diagnostic Microarray , 2006, Applied and Environmental Microbiology.
[56] Sung-Keun Rhee,et al. Improvement of Oligonucleotide Probe Design Criteria for Functional Gene Microarrays in Environmental Applications , 2006, Applied and Environmental Microbiology.
[57] John Bunge,et al. Predicting microbial species richness. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[58] Yiqi Luo,et al. Elevated CO2 stimulates net accumulations of carbon and nitrogen in land ecosystems: a meta-analysis. , 2006, Ecology.
[59] C. Boivin-Masson,et al. Microarray-Based Detection and Typing of the Rhizobium Nodulation Gene nodC: Potential of DNA Arrays To Diagnose Biological Functions of Interest , 2005, Applied and Environmental Microbiology.
[60] L. Bodrossy,et al. High-sensitivity, polymerase chain reaction-free detection of microorganisms and their functional genes using 70-mer oligonucleotide diagnostic microarray. , 2005, Analytical biochemistry.
[61] Jizhong Zhou,et al. Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation , 2005, Nucleic acids research.
[62] James R. Knight,et al. Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.
[63] Jizhong Zhou,et al. Use of Microarrays with Different Probe Sizes for Monitoring Gene Expression , 2005, Applied and Environmental Microbiology.
[64] Jizhong Zhou,et al. Empirical Establishment of Oligonucleotide Probe Design Criteria , 2005, Applied and Environmental Microbiology.
[65] T. Myers,et al. Active mixing during hybridization improves the accuracy and reproducibility of microarray results. , 2005, BioTechniques.
[66] Jizhong Zhou,et al. Fabrication of DNA microarrays on nanoengineered polymeric ultrathin film prepared by self-assembly of polyelectrolyte multilayers. , 2004, Langmuir : the ACS journal of surfaces and colloids.
[67] Jizhong Zhou,et al. Detection of Genes Involved in Biodegradation and Biotransformation in Microbial Communities by Using 50-Mer Oligonucleotide Microarrays , 2004, Applied and Environmental Microbiology.
[68] N. Stralis-Pavese,et al. Optimization of diagnostic microarray for application in analysing landfill methanotroph communities under different plant covers. , 2004, Environmental microbiology.
[69] Jizhong Zhou,et al. Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. , 2004, BioTechniques.
[70] G. Steward,et al. Fingerprinting Diazotroph Communities in the Chesapeake Bay by Using a DNA Macroarray , 2004, Applied and Environmental Microbiology.
[71] Bess B. Ward,et al. Development and Testing of a DNA Macroarray To Assess Nitrogenase (nifH) Gene Diversity , 2004, Applied and Environmental Microbiology.
[72] Vincent J. Denef,et al. Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities. , 2003, Environmental microbiology.
[73] D. Call,et al. Identifying Antimicrobial Resistance Genes with DNA Microarrays , 2003, Antimicrobial Agents and Chemotherapy.
[74] S. Brooks,et al. Geochemical reactions and dynamics during titration of a contaminated groundwater with high uranium, aluminum, and calcium , 2003 .
[75] N. Stralis-Pavese,et al. Development and validation of a diagnostic microbial microarray for methanotrophs. , 2003, Environmental microbiology.
[76] D. Nies,et al. Efflux-mediated heavy metal resistance in prokaryotes. , 2003, FEMS microbiology reviews.
[77] H. Bürgmann,et al. mRNA Extraction and Reverse Transcription-PCR Protocol for Detection of nifH Gene Expression by Azotobacter vinelandii in Soil , 2003, Applied and Environmental Microbiology.
[78] R. Fulthorpe,et al. Monitoring Gene Expression in Mixed Microbial Communities by Using DNA Microarrays , 2003, Applied and Environmental Microbiology.
[79] B. Ward,et al. Oligonucleotide Microarray for the Study of Functional Gene Diversity in the Nitrogen Cycle in the Environment , 2003, Applied and Environmental Microbiology.
[80] T. Lueders,et al. Evaluation of PCR Amplification Bias by Terminal Restriction Fragment Length Polymorphism Analysis of Small-Subunit rRNA and mcrA Genes by Using Defined Template Mixtures of Methanogenic Pure Cultures and Soil DNA Extracts , 2003, Applied and Environmental Microbiology.
[81] Thomas P. Curtis,et al. Estimating prokaryotic diversity and its limits , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[82] Dorothea K. Thompson,et al. Challenges in applying microarrays to environmental studies. , 2002, Current opinion in biotechnology.
[83] Lawrence O. Ticknor,et al. Empirical and Theoretical Bacterial Diversity in Four Arizona Soils , 2002, Applied and Environmental Microbiology.
[84] Angela Relógio,et al. Optimization of oligonucleotide-based DNA microarrays. , 2002, Nucleic acids research.
[85] L. Øvreås,et al. Prokaryotic Diversity--Magnitude, Dynamics, and Controlling Factors , 2002, Science.
[86] J. Tiedje,et al. Quantitative Detection of Microbial Genes by Using DNA Microarrays , 2002, Applied and Environmental Microbiology.
[87] Dorothea K. Thompson,et al. Development and Evaluation of Functional Gene Arrays for Detection of Selected Genes in the Environment , 2001, Applied and Environmental Microbiology.
[88] Jizhong Zhou,et al. Simultaneous Recovery of RNA and DNA from Soils and Sediments , 2001, Applied and Environmental Microbiology.
[89] P. Reich,et al. [Letters to nature] , 1975, Nature.
[90] O. Larsson,et al. Silanized nucleic acids: a general platform for DNA immobilization. , 2000, Nucleic acids research.
[91] Dietrich H. Nies,et al. Regulation of the cnr Cobalt and Nickel Resistance Determinant from Ralstonia sp. Strain CH34 , 2000, Journal of bacteriology.
[92] M. Mergeay,et al. Regulation of the cnr Cobalt and Nickel Resistance Determinant of Ralstonia eutropha (Alcaligenes eutrophus) CH34 , 2000, Journal of bacteriology.
[93] Lukas Wagner,et al. A Greedy Algorithm for Aligning DNA Sequences , 2000, J. Comput. Biol..
[94] J. Lawton. Are there general laws in ecology , 1999 .
[95] Philip Hugenholtz,et al. Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity , 1998, Journal of bacteriology.
[96] W. Whitman,et al. Prokaryotes: the unseen majority. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[97] Sean R. Eddy,et al. Profile hidden Markov models , 1998, Bioinform..
[98] M H Saier,et al. A family of gram-negative bacterial outer membrane factors that function in the export of proteins, carbohydrates, drugs and heavy metals from gram-negative bacteria. , 1997, FEMS microbiology letters.
[99] S. Clark,et al. Detection and measurement of PCR bias in quantitative methylation analysis of bisulphite-treated DNA. , 1997, Nucleic acids research.
[100] D A Stahl,et al. Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology , 1997, Applied and environmental microbiology.
[101] J. Tiedje,et al. DNA recovery from soils of diverse composition , 1996, Applied and environmental microbiology.
[102] S. Giovannoni,et al. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR , 1996, Applied and environmental microbiology.
[103] Ronald W. Davis,et al. Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray , 1995, Science.
[104] S. Harayama,et al. PCR Amplification and Direct Sequencing of gyrB Genes with Universal Primers and Their Application to the Detection and Taxonomic Analysis of Pseudomonas putida Strains , 1995 .
[105] K. Schleifer,et al. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. , 1995, Microbiological reviews.
[106] J. Thompson,et al. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.
[107] M. Saier,et al. Two novel families of bacterial membrane proteins concerned with nodulation, cell division and transport , 1994, Molecular microbiology.
[108] Rune Halvorsen Økland,et al. Canonical Correspondence Analysis with variation partitioning: some comments and an application , 1994 .
[109] H. Liesegang,et al. Characterization of the inducible nickel and cobalt resistance determinant cnr from pMOL28 of Alcaligenes eutrophus CH34 , 1993, Journal of bacteriology.
[110] K. Wilson,et al. Amplification of bacterial 16S ribosomal DNA with polymerase chain reaction , 1990, Journal of clinical microbiology.
[111] C. Braak. Canonical Correspondence Analysis: A New Eigenvector Technique for Multivariate Direct Gradient Analysis , 1986 .