GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity

[1]  Jizhong Zhou,et al.  Metagenomic analysis reveals a marked divergence in the structure of belowground microbial communities at elevated CO2. , 2010, Ecology letters.

[2]  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.

[3]  Keith A. Smith,et al.  Supporting Online Material Materials and Methods Som Text Figs. S1 to S3 Tables S1 to S6 References Elevated Co 2 Reduces Losses of Plant Diversity Caused by Nitrogen Deposition , 2022 .

[4]  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.

[5]  P. Reich,et al.  Biodiversity Under Global Change , 2009, Science.

[6]  Ye Deng,et al.  Microarray-based analysis of microbial functional diversity along an oil contamination gradient in oil field. , 2009, FEMS microbiology ecology.

[7]  Ye Deng,et al.  GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer. , 2009, Environmental microbiology.

[8]  Jizhong Zhou,et al.  Tracking Functional Guilds: “Dehalococcoides” spp. in European River Basins Contaminated with Hexachlorobenzene , 2009, Applied and Environmental Microbiology.

[9]  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.

[10]  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.

[11]  Jizhong Zhou Predictive microbial ecology , 2009, Microbial biotechnology.

[12]  Jizhong Zhou,et al.  Prokaryotic diversity, distribution, and insights into their role in biogeochemical cycling in marine basalts , 2008, The ISME Journal.

[13]  Charles T. Garten,et al.  Spatial scaling of functional gene diversity across various microbial taxa , 2008, Proceedings of the National Academy of Sciences.

[14]  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.

[15]  G. Fuchs,et al.  A 3-Hydroxypropionate/4-Hydroxybutyrate Autotrophic Carbon Dioxide Assimilation Pathway in Archaea , 2007, Science.

[16]  J. Kuever,et al.  Molecular Analysis of the Diversity of Sulfate-Reducing and Sulfur-Oxidizing Prokaryotes in the Environment, Using aprA as Functional Marker Gene , 2007, Applied and Environmental Microbiology.

[17]  H. Kasai,et al.  Comparison of gyrB gene sequences, 16S rRNA gene sequences and DNA-DNA hybridization in the Bacillus subtilis group. , 2007, International journal of systematic and evolutionary microbiology.

[18]  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.

[19]  Jizhong Zhou,et al.  Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect , 2007, The ISME Journal.

[20]  Baohua Gu,et al.  GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes , 2007, The ISME Journal.

[21]  Eoin L. Brodie,et al.  Urban aerosols harbor diverse and dynamic bacterial populations , 2007, Proceedings of the National Academy of Sciences.

[22]  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.

[23]  K. Gallagher,et al.  A framework for the use of genomics data at the EPA , 2006, Nature Biotechnology.

[24]  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.

[25]  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.

[26]  Sung-Keun Rhee,et al.  Improvement of Oligonucleotide Probe Design Criteria for Functional Gene Microarrays in Environmental Applications , 2006, Applied and Environmental Microbiology.

[27]  Lynda B. M. Ellis,et al.  The University of Minnesota Biocatalysis/Biodegradation Database: the first decade , 2005, Nucleic Acids Res..

[28]  Jizhong Zhou,et al.  Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation , 2005, Nucleic acids research.

[29]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[30]  S. Silver,et al.  A bacterial view of the periodic table: genes and proteins for toxic inorganic ions , 2005, Journal of Industrial Microbiology and Biotechnology.

[31]  Jizhong Zhou,et al.  Empirical Establishment of Oligonucleotide Probe Design Criteria , 2005, Applied and Environmental Microbiology.

[32]  T. Glenn,et al.  Elevated microbial tolerance to metals and antibiotics in metal-contaminated industrial environments. , 2005, Environmental science & technology.

[33]  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.

[34]  L. Bodrossy,et al.  Oligonucleotide microarrays in microbial diagnostics. , 2004, Current opinion in microbiology.

[35]  Jizhong Zhou,et al.  Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. , 2004, BioTechniques.

[36]  Bess B. Ward,et al.  Development and Testing of a DNA Macroarray To Assess Nitrogenase (nifH) Gene Diversity , 2004, Applied and Environmental Microbiology.

[37]  D. Nies,et al.  Efflux-mediated heavy metal resistance in prokaryotes. , 2003, FEMS microbiology reviews.

[38]  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.

[39]  A. Busch,et al.  l-Malyl-Coenzyme A Lyase/β-Methylmalyl-Coenzyme A Lyase from Chloroflexus aurantiacus, a Bifunctional Enzyme Involved in Autotrophic CO2 Fixation , 2002, Journal of bacteriology.

[40]  K. Schleifer,et al.  Oligonucleotide Microarray for 16S rRNA Gene-Based Detection of All Recognized Lineages of Sulfate-Reducing Prokaryotes in the Environment , 2002, Applied and Environmental Microbiology.

[41]  L. Øvreås,et al.  Prokaryotic Diversity--Magnitude, Dynamics, and Controlling Factors , 2002, Science.

[42]  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.

[43]  Domy C. Adriano,et al.  Trace Elements in Terrestrial Environments: Biogeochemistry, Bioavailability, and Risks of Metals , 2001 .

[44]  P. Reich,et al.  [Letters to nature] , 1975, Nature.

[45]  D. Adriano Trace elements in terrestrial environments , 2001 .

[46]  Lukas Wagner,et al.  A Greedy Algorithm for Aligning DNA Sequences , 2000, J. Comput. Biol..

[47]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[48]  S. Harayama,et al.  Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB, rpoD and 16S rRNA genes. , 1998, International journal of systematic bacteriology.

[49]  W. Whitman,et al.  Prokaryotes: the unseen majority. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[50]  Sean R. Eddy,et al.  Profile hidden Markov models , 1998, Bioinform..

[51]  José Costa,et al.  PicoGreen quantitation of DNA: effective evaluation of samples pre- or post-PCR , 1996, Nucleic Acids Res..

[52]  J. Tiedje,et al.  DNA recovery from soils of diverse composition , 1996, Applied and environmental microbiology.

[53]  S. Silver Bacterial resistances to toxic metal ions--a review. , 1996, Gene.

[54]  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, Applied and environmental microbiology.

[55]  S. Ragsdale,et al.  Enzymology of the acetyl-CoA pathway of CO2 fixation. , 1991, Critical reviews in biochemistry and molecular biology.

[56]  H. Well Childhood Lead Poisoning from the MMWR of August 19, 1988: Summary of the Report to Congress by the Agency for Toxic Substances and Disease Registry (ATSDR) , 1989 .

[57]  L. Ljungdahl The autotrophic pathway of acetate synthesis in acetogenic bacteria. , 1986, Annual review of microbiology.

[58]  S. Benkovic,et al.  Folates and pterins , 1984 .

[59]  B. Buchanan,et al.  New cyclic process for carbon assimilation by a photosynthetic bacterium. , 1966, Science.

[60]  M. Calvin Quantum conversion in photosynthesis. , 1961, Journal of theoretical biology.

[61]  P. Sassone-Corsi,et al.  Computational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil , 2022 .