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@ARTICLE{He:9598,
      author       = {He, Z. and Deng, Y. and Van Nostrand, J.D. and Tu, Q. and
                      Xu, M. and Hemme, C.L. and Li, X. and Wu, L. and Gentry,
                      T.J. and Yin, Y. and Liebich, J. and Hazen, T.C. and Zhou,
                      J.},
      title        = {{G}eo{C}hip 3.0 as a high-throughput tool for analyzing
                      microbial community composition, structure and functional
                      activity},
      journal      = {The ISME journal},
      volume       = {4},
      issn         = {1751-7362},
      address      = {Basingstoke},
      publisher    = {Nature Publishing Group},
      reportid     = {PreJuSER-9598},
      pages        = {1167 - 1179},
      year         = {2010},
      note         = {This work is supported by the Genomics: GTL program through
                      the Virtual Institute of Microbial Stress and Survival
                      (VIMSS; http://vimss.lbl.gov) as part of contract no.
                      DE-AC02-05CH11231 between the US Department of Energy and
                      Lawrence Berkeley National Laboratory, the United States
                      Department of Agriculture (Project 2007-35319-18305) through
                      NSF-USDA Microbial Observatories Program, the Environmental
                      Remediation Science Program, the Oklahoma Bioengery Center
                      (OBC) of State of Oklahoma, and the Oklahoma Applied
                      Research Support (OARS), Oklahoma Center for the Advancement
                      of Science and Technology (OCAST), the State of Oklahoma.},
      abstract     = {A new generation of functional gene arrays (FGAs; GeoChip
                      3.0) has been developed, with approximately 28 000 probes
                      covering approximately 57 000 gene variants from 292
                      functional gene families involved in carbon, nitrogen,
                      phosphorus and sulfur cycles, energy metabolism, antibiotic
                      resistance, metal resistance and organic contaminant
                      degradation. GeoChip 3.0 also has several other distinct
                      features, such as a common oligo reference standard (CORS)
                      for data normalization and comparison, a software package
                      for data management and future updating and the gyrB gene
                      for phylogenetic analysis. Computational evaluation of probe
                      specificity indicated that all designed probes would have a
                      high specificity to their corresponding targets.
                      Experimental analysis with synthesized oligonucleotides and
                      genomic DNAs showed that only $0.0036-0.025\%$
                      false-positive rates were observed, suggesting that the
                      designed probes are highly specific under the experimental
                      conditions examined. In addition, GeoChip 3.0 was applied to
                      analyze soil microbial communities in a multifactor
                      grassland ecosystem in Minnesota, USA, which showed that the
                      structure, composition and potential activity of soil
                      microbial communities significantly changed with the plant
                      species diversity. As expected, GeoChip 3.0 is a
                      high-throughput powerful tool for studying microbial
                      community functional structure, and linking microbial
                      communities to ecosystem processes and functioning.},
      keywords     = {Bacteria: classification / Bacteria: genetics / Biota /
                      Computational Biology: methods / DNA Gyrase: genetics / Drug
                      Resistance, Bacterial / Environmental Microbiology /
                      Metabolic Networks and Pathways: genetics / Metagenomics:
                      methods / Microarray Analysis: methods / Oligonucleotide
                      Array Sequence Analysis: methods / Oligonucleotide Probes:
                      genetics / Phylogeny / Sensitivity and Specificity /
                      Software / Oligonucleotide Probes (NLM Chemicals) / DNA
                      Gyrase (NLM Chemicals) / J (WoSType)},
      cin          = {ICG-4},
      ddc          = {570},
      cid          = {I:(DE-Juel1)VDB793},
      pnm          = {Terrestrische Umwelt},
      pid          = {G:(DE-Juel1)FUEK407},
      shelfmark    = {Ecology / Microbiology},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:20428223},
      UT           = {WOS:000281663700015},
      doi          = {10.1038/ismej.2010.46},
      url          = {https://juser.fz-juelich.de/record/9598},
}