• Publications
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Molecular ecological network analyses
TLDR
A novel mathematical and bioinformatics framework to construct ecological association networks named molecular ecological networks (MENs) through Random Matrix Theory (RMT)-based methods is described, which provides powerful tools to elucidate network interactions in microbial communities and their responses to environmental changes. Expand
A proposed genus boundary for the prokaryotes based on genomic insights.
TLDR
A comprehensive genomic survey indicated that the POCP can serve as a robust genomic index for establishing the genus boundary for prokaryotic groups and integration of whole-genome data into the current taxonomy system can provide comprehensive information. Expand
Nitrite Reductase Genes (nirK andnirS) as Functional Markers To Investigate Diversity of Denitrifying Bacteria in Pacific Northwest Marine Sediment Communities
  • Gesche Braker, Jizhong Zhou, Liyou Wu, Allan H. Devol, J. Tiedje
  • Biology, Medicine
  • Applied and Environmental Microbiology
  • 1 May 2000
TLDR
Findings show a very high diversity of nirsequences within small samples and that these novel nirclusters, some very divergent from known sequences, are not known in cultivated denitrifiers. Expand
Stochastic Community Assembly: Does It Matter in Microbial Ecology?
  • Jizhong Zhou, D. Ning
  • Biology, Medicine
  • Microbiology and Molecular Biology Reviews
  • 11 October 2017
TLDR
Both stochastic and deterministic components embedded in various ecological processes, including selection, dispersal, diversification, and drift are described. Expand
Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill
TLDR
The draft genome included genes for chemotaxis, motility and nutrient acquisition strategies that were also identified in the metagenomes and metatranscriptomes, which point towards a rapid response of members of the Oceanospirillales to aliphatic hydrocarbons in the deep sea. Expand
GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes
TLDR
This is the first comprehensive microarray currently available for studying biogeochemical processes and functional activities of microbial communities important to human health, agriculture, energy, global climate change, ecosystem management, and environmental cleanup and restoration. Expand
Spatial and Resource Factors Influencing High Microbial Diversity in Soil
TLDR
Examination of soil samples taken from the surface, vadose zone, and saturated subsurface using a small-subunit rRNA-based cloning approach found that spatial isolation could limit competition in surface soils, thereby supporting the high diversity and a uniform community structure. Expand
Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO2
TLDR
A novel random matrix theory (RMT)-based conceptual framework is described to discern phylogenetic molecular ecological networks of microbial communities based on high-throughput metagenomic sequencing data, among the first to document that the network interactions among different phylogenetic populations in soil microbial communities were substantially changed by a global change such as an elevated CO2 level. Expand
Microbial mediation of carbon-cycle feedbacks to climate warming
A study based on a long-term manipulation experiment in a grassland ecosystem describes the microbial mechanisms controlling feedbacks to carbon and nutrient cycling under warming. The findingsExpand
Evaluation of PCR-Generated Chimeras, Mutations, and Heteroduplexes with 16S rRNA Gene-Based Cloning
  • Xiaoyun Qiu, Liyou Wu, +4 authors Jizhong Zhou
  • Biology, Medicine
  • Applied and Environmental Microbiology
  • 1 February 2001
TLDR
PCR artifacts were significantly reduced by using AmpliTaq and fewer PCR cycles (fewer than 20 cycles), and the heteroduplexes could be effectively removed from PCR products prior to cloning by polyacrylamide gel purification or T7 endonuclease I digestion. Expand
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