List of works by Zhili He

A Slow-Release Substrate Stimulates Groundwater Microbial Communities for Long-Term in Situ Cr(VI) Reduction.

scientific article published on 2 April 2015

A comprehensive insight into functional profiles of free-living microbial community responses to a toxic Akashiwo sanguinea bloom

scientific article published on 05 October 2016

An integrated insight into the response of sedimentary microbial communities to heavy metal contamination.

scientific article published on 22 September 2015

Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris Hildenborough

scientific article

Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: a genome and transcriptome approach

scientific article

Assessing the microbial community and functional genes in a vertical soil profile with long-term arsenic contamination

scientific article

Biogeographic patterns of soil diazotrophic communities across six forests in the North America.

scientific article

Cas9-based tools for targeted genome editing and transcriptional control.

scientific article published on 03 January 2014

Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution

scientific article published on 11 April 2013

Combined genomics and experimental analyses of respiratory characteristics of Shewanella putrefaciens W3-18-1

scientific article published on 28 June 2013

Comparative metagenomics reveals impact of contaminants on groundwater microbiomes

scientific article published on 31 October 2015

Construction and evaluation of a Clostridium thermocellum ATCC 27405 whole-genome oligonucleotide microarray.

scientific article published on April 2007

Contribution of mobile genetic elements toDesulfovibrio vulgarisgenome plasticity

scientific article published on 01 September 2009

Correction to GeoChip-Based Analysis of Microbial Functional Gene Diversity in a Landfill Leachate-Contaminated Aquifer

scientific article published on 5 February 2013

Deletion of the Desulfovibrio vulgaris carbon monoxide sensor invokes global changes in transcription

scientific article

Design and analysis of mismatch probes for long oligonucleotide microarrays

scientific article

Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities

article

Development of HuMiChip for functional profiling of human microbiomes

scientific article

Development of a common oligonucleotide reference standard for microarray data normalization and comparison across different microbial communities.

scientific article

Development of functional gene microarrays for microbial community analysis.

scientific article

Development of highly fluorescent silica nanoparticles chemically doped with organic dye for sensitive DNA microarray detection.

scientific article

Differential Regulation of the Two Ferrochelatase Paralogues in Shewanella loihica PV-4 in Response to Environmental Stresses

scientific article

Distinct responses of soil microbial communities to elevated CO2 and O3 in a soybean agro-ecosystem

scientific article (publication date: March 2014)

Diversity, function and assembly of mangrove root-associated microbial communities at a continuous fine-scale

scientific article published on 12 November 2020

Dockerin-containing protease inhibitor protects key cellulosomal cellulases from proteolysis in Clostridium cellulolyticum.

scientific article published on 7 January 2014

Dramatic Increases of Soil Microbial Functional Gene Diversity at the Treeline Ecotone of Changbai Mountain

scientific article

Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction.

scientific article published on 10 April 2015

Dynamics of Microbial Community Composition and Function duringIn SituBioremediation of a Uranium-Contaminated Aquifer

article

Dynamics of microbial community composition and function during in situ bioremediation of a uranium-contaminated aquifer

scientific article

Ecogenomics reveals metals and land-use pressures on microbial communities in the waterways of a megacity

scientific article published on 21 January 2015

Efficient Genome Editing in Clostridium cellulolyticum via CRISPR-Cas9 Nickase

scientific article published on 24 April 2015

Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C4 agroecosystem.

scientific article

Elevated CO₂ influences microbial carbon and nitrogen cycling

scientific article (publication date: 29 May 2013)

Elevated carbon dioxide accelerates the spatial turnover of soil microbial communities

scientific article published on 28 September 2015

Elevated carbon dioxide alters the structure of soil microbial communities

scientific article

Elevated nitrate enriches microbial functional genes for potential bioremediation of complexly contaminated sediments

scientific article published in 2015

Elevated nitrate enriches microbial functional genes for potential bioremediation of complexly contaminated sediments.

scientific article

Empirical establishment of oligonucleotide probe design criteria

scientific article

Empirical evaluation of a new method for calculating signal-to-noise ratio for microarray data analysis

scientific article

Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough, inferred from global transcriptional analysis

scientific article

Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibrio vulgaris

scientific article published on 15 September 2020

Function of periplasmic hydrogenases in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough

scientific article published on 29 June 2007

Functional Gene Array-Based Analysis of Microbial Community Structure in Groundwaters with a Gradient of Contaminant Levels

article

Functional biogeography as evidence of gene transfer in hypersaline microbial communities

scientific article

Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough

scientific article published on 9 December 2011

Functional gene array-based analysis of microbial communities in heavy metals-contaminated lake sediments

article

Functional gene arrays-based analysis of fecal microbiomes in patients with liver cirrhosis.

scientific article

Functional gene composition, diversity and redundancy in microbial stream biofilm communities

scientific article

Functional gene differences in soil microbial communities from conventional, low-input, and organic farmlands

scientific article

Functional gene diversity of soil microbial communities from five oil-contaminated fields in China.

scientific article

Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect

scientific article published on 24 May 2007

Functional potential of soil microbial communities in the maize rhizosphere

scientific article

Functional responses of methanogenic archaea to syntrophic growth

scientific article

Fungal communities respond to long-term CO2 elevation by community reassembly

scientific article

Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site

scientific article

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

scientific article

GeoChip 4: a functional gene-array-based high-throughput environmental technology for microbial community analysis

scientific article

GeoChip as a metagenomics tool to analyze the microbial gene diversity along an elevation gradient

scientific article

GeoChip profiling of microbial community in response to global changes simulated by soil transplant and cropping.

scientific article

GeoChip-Based Analysis of Microbial Functional Gene Diversity in a Landfill Leachate-Contaminated Aquifer

scientific article published on 23 May 2012

GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer

scientific article published on 14 July 2009

GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent

scientific article

GeoChip-based analysis of the functional gene diversity and metabolic potential of microbial communities in acid mine drainage.

scientific article

GeoChip-based analysis of the functional gene diversity and metabolic potential of soil microbial communities of mangroves

scientific article published on 8 November 2012

GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes.

scientific article

Geochip-based analysis of microbial communities in alpine meadow soils in the Qinghai-Tibetan plateau

scientific article

Geochip-based functional gene analysis of anodophilic communities in microbial electrolysis cells under different operational modes

scientific article

Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough

scientific article

Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation

scientific article

High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats

scientific article

How sulphate-reducing microorganisms cope with stress: lessons from systems biology

scientific article

HuMiChip2 for strain level identification and functional profiling of human microbiomes

scientific article

Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere.

scientific article

Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough

scientific article published in October 2010

Illumina sequencing-based analysis of free-living bacterial community dynamics during an Akashiwo sanguine bloom in Xiamen sea, China.

scientific article

Impact of elevated nitrate on sulfate-reducing bacteria: a comparative study of Desulfovibrio vulgaris

scientific article published on 6 May 2010

Impacts of Shewanella oneidensis c-type cytochromes on aerobic and anaerobic respiration

scientific article published on July 2010

Impacts of the Three Gorges Dam on microbial structure and potential function

scientific article

Improvement of cellulose catabolism in Clostridium cellulolyticum by sporulation abolishment and carbon alleviation.

scientific article published on 20 February 2014

Influence of geogenic factors on microbial communities in metallogenic Australian soils.

scientific article

Isolation and characterization of Shigella flexneri G3, capable of effective cellulosic saccharification under mesophilic conditions.

scientific article

Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community

scientific article

Loss of microbial diversity in soils is coincident with reductions in some specialized functions.

scientific article published on 15 January 2014

Metagenomic analysis reveals a marked divergence in the structure of belowground microbial communities at elevated CO2.

scientific article published on 23 March 2010

Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community

scientific article

Microarray-based analysis of microbial functional diversity along an oil contamination gradient in oil field

scientific article published on 28 August 2009

Microbial Community Dynamics and Activity Link to Indigo Production from Indole in Bioaugmented Activated Sludge Systems

scientific article published on 15 September 2015

Microbial Mechanisms Mediating Increased Soil C Storage under Elevated Atmospheric N Deposition.

scientific article published in April 2013

Microbial biogeochemistry of Boiling Springs Lake: a physically dynamic, oligotrophic, low-pH geothermal ecosystem.

scientific article

Microbial communities and functional genes associated with soil arsenic contamination and the rhizosphere of the arsenic-hyperaccumulating plant Pteris vittata L

scientific article

Microbial community composition and functions are resilient to metal pollution along two forest soil gradients

scientific article published on 5 December 2014

Microbial electricity generation enhances decabromodiphenyl ether (BDE-209) degradation

scientific article

Microbial functional gene diversity with a shift of subsurface redox conditions during In Situ uranium reduction

scientific article

Microbial functional genes commonly respond to elevated carbon dioxide

scientific article published on 29 August 2020

Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume

scientific article

Microbial mechanisms mediating increased soil C storage under elevated atmospheric N deposition

scientific article

Microevolution from shock to adaptation revealed strategies improving ethanol tolerance and production in Thermoanaerobacter

scientific article published on 22 July 2013

Molecular ecological network analyses.

scientific article

More functional genes and convergent overall functional patterns detected by geochip in phenanthrene-spiked soils

article

Natural bacterial communities serve as quantitative geochemical biosensors

scientific article published on 12 May 2015

Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation

scientific article published on 14 July 2015

Over 150 years of long-term fertilization alters spatial scaling of microbial biodiversity

scientific article published on 7 April 2015

Pellicle formation in Shewanella oneidensis.

scientific article

Phylogenetic and functional diversity of microbial communities associated with subsurface sediments of the Sonora Margin, Guaymas Basin.

scientific article

Phylogenetic molecular ecological network of soil microbial communities in response to elevated CO2

scientific article (publication date: 2011)

Predicting taxonomic and functional structure of microbial communities in acid mine drainage.

scientific article published on 04 March 2016

Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris.

scientific article

Rate-specific responses of prokaryotic diversity and structure to nitrogen deposition in the Leymus chinensis steppe

article

Recovery of temperate Desulfovibrio vulgaris bacteriophage using a novel host strain

scientific article published in November 2006

Response of Desulfovibrio vulgaris to alkaline stress

scientific article

Responses of Aromatic-Degrading Microbial Communities to Elevated Nitrate in Sediments.

scientific article published on 21 September 2015

Responses of Bacterial Communities to Simulated Climate Changes in Alpine Meadow Soil of the Qinghai-Tibet Plateau.

scientific article

Responses of microbial communities to single-walled carbon nanotubes in phenol wastewater treatment systems

scientific article published on 13 March 2015

Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation

scientific article published on 18 March 2010

Responses of the functional structure of soil microbial community to livestock grazing in the Tibetan alpine grassland

scientific article published on 27 November 2012

Saliva microbiota carry caries-specific functional gene signatures

scientific article

Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach

scientific article

Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation.

scientific article

Sequencing of multiple clostridial genomes related to biomass conversion and biofuel production

scientific article

Shifts in the phylogenetic structure and functional capacity of soil microbial communities follow alteration of native tussock grassland ecosystems

scholarly article by Steven A. Wakelin et al published February 2013 in Soil Biology and Biochemistry

Shifts of functional gene representation in wheat rhizosphere microbial communities under elevated ozone

scientific article published on 15 November 2012

Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in Alaska

scientific article

Soil Amoebae Affect Iron and Chromium Reduction through Preferential Predation between Two Metal-Reducing Bacteria

scientific article published in 2022

Soil microbial community responses to a decade of warming as revealed by comparative metagenomics

scientific article

Spatial Distribution, Bioconversion and Ecological Risk of PCBs and PBDEs in the Surface Sediment of Contaminated Urban Rivers: A Nationwide Study in China

scientific article published in 2021

Stochasticity, succession, and environmental perturbations in a fluidic ecosystem

scientific article

Strain/species identification in metagenomes using genome-specific markers

scientific article published on 12 February 2014

Strain/species-specific probe design for microbial identification microarrays

scientific article published on 07 June 2013

StressChip as a high-throughput tool for assessing microbial community responses to environmental stresses

scientific article

Successional Trajectories of Rhizosphere Bacterial Communities over Consecutive Seasons

scientific article published on 4 August 2015

Temperature mediates continental-scale diversity of microbes in forest soils.

scientific article

The Diversity and Co-occurrence Patterns of N₂-Fixing Communities in a CO₂-Enriched Grassland Ecosystem

scientific article published on 18 August 2015

The Thermoanaerobacter glycobiome reveals mechanisms of pentose and hexose co-utilization in bacteria

scientific article

The complicated substrates enhance the microbial diversity and zinc leaching efficiency in sphalerite bioleaching system.

scientific article published on 13 August 2015

The electron transfer system of syntrophically grown Desulfovibrio vulgaris

scientific article published on 06 July 2009

The interactive effects of soil transplant into colder regions and cropping on soil microbiology and biogeochemistry

scientific article

The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages

scientific article published on 6 June 2016

The microbe-mediated mechanisms affecting topsoil carbon stock in Tibetan grasslands

scientific article published on 17 February 2015

The microbial gene diversity along an elevation gradient of the Tibetan grassland.

scientific article

The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system

scientific article

The shifts of sediment microbial community phylogenetic and functional structures during chromium (VI) reduction

scientific article published on 16 September 2016

Thermal disruption of soil bacterial assemblages decreases diversity and assemblage similarity

scientific article published in 2019

Transcriptome analysis of pellicle formation of Shewanella oneidensis

scientific article

Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: carbon and energy flow contribute to the distinct biofilm growth state

scientific article

Ultrasound-mediated DNA transformation in thermophilic gram-positive anaerobes.

scientific article

Use of functional gene arrays for elucidating in situ biodegradation.

scientific article

Use of microarrays with different probe sizes for monitoring gene expression.

scientific article

Warming Alters Expressions of Microbial Functional Genes Important to Ecosystem Functioning

scientific article

Whole-genome sequencing reveals novel insights into sulfur oxidation in the extremophile Acidithiobacillus thiooxidans.

scientific article

Widespread distribution of soluble di-iron monooxygenase (SDIMO) genes in Arctic groundwater impacted by 1,4-dioxane

scientific article published on 16 August 2013

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