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List of works by Ye Deng

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

scientific article published on 2 April 2015

A general framework for quantitatively assessing ecological stochasticity

scientific article published on 07 August 2019

A multiplayer game: species of Clostridium, Acinetobacter, and Pseudomonas are responsible for the persistence of antibiotic resistance genes in manure-treated soils.

scientific article

ARDEP, a Rapid Degenerate Primer Design Pipeline Based on k-mers for Amplicon Microbiome Studies

scientific article published on 17 August 2020

ARGA, a pipeline for primer evaluation on antibiotic resistance genes

scientific article published on 03 May 2019

Adaptive shifts of bacterioplankton communities in response to nitrogen enrichment in a highly polluted river

scientific article published on 07 November 2018

Analyses of the influencing factors of soil microbial functional gene diversity in tropical rainforest based on GeoChip 5.0.

scientific article published on 15 July 2015

Analysis of the functional gene structure and metabolic potential of microbial community in high arsenic groundwater

scientific article published on 21 June 2017

Annual Removal of Aboveground Plant Biomass Alters Soil Microbial Responses to Warming

scientific article

Assembly Patterns of the Rhizosphere Microbiome Along the Longitudinal Root Axis of Maize (<i>Zea mays</i> L.).

scientific article published on 12 February 2021

Assessment of microbial α-diversity in one meter squared topsoil

scientific article published in 2021

Author Correction: Continental scale structuring of forest and soil diversity via functional traits

scientific article published on 01 November 2019

Author Correction: Global diversity and biogeography of bacterial communities in wastewater treatment plants

scientific article published on 01 December 2019

Available nitrogen is the key factor influencing soil microbial functional gene diversity in tropical rainforest

scientific article

Bacterial communities and potential waterborne pathogens within the typical urban surface waters

scientific article published in Scientific Reports

Bacterioplankton assembly and interspecies interaction indicating increasing coastal eutrophication.

scientific article published on 9 March 2017

Bacterioplankton community resilience to ocean acidification: evidence from microbial network analysis

scientific article published in 2015

Biodiversity and species competition regulate the resilience of microbial biofilm community.

scientific article

Biogeographic patterns of microbial co-occurrence ecological networks in six American forests

scientific article published in 2020

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

scientific article

Chitinophaga caeni sp. nov., isolated from activated sludge

scientific article published on 11 May 2018

Climate warming restructures seasonal dynamics of grassland soil microbial communities

scientific article published in 2022

CoBacFM: Core bacteria forecast model for global grassland pH dynamics under future climate warming scenarios

scientific article published in 2024

Comparative Metagenomics of Freshwater Microbial Communities

Comparative metagenomics reveals impact of contaminants on groundwater microbiomes

scientific article published on 31 October 2015

Continental scale structuring of forest and soil diversity via functional traits

scientific article published on 19 August 2019

Contrasting Biogeographic Patterns of Bacterial and Archaeal Diversity in the Top- and Subsoils of Temperate Grasslands

scientific article published on 01 October 2019

Contrasting archaeal and bacterial community assembly processes and the importance of rare taxa along a depth gradient in shallow coastal sediments

scientific article published in 2022

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

scientific article published on 5 February 2013

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision.

scientific article

Correlation of genomic and physiological traits of thermoanaerobacter species with biofuel yields

scientific article (publication date: November 2011)

Correspondence: Reply to 'Analytical flaws in a continental-scale forest soil microbial diversity study'

scientific article

Corrigendum: NF-κB/TWIST1 Mediates Migration and Phagocytosis of Macrophages in the Mice Model of Implant-Associated Staphylococcus aureus Osteomyelitis

scientific article published on 13 August 2020

Deep-sea oil plume enriches indigenous oil-degrading bacteria

scientific article

Deforestation decreases spatial turnover and alters the network interactions in soil bacterial communities

scholarly article by Jing Tian et al published August 2018 in Soil Biology and Biochemistry

Design and analysis of mismatch probes for long oligonucleotide microarrays

scientific article

Deterministic Assembly and Diversity Gradient Altered the Biofilm Community Performances of Bioreactors

scientific article published on 18 January 2019

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

Distance-Decay Relationship for Biological Wastewater Treatment Plants

scientific article

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

scientific article (publication date: March 2014)

Divergent Responses of Forest Soil Microbial Communities under Elevated CO2 in Different Depths of Upper Soil Layers.

scientific article published on 27 October 2017

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

Dynamic Succession of Groundwater Sulfate-Reducing Communities during Prolonged Reduction of Uranium in a Contaminated Aquifer.

scientific article

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

Editorial: Microbial regulation of soil carbon cycling in terrestrial ecosystems

scientific article published in 2023

Effects of Nitrate Exposure on the Functional Structure of a Microbial Community in a Uranium-contaminated Aquifer

scholarly article published 17 May 2010

Effects of graphene oxide on PCR amplification for microbial community survey

scientific article published on 11 September 2020

Electro-driven methanogenic microbial community diversity and variability in the electron abundant niche

scientific article published on 14 January 2019

Electrostimulation triggers an increase in cross-niche microbial associations toward enhancing organic nitrogen wastewater treatment

scientific article published in 2023

Elevated CO and Warming Altered Grassland Microbial Communities in Soil Top-Layers

article

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 simplifies microbial community compositions and interactions in sulfide-rich river sediments

scientific article published on 04 August 2020

Environmental DNA metabarcoding reveals the influence of human activities on microeukaryotic plankton along the Chinese coastline

scientific article published in 2023

Euonymus japonicus phyllosphere microbiome is significantly changed by powdery mildew

scientific article published on 30 May 2019

Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform.

scientific article

Exploration of Intrinsic Microbial Community Modulators in the Rice Endosphere Indicates a Key Role of Distinct Bacterial Taxa Across Different Cultivars

scientific article published on 16 February 2021

Exploring abundance, diversity and variation of a widespread antibiotic resistance gene in wastewater treatment plants.

scientific article published on 9 May 2018

Exploring the accuracy of amplicon-based internal transcribed spacer markers for a fungal community

scientific article published on 06 November 2019

Florfenicol restructured the microbial interaction network for wastewater treatment by microbial electrolysis cells

scientific article published on 18 January 2020

Forest conversion induces seasonal variation in microbial β-diversity

scientific article published on 7 December 2017

Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities.

scientific article published on 18 June 2019

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

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 molecular ecological networks

scientific article

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

scientific article

Fungal dynamics and potential functions during anaerobic digestion of food waste

scientific article published in 2022

Fungi and cercozoa regulate methane-associated prokaryotes in wetland methane emissions

scientific article published in 2023

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

scientific article

GeoChip 3.0: A High Throughput Tool for Analyzing Microbial Community, Composition, Structure, and Functional Activity

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

scientific article

Geographical Distribution of Methanogenic Archaea in Nine Representative Paddy Soils in China

scientific article

Global diversity and biogeography of bacterial communities in wastewater treatment plants

scientific article published on 13 May 2019

Gordonia phthalatica sp. nov., a di-n-butyl phthalate-degrading bacterium isolated from activated sludge

scientific article

Grass-legume mixtures enhance forage production via the bacterial community

scientific article published in 2022

Habitat environments impacted the gut microbiome of long-distance migratory swan geese but central species conserved

scientific article published in Scientific Reports

High speciation rate of niche specialists in hot springs

scientific article published in 2023

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

scientific article

Homogeneous Selection and Dispersal Limitation Dominate the Effect of Soil Strata Under Warming Condition

scientific article published in 2022

Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough

scientific article published in October 2010

Identifying qualitative effects of different grazing types on below-ground communities and function in a long-term field experiment

scientific article

Impact of metal pollution and Thlaspi caerulescens growth on soil microbial communities.

scientific article

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

scientific article

Integrated metagenomics and network analysis of soil microbial community of the forest timberline.

scientific article

Interaction of graphene-family nanomaterials with microbial communities in sequential batch reactors revealed by high-throughput sequencing

scientific article published on 16 March 2020

Interdomain ecological networks between plants and microbes

scientific article published on 24 September 2019

Kelp Culture Enhances Coastal Biogeochemical Cycles by Maintaining Bacterioplankton Richness and Regulating Its Interactions

scientific article published in 2023

Land use change alters functional gene diversity, composition and abundance in Amazon forest soil microbial communities

scientific article published on 6 June 2014

Latitudinal distribution of ammonia-oxidizing bacteria and archaea in the agricultural soils of eastern China

scientific article

Linking NO Emissions from Biofertilizer-Amended Soil of Tea Plantations to the Abundance and Structure of NO-Reducing Microbial Communities

scientific article published on 21 September 2018

Long-Term Oil Contamination Alters the Molecular Ecological Networks of Soil Microbial Functional Genes

scientific article published on 3 February 2016

Long-term soil transplant simulating climate change with latitude significantly alters microbial temporal turnover

scientific article

Meadow degradation increases spatial turnover rates of the fungal community through both niche selection and dispersal limitation

scientific article published in 2021

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 Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers

scientific article

Microbial and chemical fertilizers for restoring degraded alpine grassland

scientific article published in 2023

Microbial diversity accumulates in a downstream direction in the Three Gorges Reservoir

scientific article published on 28 August 2020

Microbial functional diversity covaries with permafrost thaw-induced environmental heterogeneity in tundra soil

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

Molecular ecological network analyses.

scientific article

NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes

scientific article published on 01 March 2019

NF-κB/TWIST1 Mediates Migration and Phagocytosis of Macrophages in the Mice Model of Implant-Associated Staphylococcus aureus Osteomyelitis

scientific article published on 12 June 2020

Nearly a decade-long repeatable seasonal diversity patterns of bacterioplankton communities in the eutrophic Lake Donghu (Wuhan, China).

scientific article

Network analysis infers the wilt pathogen invasion associated with non-detrimental bacteria

scientific article published on 14 February 2020

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

scientific article published on 14 July 2015

Niche width of above- and belowground organisms varied in predicting biodiversity profiling along a latitudinal gradient

scientific article published on 16 April 2020

NifH-Harboring Bacterial Community Composition across an Alaskan Permafrost Thaw Gradient

scientific article

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

scientific article published on 7 April 2015

Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis.

scientific article published on 19 June 2015

Phylogenetic and functional gene structure shifts of the oral microbiomes in periodontitis patients

scientific article

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

scientific article (publication date: 2011)

Pollution Gradients Altered the Bacterial Community Composition and Stochastic Process of Rural Polluted Ponds

scientific article published on 24 February 2020

Random sampling process leads to overestimation of β-diversity of microbial communities

scientific article

Recurrent horizontal transfer of arsenite methyltransferase genes facilitated adaptation of life to arsenic.

scientific article

Relationships Between Soil Microbial Diversities Across an Aridity Gradient in Temperate Grasslands

scientific article published in 2022

Relative Importance of Deterministic and Stochastic Processes on Soil Microbial Community Assembly in Temperate Grasslands

scientific article published on 13 September 2021

Reproducibility and quantitation of amplicon sequencing-based detection

scientific article

Response of chloramphenicol-reducing biocathode resistome to continuous electrical stimulation

scientific article published on 30 October 2018

Responses of Microbial Communities and Interaction Networks to Different Management Practices in Tea Plantation Soils

scholarly article

Responses of bacterial community to dibutyl phthalate pollution in a soil-vegetable ecosystem

scientific article published on 10 April 2018

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

scientific article published on 18 March 2010

Salinity reduces bacterial diversity, but increases network complexity in Tibetan Plateau lakes

scientific article published on 01 December 2019

Saliva microbiota carry caries-specific functional gene signatures

scientific article

Scale-dependent effects of climate and geographic distance on bacterial diversity patterns across northern China's grasslands.

scientific article published on 29 October 2015

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

scientific article published on 15 November 2012

Soil Microbial Community Assembly and Interactions Are Constrained by Nitrogen and Phosphorus in Broadleaf Forests of Southern China

scientific article published in 2020

Soil bacterial diversity patterns and drivers along an elevational gradient on Shennongjia Mountain, China

scientific article published on 29 May 2015

Soil bacterial endemism and potential functional redundancy in natural broadleaf forest along a latitudinal gradient

scientific article published on 30 June 2016

Soil bacterial quantification approaches coupling with relative abundances reflecting the changes of taxa.

scientific article

Soil microbial community assembly and stability are associated with potato (Solanum tuberosum L.) fitness under continuous cropping regime

scientific article published in 2022

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

scientific article

Soil microbiome mediated nutrients decline during forest degradation process

scholarly article

Soil organic matter quantity and quality shape microbial community compositions of subtropical broadleaved forests.

scientific article published on 12 September 2015

Spatial scaling of forest soil microbial communities across a temperature gradient

scientific article published on 02 September 2018

Steeper spatial scaling patterns of subsoil microbiota are shaped by deterministic assembly process

scientific article published on 15 December 2020

Stimulation of soil microbial functioning by elevated CO2 may surpass effects mediated by irrigation in a semiarid grassland

scientific article published in 2021

Stochastic assembly leads to alternative communities with distinct functions in a bioreactor microbial community

scientific article

Stochastic processes regulate belowground community assembly in alpine grasslands on the Tibetan Plateau

scientific article published in 2021

Stochasticity, succession, and environmental perturbations in a fluidic ecosystem

scientific article

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

Succession of microbial functional communities in response to a pilot-scale ethanol-blended fuel release throughout the plume life cycle

scientific article published on 17 January 2015

Taxonomic and Functional Analyses of the Supragingival Microbiome from Caries-Affected and Caries-Free Hosts.

scientific article published on 20 September 2017

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

scientific article

The Coexistence Relationship Between Plants and Soil Bacteria Based on Interdomain Ecological Network Analysis

scientific article published on 07 December 2021

The Great Oxidation Event expanded the genetic repertoire of arsenic metabolism and cycling

scientific article published on 29 April 2020

The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities

scientific article published on 13 June 2013

The divergence between fungal and bacterial communities in seasonal and spatial variations of wastewater treatment plants

scientific article published on 20 February 2018

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

scientific article

The microbially mediated soil organic carbon loss under degenerative succession in an alpine meadow

scientific article

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

scientific article

Thirty-one years of rice-rice-green manure rotations shape the rhizosphere microbial community and enrich beneficial bacteria

scientific article published in 2017

Toward a theory for diversity gradients: the abundance-adaptation hypothesis

scientific article published in 2017

Unraveling the diversity of sedimentary sulfate-reducing prokaryotes (SRP) across Tibetan saline lakes using epicPCR

scientific article published on 04 May 2019

Warming Alters Expressions of Microbial Functional Genes Important to Ecosystem Functioning

scientific article

Warming enhances old organic carbon decomposition through altering functional microbial communities

scientific article

Warming-driven migration of core microbiota indicates soil property changes at continental scale

scholarly 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

[Expert consensus on microbiome sequencing and analysis]

scientific article published on 01 December 2020

mcrA sequencing reveals the role of basophilic methanogens in a cathodic methanogenic community.

scientific article published on 2 March 2018

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