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2025
Host Adaptation, Virulence, and Evolution
2025
Extensive and diverse lanthanide-dependent metabolism in the ocean
The ISME Journal
2025
Lanthanides in Enzymology and Microbiology
2025
Enhancing peptide identification in metaproteomics through curriculum learning in deep learning
Nature Communications
2025
High-affinity PQQ import is widespread in Gram-negative bacteria
Science Advances
2024
Diverse and unconventional methanogens, methanotrophs, and methylotrophs in metagenome-assembled genomes from subsurface sediments of the Slate River floodplain, Crested Butte, CO, USA
mSystems
2024
Insights into chemoautotrophic traits of a prevalent bacterial phylum CSP1-3, herein Sysuimicrobiota
National Science Review
2024
Weathered granites and soils harbour microbes with lanthanide-dependent methylotrophic enzymes
BMC Biology
2024
Changes in growth, lanthanide binding, and gene expression in Pseudomonas alloputida KT2440 in response to light and heavy lanthanides
mSphere
2023
Genome-Resolved Metagenomics of Nitrogen Transformations in the Switchgrass Rhizosphere Microbiome on Marginal Lands
Agronomy
2023
Metagenomic profiles of archaea and bacteria within thermal and geochemical gradients of the Guaymas Basin deep subsurface
Nature Communications
2023
Different lanthanide elements induce strong gene expression changes in a lanthanide-accumulating methylotroph
Microbiology Spectrum
2023
Metaproteomics reveals functional partitioning and vegetational variation among permafrost-affected Arctic soil bacterial communities
mSystems
2023
Rhizobiome
2023
Microbial communities from weathered outcrops of a sulfide‐rich ultramafic intrusion, and implications for mine waste management
Environmental Microbiology
2023
Trait biases in microbial reference genomes
Scientific Data
2023
The Deep Soil Organic Carbon Response to Global Change
Annual Review of Ecology, Evolution, and Systematics
2022
Quantitative Stable-Isotope Probing (qSIP) with Metagenomics Links Microbial Physiology and Activity to Soil Moisture in Mediterranean-Climate Grassland Ecosystems
mSystems
2022
Metagenomic analysis of bacterial communities of Wadi Namar Lake, Riyadh, Saudi Arabia
Saudi Journal of Biological Sciences
2022
MetaLP: An integrative linear programming method for protein inference in metaproteomics
PLOS Computational Biology
2022
Soils and sediments host Thermoplasmata archaea encoding novel copper membrane monooxygenases (CuMMOs)
The ISME Journal
2022
Methanol utilizers of the rhizosphere and phyllosphere of a common grass and forb host species
Environmental Microbiome
2022
Effects of environmental factors on low temperature anaerobic digestion of pig manure
Environmental Research Communications
2022
Strain Klebsiella ZP-2 inoculation activating soil nutrient supply and altering soil phosphorus cycling
Journal of Soils and Sediments
2022
Deep-C storage: Biological, chemical and physical strategies to enhance carbon stocks in agricultural subsoils
Soil Biology and Biochemistry
2022
Chiral resolution of N-methyl-d,l-aspartic acid using a predicted N-demethylase from Chloroflexi bacterium 54-19
Systems Microbiology and Biomanufacturing
2022
2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
2022
Biotechnological Combination for Co-contaminated Soil Remediation: Focus on Tripartite “Meta-Enzymatic” Activity
Frontiers in Plant Science
2022
A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry
Journal of Bacteriology
2022
Relationships among phosphatase activities, functional genes and soil properties following amendment with the bacterium Burkholderia sp. ZP‐4
Land Degradation & Development
2022
Protein sequence databases generated from metagenomics and public databases produced similar soil metaproteomic results of microbial taxonomic and functional changes
Pedosphere
2021
Germplasm Screening of Green Manure Rapeseed through the Effects of Short-Term Decomposition on Soil Nutrients and Microorganisms
Agriculture
2021
High Temperature Acclimation of Leaf Gas Exchange, Photochemistry, and Metabolomic Profiles in Populus trichocarpa
ACS Earth and Space Chemistry
2021
The phylogenetic and global distribution of bacterial polyhydroxyalkanoate bioplastic‐degrading genes
Environmental Microbiology
2021
Microbiome Stimulants for Crops
2021
Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil
mSphere
2021
Genomic Analysis of the Yet-Uncultured Binatota Reveals Broad Methylotrophic, Alkane-Degradation, and Pigment Production Capacities
mBio
2021
Extracellular and Intracellular Lanthanide Accumulation in the Methylotrophic Beijerinckiaceae Bacterium RH AL1
Applied and Environmental Microbiology
2021
Genomic Analysis of Family UBA6911 (Group 18 Acidobacteria ) Expands the Metabolic Capacities of the Phylum and Highlights Adaptations to Terrestrial Habitats
Applied and Environmental Microbiology
2021
Rokubacteria in Northern Peatlands: Habitat Preferences and Diversity Patterns
Microorganisms
2021
Comparative Genomics Reveals Thermal Adaptation and a High Metabolic Diversity in “ Candidatus Bathyarchaeia”
mSystems
2021
Secondary lanthanide phosphate mineralisation in weathering profiles of I-, S- and A-type granites
Mineralogical Magazine
2021
Comparative Metagenomic and Metabolomic Profiling of Rhizospheres of Panax notoginseng Grown under Forest and Field Conditions
Agronomy
2021
Deep learning for peptide identification from metaproteomics datasets
Journal of Proteomics
2021
Soil Bacterial Diversity Is Positively Correlated with Decomposition Rates during Early Phases of Maize Litter Decomposition
Microorganisms
2020
Biomass-degrading glycoside hydrolases of archaeal origin
Biotechnology for Biofuels
2020
Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow
The ISME Journal
2020
Preserved antibacterial activity of ribosomal protein S15 during evolution
Molecular Immunology
2020
Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type
mBio
2020
Soil metaproteomics as a tool for monitoring functional microbial communities: promises and challenges
Reviews in Environmental Science and Bio/Technology
2020
Molecular and ecological perspectives of nitrous oxide producing microbial communities in agro-ecosystems
Reviews in Environmental Science and Bio/Technology
2020
An EDTA-resistant pyrazinamidase from non-pathogen Pseudonocardia carboxydivorans
Biotechnology Letters
2020
Soil Metaproteomics for the Study of the Relationships Between Microorganisms and Plants: A Review of Extraction Protocols and Ecological Insights
International Journal of Molecular Sciences
2020
Microbial Activity in Subterranean Ecosystems: Recent Advances
Applied Sciences
2019
An archaeal origin of the Wood–Ljungdahl H4MPT branch and the emergence of bacterial methylotrophy
Nature Microbiology
2019
Soluble expression of Thermomicrobium roseum sarcosine oxidase and characterization of N-demethylation activity
Molecular Catalysis
2019
A Bioinformatics Guide to Plant Microbiome Analysis
Frontiers in Plant Science
2019
Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms
Nature Microbiology
2019
Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil
Proceedings of the National Academy of Sciences
2019
Lanthanide-Dependent Methylotrophs of the Family Beijerinckiaceae : Physiological and Genomic Insights
Applied and Environmental Microbiology
2019
Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using 13CO2 and 13C-Methanol
Frontiers in Microbiology
2019
Core Metabolic Features and Hot Origin of Bathyarchaeota
Engineering
2019
Identification of Molecular Markers That Are Specific to the Class Thermoleophilia
Frontiers in Microbiology
2019
Differences in Bacterial Diversity, Composition and Function due to Long-Term Agriculture in Soils in the Eastern Free State of South Africa
Diversity
2019
Microbiology Monographs
2019
Microbial diversity analysis and screening for novel xylanase enzymes from the sediment of the Lobios Hot Spring in Spain
Scientific Reports
2019
Microbial Diversity in the Genomic Era
2018
Chloromethane Degradation in Soils: A Combined Microbial and Two‐Dimensional Stable Isotope Approach
Journal of Environmental Quality
2018
Archaea are prominent members of the prokaryotic communities colonizing common forest mushrooms
Canadian Journal of Microbiology
2018
A simple cleanup method for the removal of humic substances from soil protein extracts using aluminum coagulation
Environmental Science and Pollution Research
2018
Group I introns are widespread in archaea
Nucleic Acids Research
2018
Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil
Nature Ecology & Evolution
2018
Current Trends in Methylotrophy
Trends in Microbiology
2018
Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy
Nature Microbiology
2018
New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes
Frontiers in Microbiology
2018
Elucidating Bacterial Gene Functions in the Plant Microbiome
Cell Host & Microbe
2018
Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis
Nature
2018
Sipros Ensemble improves database searching and filtering for complex metaproteomics
Bioinformatics
2018
Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life
Cell
2017
Drivers of Plot-Scale Variability of CH4 Consumption in a Well-Aerated Pine Forest Soil
Forests
2017
The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis
mBio
2017
Microbial network, phylogenetic diversity and community membership in the active layer across a permafrost thaw gradient
Environmental Microbiology
2017
Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla
Frontiers in Microbiology
2017
Lifestyle‐determining extrachromosomal replicon pAMV1 and its contribution to the carbon metabolism of the methylotrophic bacterium Paracoccus aminovorans JCM 7685
Environmental Microbiology
2017
Pheno- and Genotyping of Hopanoid Production in Acidobacteria
Frontiers in Microbiology
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