Citation sources

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2025
Development of a quantitative metagenomic approach to establish quantitative limits and its application to viruses
Nucleic Acids Research
2025
Leveraging strain competition to address antimicrobial resistance with microbiota therapies
Gut Microbes
2025
CoverM: read alignment statistics for metagenomics
Bioinformatics
2025
Quantifying the contribution of the rare biosphere to natural disturbances
The ISME Journal
2025
Detection of parasites in food and water matrices by shotgun metagenomics: A narrative review
Food and Waterborne Parasitology
2025
The physical biogeography of Fusobacterium nucleatum in health and disease
mBio
2025
A practical guide on environmental genomics for prokaryotic systematics
Systematic and Applied Microbiology
2024
Recruitment of complete crAss-like phage genomes reveals their presence in chicken viromes, few human-specific phages, and lack of universal detection
The ISME Journal
2024
Experimental evolution at ecological scales allows linking of viral genotypes to specific host strains
The ISME Journal
2024
Metagenomic insights into the impact of litter from poultry Concentrated Animal Feeding Operations (CAFOs) to adjacent soil and water microbial communities
Science of The Total Environment
2024
A user's guide to the bioinformatic analysis of shotgun metagenomic sequence data for bacterial pathogen detection
International Journal of Food Microbiology
2023
Fecal microbiota transplantation promotes reduction of antimicrobial resistance by strain replacement
Science Translational Medicine
2023
Pathogen Detection Using Metagenomic Next-Generation Sequencing of Plasma Samples from Patients with Sepsis in Uganda
Microbiology Spectrum
2023
A genome catalogue of lake bacterial diversity and its drivers at continental scale
Nature Microbiology
2022
Toward shotgun metagenomic approaches for microbial source tracking sewage spills based on laboratory mesocosms
Water Research
2022
Metagenomics indicate that public health risk may be higher from flooding following dry versus rainy periods
Environmental Microbiology Reports
2022
The search for Schizosaccharomyces fission yeasts in environmental metatranscriptomes
Yeast
2021
Description of Candidatus Mesopelagibacter carboxydoxydans and Candidatus Anoxipelagibacter denitrificans: Nitrate-reducing SAR11 genera that dominate mesopelagic and anoxic marine zones
Systematic and Applied Microbiology
2021
Longitudinal study on the effects of growth-promoting and therapeutic antibiotics on the dynamics of chicken cloacal and litter microbiomes and resistomes
Microbiome
2020
Genome repository of oil systems: An interactive and searchable database that expands the catalogued diversity of crude oil‐associated microbes
Environmental Microbiology
2020
Metagenomics as a Public Health Risk Assessment Tool in a Study of Natural Creek Sediments Influenced by Agricultural and Livestock Runoff: Potential and Limitations
Applied and Environmental Microbiology
2020
Iterative subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences
Environmental Microbiology
2019
Ecogenomic characterization of widespread, closely-related SAR11 clades of the freshwater genus “Candidatus Fonsibacter” and proposal of Ca. Fonsibacter lacus sp. nov
Systematic and Applied Microbiology
2019
Metagenomic Signatures of Gut Infections Caused by Different Escherichia coli Pathotypes
Applied and Environmental Microbiology
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