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2023
Use of a taxon-specific reference database for accurate metagenomics-based pathogen detection of Listeria monocytogenes in turkey deli meat and spinach
BMC Genomics
2023
Environmental DNA and RNA in aquatic community ecology: Toward methodological standardization
Environmental DNA
2022
How Scalable Are Clade-Specific Marker K-Mer Based Hash Methods for Metagenomic Taxonomic Classification?
Frontiers in Signal Processing
2022
Ranking the biases: The choice of OTUs vs. ASVs in 16S rRNA amplicon data analysis has stronger effects on diversity measures than rarefaction and OTU identity threshold
PLOS ONE
2022
Over‐optimism in benchmark studies and the multiplicity of design and analysis options when interpreting their results
WIREs Data Mining and Knowledge Discovery
2022
Crowdsourced benchmarking of taxonomic metagenome profilers: lessons learned from the sbv IMPROVER Microbiomics challenge
BMC Genomics
2022
Drastic reduction of false positive species in samples of insects by intersecting the default output of two popular metagenomic classifiers
PLOS ONE
2021
Benchmarking bioinformatic tools for fast and accurate eDNA metabarcoding species identification
Molecular Ecology Resources
2021
Beating Naive Bayes at Taxonomic Classification of 16S rRNA Gene Sequences
Frontiers in Microbiology
2021
Soil Biology
2021
On the optimistic performance evaluation of newly introduced bioinformatic methods
Genome Biology
2021
HCK and ABAA: A Newly Designed Pipeline to Improve Fungi Metabarcoding Analysis
Frontiers in Microbiology
2021
Assessment of current taxonomic assignment strategies for metabarcoding eukaryotes
Molecular Ecology Resources
2020
Spatial and temporal turnover of soil microbial communities is not linked to function in a primary tropical forest
Ecology
2020
TAMA: improved metagenomic sequence classification through meta-analysis
BMC Bioinformatics
2020
Metagenomics as a Tool To Monitor Reclaimed-Water Quality
Applied and Environmental Microbiology
2020
Secret lifestyles of pyrophilous fungi in the genus Sphaerosporella
American Journal of Botany
2020
LEMMI: a continuous benchmarking platform for metagenomics classifiers
Genome Research
2020
Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline
Frontiers in Microbiology
2020
A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses
Ecology and Evolution
2019
Essential guidelines for computational method benchmarking
Genome Biology
2019
Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance
GigaScience
2019
A Cautionary Report for Pathogen Identification Using Shotgun Metagenomics; A Comparison to Aerobic Culture and Polymerase Chain Reaction for Salmonella enterica Identification
Frontiers in Microbiology
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