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2025
Clinical metagenomics for diagnosis and surveillance of viral pathogens
Nature Reviews Microbiology
2024
Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters
Genome Research
2024
Drug-induced liver injury associated with elexacaftor/tezacaftor/ivacaftor: A pharmacovigilance analysis of the FDA adverse event reporting system (FAERS)
Journal of Cystic Fibrosis
2023
Evaluation of tools for taxonomic classification of viruses
Briefings in Functional Genomics
2023
KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping
Bioinformatics
2022
Computational Biology
2022
Zebra: Static and Dynamic Genome Cover Thresholds with Overlapping References
mSystems
2022
Gut Microbial Signatures of Distinct Trimethylamine N-Oxide Response to Raspberry Consumption
Nutrients
2022
Raspberry consumption: identification of distinct immune-metabolic response profiles by whole blood transcriptome profiling
The Journal of Nutritional Biochemistry
2022
PathoLive—Real-Time Pathogen Identification from Metagenomic Illumina Datasets
Life
2021
Analysis of oral microbial dysbiosis associated with early childhood caries
BMC Oral Health
2020
MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota
mSystems
2020
A big data approach to metagenomics for all-food-sequencing
BMC Bioinformatics
2020
CSMD: a computational subtraction-based microbiome discovery pipeline for species-level characterization of clinical metagenomic samples
Bioinformatics
2020
Long-read sequencing based clinical metagenomics for the detection and confirmation of Pneumocystis jirovecii directly from clinical specimens: A paradigm shift in mycological diagnostics
Medical Mycology
2020
Blueberry proanthocyanidins and anthocyanins improve metabolic health through a gut microbiota-dependent mechanism in diet-induced obese mice
American Journal of Physiology-Endocrinology and Metabolism
2019
Resolving Phylogenetic Relationships for Streptococcus mitis and Streptococcus oralis through Core- and Pan-Genome Analyses
Genome Biology and Evolution
2019
The gut microbiome of horses: current research on equine enteral microbiota and future perspectives
Animal Microbiome
2018
DREAM-Yara: an exact read mapper for very large databases with short update time
Bioinformatics
2018
Identification of fungi in shotgun metagenomics datasets
PLOS ONE
2018
Formula Feeding Predisposes Neonatal Piglets to Clostridium difficile Gut Infection
The Journal of Infectious Diseases
2018
Species classifier choice is a key consideration when analysing low-complexity food microbiome data
Microbiome
2018
KrakenUniq: confident and fast metagenomics classification using unique k-mer counts
Genome Biology
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