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2025
Whole-genome sequencing surveillance of vancomycin-resistant Enterococcus faecium (VRE) detects hospital outbreaks and identifies the postanesthesia care unit as a transmission locus
Infection Control & Hospital Epidemiology
2025
A network analysis of carbapenem-resistant Klebsiella pneumoniae among healthcare facilities
Scientific Reports
2025
Genomic Characterization of Pan‐Drug Resistant Klebsiella pneumoniae KPNW Isolated From UTI Patient in Bangladesh
MicrobiologyOpen
2025
The Clinical and Molecular Characteristics of Community-Associated Staphylococcus aureus Bacteremia in Persons who Inject Drugs at a New York City Tertiary Care Facility During the Opioid Epidemic
Open Forum Infectious Diseases
2025
Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives
Briefings in Bioinformatics
2024
A survey of k-mer methods and applications in bioinformatics
Computational and Structural Biotechnology Journal
2024
Increasing Incidence of Streptococcus anginosus Group Intracranial Infections Associated With Sinusitis, Otitis Media, and Mastoiditis in Children
Pediatric Infectious Disease Journal
2024
Disseminated Infection Caused by <i>Nocardia cyriacigeorgica</i> in Immunocompromised Patient Confirmed by Whole Genome Sequencing
Chemotherapy
2023
Development of a novel real-time PCR multiplex assay for detection of Streptococcus equi subspecies equi and Streptococcus equi subspecies zooepidemicus
Veterinary Microbiology
2023
Mixed infections in genotypic drug-resistant Mycobacterium tuberculosis
Scientific Reports
2023
Lecture Notes in Computer Science
2023
Transmission of Carbapenem-Resistant Klebsiella pneumoniae in US Hospitals
Clinical Infectious Diseases
2023
Are the predicted known bacterial strains in a sample really present? A case study
PLOS ONE
2023
High-resolution strain-level microbiome composition analysis from short reads
Microbiome
2022
Toward accurate diagnosis and surveillance of bacterial infections using enhanced strain-level metagenomic next-generation sequencing of infected body fluids
Briefings in Bioinformatics
2022
Computational analyses of bacterial strains from shotgun reads
Briefings in Bioinformatics
2022
Genomic, morphological, and biochemical analyses of a multi-metal resistant but multi-drug susceptible strain of Bordetella petrii from hospital soil
Scientific Reports
2022
Identification of Antimicrobial Compounds in Two Streptomyces sp. Strains Isolated From Beehives
Frontiers in Microbiology
2022
VirStrain: a strain identification tool for RNA viruses
Genome Biology
2022
Respiratory tract infections and gut microbiome modifications: A systematic review
PLOS ONE
2021
Identification of isolated or mixed strains from long reads: a challenge met on Streptococcus thermophilus using a MinION sequencer
Microbial Genomics
2021
mixtureS: a novel tool for bacterial strain genome reconstruction from reads
Bioinformatics
2021
Genomic Sequence Analysis of Methicillin- and Carbapenem-Resistant Bacteria Isolated from Raw Sewage
Microbiology Spectrum
2021
Differences in the genome, methylome, and transcriptome do not differentiate isolates of Streptococcus equi subsp. equi from horses with acute clinical signs from isolates of inapparent carriers
PLOS ONE
2021
Genomics of Staphylococcus aureus ocular isolates
PLOS ONE
2021
Molecular Characterization of Enterococcus Isolates From Different Sources in Estonia Reveals Potential Transmission of Resistance Genes Among Different Reservoirs
Frontiers in Microbiology
2021
Risk Factors for and Mechanisms of COlistin Resistance Among Enterobacterales: Getting at the CORE of the Issue
Open Forum Infectious Diseases
2021
Large-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy
PLOS ONE
2020
QuantTB – a method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data
BMC Genomics
2020
Method for the Identification of Plant DNA in Food Using Alignment-Free Analysis of Sequencing Reads: A Case Study on Lupin
Frontiers in Plant Science
2019
SEPATH: benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines
Genome Biology
2019
Machine Learning Approaches for Epidemiological Investigations of Food-Borne Disease Outbreaks
Frontiers in Microbiology
2019
Methods in Molecular Biology
2019
UltraStrain: An NGS-Based Ultra Sensitive Strain Typing Method for Salmonella enterica
Frontiers in Genetics
2019
Genomic metrics made easy: what to do and where to go in the new era of bacterial taxonomy
Critical Reviews in Microbiology
2019
Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications
2019
Lactobacilli Isolated From Wild Boar (Sus scrofa) Antagonize Mycobacterium bovis Bacille Calmette-Guerin (BCG) in a Species-Dependent Manner
Frontiers in Microbiology
2019
Kmer-db: instant evolutionary distance estimation
Bioinformatics
2018
PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads
PeerJ
2018
MentaLiST – A fast MLST caller for large MLST schemes
Microbial Genomics
2018
Method for the Identification of Taxon-Specific k-mers from Chloroplast Genome: A Case Study on Tomato Plant (Solanum lycopersicum)
Frontiers in Plant Science
2017
Alignment-free sequence comparison: benefits, applications, and tools
Genome Biology
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