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2025
Solu: a cloud platform for real-time genomic pathogen surveillance
BMC Bioinformatics
2025
Validation of Core and Whole-Genome Multi-Locus Sequence Typing Schemes for Shiga-Toxin-Producing E. coli (STEC) Outbreak Detection in a National Surveillance Network, PulseNet 2.0, USA
Microorganisms
2025
dTOURS: Dense-region tagging for outbreak detection using ratio statistics
PLOS One
2023
Evaluation of whole and core genome multilocus sequence typing allele schemes for Salmonella enterica outbreak detection in a national surveillance network, PulseNet USA
Frontiers in Microbiology
2023
Trending Topics in Escherichia coli Research
2023
Accelerating bioinformatics implementation in public health
Microbial Genomics
2023
ClinMicroNow
2023
Pipeline validation for the identification of antimicrobial-resistant genes in carbapenem-resistant Klebsiella pneumoniae
Scientific Reports
2023
PRAWNS: compact pan-genomic features for whole-genome population genomics
Bioinformatics
2023
Molecular detection and characterization of foodborne bacteria: Recent progresses and remaining challenges
Comprehensive Reviews in Food Science and Food Safety
2023
Food Microbiology and Food Safety
2022
The Handbook of Environmental Chemistry
2022
Optimization and Validation of Candida auris Short Tandem Repeat Analysis
Microbiology Spectrum
2022
Benchmarking the topological accuracy of bacterial phylogenomic workflows using in silico evolution
Microbial Genomics
2022
PM 7/151 (1) Considerations for the use of high throughput sequencing in plant health diagnostics1
EPPO Bulletin
2022
A review on the application of bioinformatics tools in food microbiome studies
Briefings in Bioinformatics
2022
Benchmark datasets for SARS-CoV-2 surveillance bioinformatics
PeerJ
2022
Smart traceability for food safety
Critical Reviews in Food Science and Nutrition
2022
Use of Whole Genome Sequencing by the Federal Interagency Collaboration for Genomics for Food and Feed Safety in the United States
Journal of Food Protection
2021
Candida auris Whole-Genome Sequence Benchmark Dataset for Phylogenomic Pipelines
Journal of Fungi
2021
Validation strategy of a bioinformatics whole genome sequencing workflow for Shiga toxin-producing Escherichia coli using a reference collection extensively characterized with conventional methods
Microbial Genomics
2021
Comprehensive Foodomics
2021
Whole-Genome Sequence Datasets: A Powerful Resource for the Food Microbiology Laboratory Toolbox
Frontiers in Sustainable Food Systems
2020
Whole-genome sequencing as part of national and international surveillance programmes for antimicrobial resistance: a roadmap
BMJ Global Health
2020
Closed Genome Sequences of 28 Foodborne Pathogens from the CFSAN Verification Set, Determined by a Combination of Long and Short Reads
Microbiology Resource Announcements
2020
Large scale automated phylogenomic analysis of bacterial isolates and the Evergreen Online platform
Communications Biology
2020
Ten recommendations for supporting open pathogen genomic analysis in public health
Nature Medicine
2019
Emerging strategies for the development of food industries
Bioengineered
2019
Mashtree: a rapid comparison of whole genome sequence files
Journal of Open Source Software
2019
Validation of a Bioinformatics Workflow for Routine Analysis of Whole-Genome Sequencing Data and Related Challenges for Pathogen Typing in a European National Reference Center: Neisseria meningitidis as a Proof-of-Concept
Frontiers in Microbiology
2019
All for one and one for all: the true potential of whole-genome sequencing
The Lancet Infectious Diseases
2019
Rapid, multiplexed, whole genome and plasmid sequencing of foodborne pathogens using long-read nanopore technology
Scientific Reports
2019
Methods in Molecular Biology
2019
GenBank
Nucleic Acids Research
2019
In-depth comparison of library pooling strategies for multiplexing bacterial species in NGS
Diagnostic Microbiology and Infectious Disease
2019
A Simple and Robust Statistical Method to Define Genetic Relatedness of Samples Related to Outbreaks at the Genomic Scale – Application to Retrospective Salmonella Foodborne Outbreak Investigations
Frontiers in Microbiology
2019
The use of next generation sequencing for improving food safety: Translation into practice
Food Microbiology
2019
An Overview of PulseNet USA Databases
Foodborne Pathogens and Disease
2019
Detailed Evaluation of Data Analysis Tools for Subtyping of Bacterial Isolates Based on Whole Genome Sequencing: Neisseria meningitidis as a Proof of Concept
Frontiers in Microbiology
2019
The Cano-eMLST Program: An Approach for the Calculation of Canonical Extended Multi-Locus Sequence Typing, Making Comparison of Genetic Differences Among Bunches of Bacterial Strains
Microorganisms
2019
Changes detected in the genome sequences of Escherichia coli, Listeria monocytogenes, Vibrio parahaemolyticus, and Salmonella enterica after serial subculturing
Canadian Journal of Microbiology
2019
cano-wgMLST_BacCompare: A Bacterial Genome Analysis Platform for Epidemiological Investigation and Comparative Genomic Analysis
Frontiers in Microbiology
2019
Phylogenetic Concepts and Tools Applied to Epidemiologic Investigations of Infectious Diseases
Microbiology Spectrum
2019
OutbreakFinder: a visualization tool for rapid detection of bacterial strain clusters based on optimized multidimensional scaling
PeerJ
2019
Phylogenomic Pipeline Validation for Foodborne Pathogen Disease Surveillance
Journal of Clinical Microbiology
2018
Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study
Wellcome Open Research
2018
Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene–based approaches
Clinical Microbiology and Infection
2018
Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study
Wellcome Open Research
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