be.Prepared: Setting up a cloud-based bioinformatics platform and coupled NRC usability platform for integrated genomic-epidemiological analysis at a national level, Gori, A., Kelchtermans Michael, Millis Kato, Van Laer Amber, Mairiaux Eric, initiative Members of the H. E. R., Van den Bossche An, Ceyssens Pieter-Jan, Mattheus Wesley, Mathys Vanessa, et al. , Applied Bioinformatics and Public Health Microbiology, 22/05/2025, Hixton, UK, (2025)

Galaxy @Sciensano: a comprehensive bioinformatics portal for genomics-based microbial typing, characterization, and outbreak detection., Bogaerts, Bert, Van Braekel Julien, Van Uffelen Alexander, D'aes Jolien, Godfroid Maxime, Delcourt Thomas, Kelchtermans Michael, Milis Kato, Goeders Nathalie, De Keersmaecker Sigrid C. J., et al. , BMC Genomics, 2025 Jan 08, Volume 26, Issue 1, (2025)

Metagenomics-based tracing of genetically modified microorganism contaminations in commercial fermentation products, D'aes, Jolien, Fraiture Marie-Alice, Bogaerts Bert, Van Laere Yari, De Keersmaecker Sigrid C. J., Roosens Nancy, and Vanneste Kevin , Food Chemistry: Molecular Sciences, June-2025, Volume 10, (2025)

Molecular and WGS-based characterization of invasive Neisseria meningitidis isolates collected in Belgium (2016-2022) and MenB-FHbp vaccine coverage estimation of serogroup B., Goeders, Nathalie, Vanneste Kevin, Roosens Nancy, Bogaerts Bert, and Mattheus Wesley , Vaccine, 2025 May 10, Volume 55, (2025)

Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens., Bogaerts, Bert, Van den Bossche An, Verhaegen Bavo, Delbrassinne Laurence, Mattheus Wesley, Nouws Stéphanie, Godfroid Maxime, Hoffman Stefan, Roosens Nancy, De Keersmaecker Sigrid C. J., et al. , J Clin Microbiol, 2024 Mar 05, (2024)

Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens., Bogaerts, Bert , J Clin Microbiol, 2024 Mar 05, (2024)

Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens., Bogaerts, Bert , J Clin Microbiol, 2024 Mar 05, (2024)

Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens., Bogaerts, Bert , J Clin Microbiol, 2024 Mar 05, (2024)

Genomic comparison between  and  and  analysis of peptide-based biomarkers for serodiagnosis., Moens, Charlotte, Bogaerts Bert, Lorente-Leal Victor, Vanneste Kevin, De Keersmaecker Sigrid C. J., Roosens Nancy, Mostin Laurent, Fretin David, and Marché Sylvie , Front Vet Sci, 2024, Volume 11, (2024)

Phage-Mediated Digestive Decolonization in a Gut-On-A-Chip Model: A Tale of Gut-Specific Bacterial Prosperity., Van Nieuwenhuyse, Brieuc, Merabishvili Maya, Goeders Nathalie, Vanneste Kevin, Bogaerts Bert, de Jode Mathieu, Ravau Joachim, Wagemans Jeroen, Belkhir Leïla, and Van der Linden Dimitri , Viruses, 2024 Jun 28, Volume 16, Issue 7, (2024)

Retrospective surveillance of viable Bacillus cereus group contaminations in commercial food and feed vitamin B2 products sold on the Belgian market using whole-genome sequencing, Bogaerts, Bert, Fraiture Marie-Alice, Van Nieuwenhuysen Tom, Jacobs Bram, Van Hoorde Koenraad, De Keersmaecker Sigrid C. J., Roosens Nancy, and Vanneste Kevin , Frontiers in Microbiology, Sep-06-2024, Volume 14, (2023)

Transforming Shiga toxin-producing  surveillance through whole genome sequencing in food safety practices., Nouws, Stéphanie, Verhaegen Bavo, Denayer Sarah, Crombé Florence, Piérard Denis, Bogaerts Bert, Vanneste Kevin, Marchal Kathleen, Roosens Nancy, and De Keersmaecker Sigrid C. J. , Front Microbiol, 2023, Volume 14, (2023)

Whole-genome sequencing-based phylogenomic investigation of unexpected Bacillus cereus contaminations collected from commercial vitamin B2 food and feed additives sold on the Belgian market, Bogaerts, Bert, Fraiture Marie-Alice, Huwaert Astrid, Van Nieuwenhuysen Tom, Jacobs Bram, Van Hoorde Koenraad, De Keersmaecker Sigrid C. J., Roosens Nancy, and Vanneste Kevin , Applied Bioinformatics and Public Health Microbiology , 2023, Hinxton, OK, (2023)

Whole-Genome Sequencing-Based Screening of MRSA in Patients and Healthcare Workers in Public Hospitals in Benin., Yehouenou, Laurence Carine, Bogaerts Bert, Vanneste Kevin, De Keersmaecker Sigrid C. J., Roosens Nancy, Kpangon Arsène A., Dissou Affolabi, Simon Anne, Dossou Francis Moise, and Dalleur Olivia , Microorganisms, 2023 Jul 31, Volume 11, Issue 8, (2023)

The key role of WGS-based surveillance of Listeria monocytogenes in both human and food isolates in outbreak investigations, Van den Bossche, An, De Keersmaecker Sigrid C. J., Mattheus Wesley, Roosens Nancy, Bogaerts Bert, Vanneste Kevin, Van Hoorde Koenraad, and Verhaegen Bavo , 26th Conference on Food Microbiology, 13-14/10/2022, Issue BSFM, Brussels, Belgium, (2022)

Metagenomic Characterization of Multiple Genetically Modified Bacillus Contaminations in Commercial Microbial Fermentation Products, D'aes, Jolien, Fraiture Marie-Alice, Bogaerts Bert, De Keersmaecker Sigrid C. J., Roosens Nancy, and Vanneste Kevin , Life, 25/11/2022, Volume 12, Issue 12, (2022)

Population Analysis of O26 Shiga Toxin-Producing  Causing Hemolytic Uremic Syndrome in Italy, 1989-2020, Through Whole Genome Sequencing., Michelacci, Valeria, Montalbano Di Filippo Margherita, Gigliucci Federica, Arancia Silvia, Chiani Paola, Minelli Fabio, Roosens Nancy, De Keersmaecker Sigrid C. J., Bogaerts Bert, Vanneste Kevin, et al. , Front Cell Infect Microbiol, 2022, Volume 12, (2022)

Shotgun metagenomics as a ONE Health tool for better protecting human health, Gand, Mathieu, Buytaers Florence E., Bloemen Bram, Saltykova Assia, Denayer Sarah, Verhaegen Bavo, Mattheus Wesley, Piérard Denis, Bogaerts Bert, Marchal Kathleen, et al. , EFSA One, 21/06/2022, Issue EFSA, (2022)

A Bioinformatics Whole-Genome Sequencing Workflow for Clinical Mycobacterium tuberculosis Complex Isolate Analysis, Validated Using a Reference Collection Extensively Characterized with Conventional Methods and In Silico Approaches, Bogaerts, Bert, Delcourt Thomas, Soetaert Karine, Boarbi Samira, Ceyssens Pieter-Jan, Winand Raf, Van Braekel Julien, De Keersmaecker Sigrid C. J., Roosens Nancy, Marchal Kathleen, et al. , J Clin Microbiol, 2021 Mar 31, (2021)

Characterization of Genetically Modified Microorganisms Using Short- and Long-Read Whole-Genome Sequencing Reveals Contaminations of Related Origin in Multiple Commercial Food Enzyme Products., D'aes, Jolien, Fraiture Marie-Alice, Bogaerts Bert, De Keersmaecker Sigrid C. J., Roosens Nancy, and Vanneste Kevin , Foods, 2021 Oct 30, Volume 10, Issue 11, (2021)

Development of a data-intensive centralized system for surveillance and outbreak investigation of bacterial pathogens using whole-genome sequencing, Bogaerts, Bert , 14/02/2022, Gh, p.250, (2021)

Evaluation of WGS performance for bacterial pathogen characterization with the Illumina technology optimized for time-critical situations., Bogaerts, Bert, Winand Raf, Van Braekel Julien, Hoffman Stefan, Roosens Nancy, De Keersmaecker Sigrid C. J., Marchal Kathleen, and Vanneste Kevin , Microb Genom, 2021 11, Volume 7, Issue 11, (2021)

First detection of a plasmid-encoded New-Delhi metallo-beta-lactamase-1 (NDM-1) producing Acinetobacter baumannii using whole genome sequencing, isolated in a clinical setting in Benin., Yehouenou, Carine, Bogaerts Bert, Vanneste Kevin, Roosens Nancy, De Keersmaecker Sigrid C. J., Marchal Kathleen, Dissou Affolabi, Soleimani Reza, Rodriguez-Villalobos Hector, Van Bambeke Françoise, et al. , Ann Clin Microbiol Antimicrob, 2021 Jan 06, Volume 20, Issue 1, (2021)

Large diversity of linezolid-resistant isolates discovered in food-producing animals through linezolid selective monitoring in Belgium in 2019., Timmermans, Michaël, Bogaerts Bert, Vanneste Kevin, De Keersmaecker Sigrid C. J., Roosens Nancy, Kowalewicz Carole, Simon Guillaume, M Argudín Angeles, Deplano Ariane, Hallin Marie, et al. , J Antimicrob Chemother, 2021 Oct 21, (2021)

Large diversity of linezolid-resistant isolates discovered in food-producing animals through linezolid selective monitoring in Belgium in 2019, Timmermans, Michaël, Bogaerts Bert, Vanneste Kevin, De Keersmaecker Sigrid C. J., Roosens Nancy, Kowalewicz Carole, Simon Guillaume, Argudín Maria A., Deplano Ariane, Hallin Marie, et al. , Journal of Antimicrobial Chemotherapy, Sep-10-2022, Volume 77, Issue 1, (2021)

Phylogenomic Investigation of Increasing Fluoroquinolone Resistance among Belgian Cases of Shigellosis between 2013 and 2018 Indicates Both Travel-Related Imports and Domestic Circulation., Bogaerts, Bert, Winand Raf, Van Braekel Julien, Mattheus Wesley, De Keersmaecker Sigrid C. J., Roosens Nancy, Marchal Kathleen, Vanneste Kevin, and Ceyssens Pieter-Jan , Microorganisms, 2021 Apr 06, Volume 9, Issue 4, (2021)

Retrospective evaluation of routine whole genome sequencing of Mycobacterium tuberculosis at the Belgian National Reference Center, 2019., Soetaert, Karine, Ceyssens Pieter-Jan, Boarbi Samira, Bogaerts Bert, Delcourt Thomas, Vanneste Kevin, De Keersmaecker Sigrid C. J., Roosens Nancy, Vodolazkaia Alexandra, Mukovnikova Marina, et al. , Acta Clin Belg, 2021 Nov 09, (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, Bogaerts, Bert, Nouws Stéphanie, Verhaegen Bavo, Denayer Sarah, Van Braekel Julien, Winand Raf, Fu Qiang, Crombé Florence, Piérard Denis, Marchal Kathleen, et al. , Microbial Genomics, Jan-03-2021, Volume 7, Issue 3, (2021)

Whole Genome Sequencing Provides an Added Value to the Investigation of Staphylococcal Food Poisoning Outbreaks, Nouws, Stéphanie, Bogaerts Bert, Verhaegen Bavo, Denayer Sarah, Laeremans Lasse, Marchal Kathleen, Roosens Nancy, Vanneste Kevin, and De Keersmaecker Sigrid C. J. , Frontiers in Microbiology, Feb-11-2021, Volume 12, (2021)

Whole-Genome Sequencing-Based Antimicrobial Resistance Characterization and Phylogenomic Investigation of 19 Multidrug-Resistant and Extended-Spectrum Beta-Lactamase-Positive Escherichia coli Strains Collected From Hospital Patients in Benin in 2019., Yehouenou, Carine Laurence, Bogaerts Bert, De Keersmaecker Sigrid C. J., Roosens Nancy, Marchal Kathleen, Tchiakpe Edmond, Dissou Affolabi, Simon Anne, Dossou Francis Moise, Vanneste Kevin, et al. , Front Microbiol, 2021, Volume 12, (2021)

Whole-genome-based phylogenomic analysis of the Belgian 2016-2017 influenza A(H3N2) outbreak season allows improved surveillance., Van Poelvoorde, Laura, Bogaerts Bert, Qiang Fu, De Keersmaecker Sigrid C. J., Thomas Isabelle, Van Goethem Nina, Van Gucht Steven, Winand Raf, Saelens Xavier, Roosens Nancy, et al. , Microb Genom, 2021 09, Volume 7, Issue 9, (2021)

The Benefits of Whole Genome Sequencing for Foodborne Outbreak Investigation from the Perspective of a National Reference Laboratory in a Smaller Country., Nouws, Stéphanie, Bogaerts Bert, Verhaegen Bavo, Denayer Sarah, Crombé Florence, De Rauw Klara, Piérard Denis, Marchal Kathleen, Vanneste Kevin, Roosens Nancy, et al. , Foods, 2020 Aug 01, Volume 9, Issue 8, (2020)

Identification of an unauthorized genetically modified bacteria in food enzyme through whole-genome sequencing., Fraiture, Marie-Alice, Bogaerts Bert, Winand Raf, Deckers Marie, Papazova N., Vanneste Kevin, De Keersmaecker Sigrid C. J., and Roosens Nancy , Sci Rep, 2020 04 27, Volume 10, Issue 1, (2020)

Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates, Nouws, Stéphanie, Bogaerts Bert, Verhaegen Bavo, Denayer Sarah, Piérard Denis, Marchal Kathleen, Roosens Nancy, Vanneste Kevin, and De Keersmaecker Sigrid C. J. , Scientific Reports, Jan-12-2020, Volume 10, Issue 1, (2020)

Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates., Nouws, Stéphanie, Bogaerts Bert, Verhaegen Bavo, Denayer Sarah, Piérard Denis, Marchal Kathleen, Roosens Nancy, Vanneste Kevin, and De Keersmaecker Sigrid C. J. , Sci Rep, 2020 09 04, Volume 10, Issue 1, (2020)

Isolation of Drug-Resistant Gallibacterium anatis from Calves with Unresponsive Bronchopneumonia, Belgium., Van Driessche, Laura, Vanneste Kevin, Bogaerts Bert, De Keersmaecker Sigrid C. J., Roosens Nancy, Haesebrouck Freddy, De Cremer Lieze, Deprez Piet, Pardon Bart, and Boyen Filip , Emerg Infect Dis, 2020 04, Volume 26, Issue 4, (2020)

Shifting national surveillance of Shigella infections toward geno-serotyping by the development of a tailored Luminex assay and NGS workflow., Ventola, Eleonora, Bogaerts Bert, De Keersmaecker Sigrid C. J., Vanneste Kevin, Roosens Nancy, Mattheus Wesley, and Ceyssens Pieter-Jan , Microbiologyopen, 2019 Mar 28, (2019)

Targeting the 16S rRNA gene for bacterial identification in complex mixed samples: comparative evaluation of second (Illumina) and third (Oxford Nanopore Technologies) generation sequencing technologies., Winand, Raf, Bogaerts Bert, Hoffman Stefan, Lefèvre Loic, Delvoye Maud, Van Braekel Julien, Qiang Fu, Roosens Nancy, De Keersmaecker Sigrid C. J., and Vanneste Kevin , Int J Mol Sci, 2019 Dec 31, Volume 21, Issue 1, (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:  as a Proof-of-Concept., Bogaerts, Bert, Winand Raf, Qiang Fu, Van Braekel Julien, Ceyssens Pieter-Jan, Mattheus Wesley, Bertrand Sophie, De Keersmaecker Sigrid C. J., Roosens Nancy, and Vanneste Kevin , Front Microbiol, 2019, Volume 10, (2019)

Development and implementation of a transversal NGS & bioinformatics platform at the Belgian Institute of Public Health, Vanneste, Kevin, Bogaerts Bert, Fu Q., Winand Raf, Romeu A.G., Brown I., De Keersmaecker Sigrid C. J., and Roosens Nancy , Applied Bioinformatics in Life Sciences, 17/3/2016, Issue VIB, NA, (2016)

Development and implementation of a transversal NGS & bioinformatics platform at the Belgian Institute of Public Health: deployment of user-friendly pipelines for routine use, Vanneste, Kevin, Fu Q., Bogaerts Bert, Winand Raf, Romeu A.G., Brown I., Van Braekel Julien, De Keersmaecker Sigrid C. J., and Roosens Nancy , 15th European Conference on Computational Biology, 0/0/2016, Issue VU Amsterdam,  TU Delft,  DTL,  BioSB,  UMC Utrecht, NA, (2016)

Development of a bioinformatics pipeline for routine analysis of whole genome sequencing data for typing of Neisseria meningitidis, Bogaerts, Bert , Big Data in Biology and Health, 0/0/2016, Issue EMBL, NA, (2016)

Metagenomics-based tracing of genetically modified microorganism contaminations in commercial fermentation products, D'aes, Jolien, Fraiture Marie-Alice, Bogaerts Bert, Van Laere Yari, De Keersmaecker Sigrid C. J., Roosens Nancy, and Vanneste Kevin , (0)