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2025
Assessing the authenticity and purity of a commercial Bacillus thuringiensis bioinsecticide through whole genome sequencing and metagenomics approaches, Van Laere, Yari, Fraiture Marie-Alice, Gobbo Andrea, De Keersmaecker Sigrid C. J., Marchal Kathleen, Roosens Nancy, and Vanneste Kevin , Frontiers in Microbiology, Jul-01-2027, Volume 16, (2025)
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)
Development of a shotgun metagenomics workflow for the comprehensive surveillance of biological impurities in vitamin-containing food products, Orval, Rik, Jolien D'aes, De Keersmaecker Sigrid C. J., Vanneste Kevin, Deforce Dieter, Roosens Nancy, and Fraiture Marie-Alice , LWT, Jan-09-2025, Volume 231, (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)
Genetic and epigenetic biomarkers in human biomonitoring: why needed and how can Oxford Nanopore sequencing contribute?, Gand, Mathieu, Soubry Adelheid, Mertens Birgit, Roosens Nancy, and De Keersmaecker Sigrid C. J. , Frontiers in Public Health, Jan-07-2025, Volume 13, (2025)
Investigating fungal diversity through metabarcoding for environmental samples: assessment of ITS1 and ITS2 Illumina sequencing using multiple defined mock communities with different classification methods and reference databases., Winand, Raf, Elizabet D'hooge, Van Uffelen Alexander, Bogaerts Bert, Van Braekel Julien, Hoffman Stefan, Roosens Nancy, Pierre Becker, De Keersmaecker Sigrid C. J., and Vanneste Kevin , BMC Genomics, 2025 Aug 06, Volume 26, Issue 1, (2025)
Mapping the spread of fluoroquinolone resistance: continued presence of non-susceptible in broilers., Moniek, Ringenier, Boyen Filip, Bogaerts Bert, Gand Mathieu, Vanneste Kevin, De Keersmaecker Sigrid C. J., Ilias Chantziaras, Nelima Ibrahim, Devreese Mathias, and Dewulf Jeroen , Front Vet Sci, 2025, Volume 12, (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)
Overcoming challenges in metagenomic AMR surveillance with nanopore sequencing: a case study on fluoroquinolone resistance., Bloemen, Bram, Gand Mathieu, Moniek Ringenier, Bogaerts Bert, Vanneste Kevin, Marchal Kathleen, Roosens Nancy, Dewulf Jeroen, Boyen Filip, and De Keersmaecker Sigrid C. J. , Front Microbiol, 2025, Volume 16, (2025)
Oxford Nanopore Technologies R10 sequencing enables accurate cgMLST-based bacterial outbreak investigation of and when accounting for methylation-related errors., Bogaerts, Bert, Margo Maex, Florian Commans, Goeders Nathalie, Van den Bossche An, De Keersmaecker Sigrid C. J., Roosens Nancy, Ceyssens Pieter-Jan, Mattheus Wesley, and Vanneste Kevin , J Clin Microbiol, 2025 Oct 08, Volume 63, Issue 10, (2025)
Recent and chronic ambient air pollution exposure in association with telomere length and mitochondrial DNA content in the general population, Pauline, Hautekiet, Nawrot Tim S., Martens Dries S., Bijnens Esmée M., De Keersmaecker Sigrid C. J., Van der Heyden Johan, De Clercq Eva M., and D. Saenen, Nelly , Environmental Research, Jan-07-2025, Volume 276, (2025)
Salmonella spp. as a be.Prepared Case Study for Integrating Microbial Genomic and Health Data in Public Health Surveillance, Van Laer, Amber, Commans Florian, Mattheus Wesley, Van den Bossche An, Ceyssens Pieter-Jan, Vanneste Kevin, De Keersmaecker Sigrid C. J., Gori A., Kelchtermans Michael, Milis Kato, et al. , Scientific seminar for Infectious Diseases, 22/05/2025, Brussels, Belgium, (2025)
Whole-genome sequencing of soil- and foodborne Bacillus cereus sensu lato indicates no clear association between their virulence repertoire, genomic diversity and food matrix, Jacobs, Bram, Bert Bogaerts, Marie Verhaegen, Kevin Vanneste, De Keersmaecker Sigrid C. J., Roosens Nancy, Rajkovic Andreja, Mahillon Jacques, Van Nieuwenhuysen Tom, and Van Hoorde Koenraad , International Journal of Food Microbiology, Jan-08-2025, Volume 439, (2025)
2024
Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities, Van Uffelen, Alexander, Posadas Andrés, Roosens Nancy, Marchal Kathleen, De Keersmaecker Sigrid C. J., and Vanneste Kevin , Scientific Data, 2024/08/10, Volume 11, Issue 1, (2024)
be.Prepared: An architecture to increase Belgian integration of health data as a way of strengthening preparedness for infectious diseases, Van Laer, Amber, Kelchtermans Michael, Millis Kato, Gori A., Van Cauteren Dieter, Brondeel Ruben, De Keersmaecker Sigrid C. J., Herman Philippe, Roosens Nancy, De Ridder Karin, et al. , The Belgian Presidency of the Council of the European Union, March 2024, (2024)
be.Prepared to increase Belgian integration of health data as a way of strengthening preparedness for infectious diseases, Masset, Heleen, Van Laer Amber, Kelchtermans Michael, Millis Kato, Gori A., Winand Raf, De Keersmaecker Sigrid C. J., Roosens Nancy, Herman Philippe, Brondeel Ruben, et al. , ESCMID Global 2024, 27/04/2024, Barcelona, (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, 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)
Development of a reverse transcriptase digital droplet polymerase chain reaction‐based approach for SARS‐CoV‐2 variant surveillance in wastewater, Van Poelvoorde, Laura, Gobbo Andrea, Nauwelaerts S., Verhaegen Bavo, Lesenfants Marie, Janssens Raphael, Hutse Veronik, Fraiture Marie-Alice, De Keersmaecker Sigrid C. J., Herman Philippe, et al. , Water Environment Research, Jan-03-2024, Volume 96, Issue 3, (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)
How to develop a controlled human infection model for Clostridioides difficile, Hensen, Annefleur D. O., Vehreschild Maria J. G. T., Gerding Dale N., Krut Oleg, Chen Wilbur, Young Vincent B., Tzipori Saul, Solbach Philipp, Gibani Malick Mahdi, Chiu Christopher, et al. , Clinical Microbiology and Infection, Jan-08-2024, (2024)
The potential of including the microbiome as biomarker in population-based health studies: methods and benefits, Buytaers, Florence E., Berger Nicolas, Van der Heyden Johan, Roosens Nancy, and De Keersmaecker Sigrid C. J. , Frontiers in Public Health, (2024)
Sheeppox virus genome sequences from the European outbreaks in Spain, Bulgaria, and Greece in 2022-2024., Breman, Floris C., Haegeman Andy, Philips Wannes, Krešić Nina, Hoffman Stefan, De Keersmaecker Sigrid C. J., Roosens Nancy, Montserrat Agüero, Villalba Rubén, Miteva Aleksandra, et al. , Arch Virol, 2024 Oct 30, Volume 169, Issue 11, (2024)

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