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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)
2020
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)
2019
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)
2016
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)
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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)

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