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)

Detection and identification of authorized and unauthorized GMOs using high-throughput sequencing with the support of a sequence-based GMO database, Saltykova, Assia, Van Braekel Julien, Papazova N., Fraiture Marie-Alice, Deforce Dieter, Vanneste Kevin, De Keersmaecker Sigrid C. J., and Roosens Nancy , Food Chemistry: Molecular Sciences, Jan-07-2022, Volume 4, (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)

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)

Food Enzyme Database (FEDA): a web application gathering information about food enzyme preparations available on the European market., Deckers, Marie, Van Braekel Julien, Vanneste Kevin, Deforce Dieter, Fraiture Marie-Alice, and Roosens Nancy , Database (Oxford), 2021 10 09, Volume 2021, (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)

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)

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 of a bioinformatics pipeline for the routine analysis of Influenza whole genome sequencing data, Fu, Qiang, Winand Raf, Van Braekel Julien, Barbezange Cyril, Hutse Veronik, Thomas Isabelle, Van Gucht Steven, De Keersmaecker Sigrid C. J., Roosens Nancy, and Vanneste Kevin , European Conference on Computational Biology 2018 conference (http://eccb18.org/). 8 ? 12 September, 2018, Athens, Greece, (2018)

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)