FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data. - Youri Hoogstrate; Guido Jenster; Elena S. Martens-Uzunova (Bioinform., 2015)

FuMa: reporting overlap in RNA-seq detected fusion genes. - Youri Hoogstrate; René Böttcher; Saskia D. Hiltemann; Peter J. van der Spek; Guido Jenster; Andrew Stubbs (Bioinform., 2016)

Integration of EGA secure data access into Galaxy. - Youri Hoogstrate; Chao Zhang; Alexander Senf; Jochem Bijlard; Saskia D. Hiltemann; David van Enckevort; Susanna Repo; Jaap Heringa; Guido Jenster; Remond J. A. Fijneman; Jan-Willem Boiten; Gerrit A. Meijer; et al. (F1000Research, 2016)

Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data. - Chao Zhang; Jochem Bijlard; Christine Staiger; Serena A. Scollen; David van Enckevort; Youri Hoogstrate; Alexander Senf; Saskia D. Hiltemann; Susanna Repo; Wibo Pipping; Mariska Bierkens; Stefan Payralbe; et al. (F1000Research, 2017)

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy. - Björn A. Grüning; Jörg Fallmann; Dilmurat Yusuf; Sebastian Will; Anika Erxleben; Florian Eggenhofer; Torsten Houwaart; Bérénice Batut; Pavankumar Videm; Andrea Bagnacani; Markus Wolfien; Steffen Lott; et al. (Nucleic Acids Res., 2017)

FASTAFS: file system virtualisation of random access compressed FASTA files. - Youri Hoogstrate; Guido Jenster; Harmen J. G. van de Werken (BMC Bioinform., 2021)