tranSMART. - Mariska Bierkens; Wim van der Linden; Kees van Bochove; Ward Weistra; Remond J. A. Fijneman; Rita Azevedo; Jan-Willem Boiten; Jeroen Beliën; Gerrit A. Meijer (J. Clin. Bioinform., 2015)

GeneBreak: detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes. - Evert van den Broek; Stef van Lieshout; Christian Rausch; Bauke Ylstra; Mark A. van de Wiel; Gerrit A. Meijer; Remond J. A. Fijneman; Sanne Abeln (F1000Research, 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)

CIBRA identifies genomic alterations with a system-wide impact on tumor biology. - Soufyan Lakbir; Caterina Buranelli; Gerrit A. Meijer; Jaap Heringa; Remond J. A. Fijneman; Sanne Abeln (Bioinform., 2024)

TrialMatchAI: An End-to-End AI-powered Clinical Trial Recommendation System to Streamline Patient-to-Trial Matching. - Majd Abdallah; Sigve Nakken; Mariska Bierkens; Johanna Galvis; Alexis Groppi; Slim Karkar; Lana Meiqari; Maria Alexandra Rujano; Steve Canham; Rodrigo Dienstmann; Remond J. A. Fijneman; Eivind Hovig; et al. (CoRR, 2025)