CGHMultiArray: exact P-values for multi-array comparative genomic hybridization data. - Mark A. van de Wiel; Serge J. Smeets; Ruud H. Brakenhoff; Bauke Ylstra (Bioinform., 2005)

tigaR: integrative significance analysis of temporal differential gene expression induced by genomic abnormalities. - Viktorian Miok; Saskia M. Wilting; Mark A. van de Wiel; Annelieke Jaspers; Paula I. van Noort; Ruud H. Brakenhoff; Peter J. F. Snijders; Renske D. M. Steenbergen; Wessel N. van Wieringen (BMC Bioinform., 2014)

Oramod - Software-basierte multimodale Prädiktion des Outcome von Patienten mit Mundhöhlenkarzinomen. - Kathrin Scheckenbach; Lena Colter; Vera Okpanyi; Jörg Schipper; Thomas Klenzner; Stefan Wesarg; Florian Jung; Ruud H. Brakenhoff; Steven W. Mes; Marc van de Wiel; V. Karampali; A. Ruggeri; et al. (CURAC, 2016)

Discovery of Salivary Gland Tumors' Biomarkers via Co-Regularized Sparse-Group Lasso. - Sultan Imangaliyev; Johannes H. Matse; Jan G. M. Bolscher; Ruud H. Brakenhoff; David T. W. Wong; Elisabeth Bloemena; Enno C. I. Veerman; Evgeni Levin (DS, 2017)

Improved high-dimensional prediction with Random Forests by the use of co-data. - Dennis E. te Beest; Steven W. Mes; Saskia M. Wilting; Ruud H. Brakenhoff; Mark A. van de Wiel (BMC Bioinform., 2017)

Rscreenorm: normalization of CRISPR and siRNA screen data for more reproducible hit selection. - Costa Bachas; Jasmina Hodzic; Johannes C. van der Mijn; Chantal Stoepker; Henk M. W. Verheul; Rob M. F. Wolthuis; Emanuela Felley-Bosco; Wessel N. van Wieringen; Victor W. van Beusechem; Ruud H. Brakenhoff; Renée X. de Menezes (BMC Bioinform., 2018)

ACE: absolute copy number estimation from low-coverage whole-genome sequencing data. - Jos B. Poell; Matias Mendeville; Daoud Sie; Arjen Brink; Ruud H. Brakenhoff; Bauke Ylstra (Bioinform., 2019)

HeNeCOn: An ontology for integrative research in Head and Neck cancer. - Liss Hernández; Estefanía Estévez-Priego; Laura Lopez-Perez; María Fernanda Cabrera-Umpiérrez; María Teresa Arredondo; Giuseppe Fico; Tito Poli; Silvia Rossi 004; Elena Martinelli; Lisa Licitra; Stefano Cavalieri; Loris De Cecco; et al. (Int. J. Medical Informatics, 2024)