CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes. - Matthew S. Hestand; Michiel van Galen; Michel P. Villerius; Gert-Jan B. van Ommen; Johan T. den Dunnen; Peter A. C. 't Hoen (BMC Bioinform., 2008)

Literature-aided meta-analysis of microarray data: a compendium study on muscle development and disease. - Rob Jelier; Peter A. C. 't Hoen; Ellen Sterrenburg; Johan T. den Dunnen; Gert-Jan B. van Ommen; Jan A. Kors; Barend Mons (BMC Bioinform., 2008)

Microarray retriever: a web-based tool for searching and large scale retrieval of public microarray data. - Alexander E. Ivliev; Peter A. C. 't Hoen; Michel P. Villerius; Johan T. den Dunnen; Bernd W. Brandt (Nucleic Acids Res., 2008)

CLI-mate: an interface generator for command line programs. - Zuotian Tatum; Johan T. den Dunnen; Jeroen F. J. Laros (SWAT4LS, 2011)

Literature-aided interpretation of gene expression data with the weighted global test. - Rob Jelier; Jelle J. Goeman; Kristina M. Hettne; Martijn J. Schuemie; Johan T. den Dunnen; Peter A. C. 't Hoen (Briefings Bioinform., 2011)

A formalized description of the standard human variant nomenclature in Extended Backus-Naur Form. - Jeroen F. J. Laros; André Blavier; Johan T. den Dunnen; Peter E. M. Taschner (BMC Bioinform., 2011)

mRNA degradation controls differentiation state-dependent differences in transcript and splice variant abundance. - Peter A. C. 't Hoen; Michael Hirsch 003; Emile J. de Meijer; Renée X. de Menezes; Gert-Jan B. van Ommen; Johan T. den Dunnen (Nucleic Acids Res., 2011)

TSSV: a tool for characterization of complex allelic variants in pure and mixed genomes. - Seyed Yahya Anvar; Kristiaan J. van der Gaag; Jaap W. F. van der Heijden; Marcel H. A. M. Veltrop; Rolf H. A. M. Vossen; Rick H. de Leeuw; Cor Breukel; Henk P. J. Buermans; J. Sjef Verbeek; Peter de Knijff; Johan T. den Dunnen; Jeroen F. J. Laros (Bioinform., 2014)

Finding Novel Associations Across Domains Using Linked Data: a Case Study on Genetic Variants Disrupting Transcription Start Sites. - Eelke van der Horst; Rajaram Kaliyaperumal; Zuotian Tatum; Mark Thompson 002; Erik A. Schultes; Eleni Mina; Ivo Fokkema; Johan T. den Dunnen; Marco Roos; Jeroen F. J. Laros; Barend Mons; Kristina M. Hettne; et al. (SWAT4LS, 2015)

Mutalyzer 2: next generation HGVS nomenclature checker. - Mihai Lefter; Jonathan K. Vis; Martijn Vermaat; Johan T. den Dunnen; Peter E. M. Taschner; Jeroen F. J. Laros (Bioinform., 2021)