FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes. - Evert-Jan Blom; Dinne W. J. Bosman; Sacha A. F. T. van Hijum; Rainer Breitling; Lars Tijsma; Remko Silvis; Jos B. T. M. Roerdink; Oscar P. Kuipers (Bioinform., 2007)

MOVE: A Multi-Level Ontology-Based Visualization and Exploration Framework for Genomic Networks. - Diederik W. J. Bosman; Evert-Jan Blom; Patrick J. Ogao; Oscar P. Kuipers; Jos B. T. M. Roerdink (Silico Biol., 2007)

DISCLOSE : DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites. - Evert-Jan Blom; Sacha A. F. T. van Hijum; Klaas J. Hofstede; Remko Silvis; Jos B. T. M. Roerdink; Oscar P. Kuipers (BMC Bioinform., 2008)

MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data. - Evert-Jan Blom; Jos B. T. M. Roerdink; Oscar P. Kuipers; Sacha A. F. T. van Hijum (Bioinform., 2009)