UniFrag and GenomePrimer: selection of primers for genome-wide production of unique amplicons. - Sacha A. F. T. van Hijum; Anne de Jong; Girbe Buist; Jan Kok; Oscar P. Kuipers (Bioinform., 2003)

Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases. - Morris A. Swertz; Engbert O. de Brock; Sacha A. F. T. van Hijum; Anne de Jong; Girbe Buist; Richard J. S. Baerends; Jan Kok; Oscar P. Kuipers; Ritsert C. Jansen (Bioinform., 2004)

Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies. - Sacha A. F. T. van Hijum; Aldert L. Zomer; Oscar P. Kuipers; Jan Kok (Nucleic Acids Res., 2005)

SIMAGE: simulation of DNA-microarray gene expression data. - Casper J. Albers; Ritsert C. Jansen; Jan Kok; Oscar P. Kuipers; Sacha A. F. T. van Hijum (BMC Bioinform., 2006)

BAGEL: a web-based bacteriocin genome mining tool. - Anne de Jong; Sacha A. F. T. van Hijum; Jetta J. E. Bijlsma; Jan Kok; Oscar P. Kuipers (Nucleic Acids Res., 2006)

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)

Interactive Visualization of Gene Regulatory Networks with Associated Gene Expression Time Series Data. - Michel A. Westenberg; Sacha A. F. T. van Hijum; Andrzej T. Lulko; Oscar P. Kuipers; Jos B. T. M. Roerdink (Visualization in Medicine and Life Sciences, 2008)

The relative value of operon predictions. - Rutger W. W. Brouwer; Oscar P. Kuipers; Sacha A. F. T. van Hijum (Briefings Bioinform., 2008)

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)

Supervised Lowess normalization of comparative genome hybridization data - application to lactococcal strain comparisons. - Sacha A. F. T. van Hijum; Richard J. S. Baerends; Aldert L. Zomer; Harma A. Karsens; Victoria Martin-Requena; Oswaldo Trelles; Jan Kok; Oscar P. Kuipers (BMC Bioinform., 2008)

Visualizing Genome Expression and Regulatory Network Dynamics in Genomic and Metabolic Context. - Michel A. Westenberg; Sacha A. F. T. van Hijum; Oscar P. Kuipers; Jos B. T. M. Roerdink (Comput. Graph. Forum, 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)

MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context. - Rutger W. W. Brouwer; Sacha A. F. T. van Hijum; Oscar P. Kuipers (Bioinform., 2009)

SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks. - Michel A. Westenberg; Jos B. T. M. Roerdink; Oscar P. Kuipers; Sacha A. F. T. van Hijum (Bioinform., 2010)

BAGEL2: mining for bacteriocins in genomic data. - Anne de Jong; Auke J. van Heel; Jan Kok; Oscar P. Kuipers (Nucleic Acids Res., 2010)

BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides. - Auke J. van Heel; Anne de Jong; Manuel Montalbán-López; Jan Kok; Oscar P. Kuipers (Nucleic Acids Res., 2013)

SporeWeb: an interactive journey through the complete sporulation cycle of Bacillus subtilis. - Robyn T. Eijlander; Anne de Jong; Antonina O. Krawczyk; Siger Holsappel; Oscar P. Kuipers (Nucleic Acids Res., 2014)

BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins. - Auke J. van Heel; Anne de Jong; Chunxu Song; Jakob H. Viel; Jan Kok; Oscar P. Kuipers (Nucleic Acids Res., 2018)

FUNAGE-Pro: comprehensive web server for gene set enrichment analysis of prokaryotes. - Anne de Jong; Oscar P. Kuipers; Jan Kok (Nucleic Acids Res., 2022)