On choosing test criteria for behavioral level hardware design verification. - Anneliese von Mayrhauser; Tom Chen 001; Jan Kok; Chuck Anderson 001; Anita Read; Amjad Hajjar (HLDVT, 2000)

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)

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)

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

Analysis of the BotNet Ecosystem. - Jan Kok; Bernhard Kurz (CTTE, 2011)

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)

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)