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)

PreP: gene expression data pre-processing. - Jorge García de la Nava; Sacha A. F. T. van Hijum; Oswaldo Trelles (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)

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)

PanCGHweb: a web tool for genotype calling in pangenome CGH data. - Jumamurat R. Bayjanov; Roland J. Siezen; Sacha A. F. T. van Hijum (Bioinform., 2010)

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)

FACIL: Fast and Accurate Genetic Code Inference and Logo. - Bas E. Dutilh; Rasa Jurgelenaite; Radek Szklarczyk; Sacha A. F. T. van Hijum; Harry R. Harhangi; Markus Schmid 002; Bart de Wild; Kees-Jan Françoijs; Henk Stunnenberg; Marc Strous; Mike S. M. Jetten; Huub J. M. Op den Camp; et al. (Bioinform., 2011)

Comparison of Multiple Weighted Hierarchies: Visual Analytics for Microbe Community Profiling. - Kasper Dinkla; Michel A. Westenberg; H. M. Timmerman; Sacha A. F. T. van Hijum; Jarke J. van Wijk (Comput. Graph. Forum, 2011)

Data mining in the Life Sciences with Random Forest: a walk in the park or lost in the jungle? - Wouter G. Touw; Jumamurat R. Bayjanov; Lex Overmars; Lennart Backus; Jos Boekhorst; Michiel Wels; Sacha A. F. T. van Hijum (Briefings Bioinform., 2013)

CiVi: circular genome visualization with unique features to analyze sequence elements. - Lex Overmars; Sacha A. F. T. van Hijum; Roland J. Siezen; Christof Francke (Bioinform., 2015)

Microbial bioinformatics for food safety and production. - Wynand Alkema; Jos Boekhorst; Michiel Wels; Sacha A. F. T. van Hijum (Briefings Bioinform., 2016)