Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm. - Öjvind Johansson; Wynand Alkema; Wyeth W. Wasserman; Jens Lagergren (ISMB (Supplement of Bioinformatics), 2003)

MSCAN: identification of functional clusters of transcription factor binding sites. - Wynand Alkema; Öjvind Johansson; Jens Lagergren; Wyeth W. Wasserman (Nucleic Acids Res., 2004)

JASPAR: an open-access database for eukaryotic transcription factor binding profiles. - Albin Sandelin; Wynand Alkema; Pär G. Engström; Wyeth W. Wasserman; Boris Lenhard (Nucleic Acids Res., 2004)

CoPub: a literature-based keyword enrichment tool for microarray data analysis. - Raoul Frijters; Bart Heupers; Pieter van Beek; Maurice Bouwhuis; René C. van Schaik; Jacob de Vlieg; Jan Polman; Wynand Alkema (Nucleic Acids Res., 2008)

PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood. - Tim Hulsen; Peter M. A. Groenen; Jacob de Vlieg; Wynand Alkema (Nucleic Acids Res., 2009)

Literature Mining for the Discovery of Hidden Connections between Drugs, Genes and Diseases. - Raoul Frijters; Marianne van Vugt; Ruben Smeets; René C. van Schaik; Jacob de Vlieg; Wynand Alkema (PLoS Comput. Biol., 2010)

ss-TEA: Entropy based identification of receptor specific ligand binding residues from a multiple sequence alignment of class A GPCRs. - Marijn P. A. Sanders; Wilco W. M. Fleuren; Stefan Verhoeven; Sven van den Beld; Wynand Alkema; Jacob de Vlieg; Jan P. G. Klomp (BMC Bioinform., 2011)

CoPub update: CoPub 5.0 a text mining system to answer biological questions. - Wilco W. M. Fleuren; Stefan Verhoeven; Raoul Frijters; Bart Heupers; Jan Polman; René C. van Schaik; Jacob de Vlieg; Wynand Alkema (Nucleic Acids Res., 2011)

Identification of new biomarker candidates for glucocorticoid induced insulin resistance using literature mining. - Wilco W. M. Fleuren; Erik J. M. Toonen; Stefan Verhoeven; Raoul Frijters; Tim Hulsen; Ton Rullmann; René C. van Schaik; Jacob de Vlieg; Wynand Alkema (BioData Min., 2013)

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