Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data. - Feng Gao; Barrett C. Foat; Harmen J. Bussemaker (BMC Bioinform., 2004)

T-profiler: scoring the activity of predefined groups of genes using gene expression data. - André Boorsma; Barrett C. Foat; Daniel J. Vis; Frans Klis; Harmen J. Bussemaker (Nucleic Acids Res., 2005)

Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE. - Barrett C. Foat; Alexandre V. Morozov; Harmen J. Bussemaker (ISMB (Supplement of Bioinformatics), 2006)

TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors. - Barrett C. Foat; Ronald G. Tepper; Harmen J. Bussemaker (Nucleic Acids Res., 2008)