Regulatory Element Detection Using a Probabilistic Segmentation Model. - Harmen J. Bussemaker; Hao Li; Eric D. Siggia (ISMB, 2000)

Regulatory element detection using correlation with expression (abstract only). - Harmen J. Bussemaker; Hao Li; Eric D. Siggia (RECOMB, 2001)

REDUCE: an online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data. - Crispin Roven; Harmen J. Bussemaker (Nucleic Acids Res., 2003)

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)

Dissecting complex transcriptional responses using pathway-level scores based on prior information. - Harmen J. Bussemaker; Lucas D. Ward; André Boorsma (BMC Bioinform., 2007)

Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences. - Lucas D. Ward; Harmen J. Bussemaker (ISMB, 2008)

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)