@article{Thompson01102004,
author = {Thompson, William and Palumbo, Michael J. and Wasserman, Wyeth W. and Liu, Jun S. and Lawrence, Charles E.}, 
title = {Decoding Human Regulatory Circuits},
volume = {14}, 
number = {10a}, 
pages = {1967-1974}, 
year = {2004}, 
doi = {10.1101/gr.2589004}, 
abstract ={Clusters of transcription factor binding sites (TFBSs) which direct gene expression constitute cis-regulatory modules (CRMs). We present a novel algorithm, based on Gibbs sampling, which locates, de novo, the cis features of these CRMs, their component TFBSs, and the properties of their spatial distribution. The algorithm finds 69% of experimentally reported TFBSs and 85% of the CRMs in a reference data set of regions upstream of genes differentially expressed in skeletal muscle cells. A discriminant procedure based on the output of the model specifically discriminated regulatory sequences in muscle-specific genes in an independent test set. Application of the method to the analysis of 2710 10-kb fragments upstream of annotated human genes identified 17 novel candidate modules with a false discovery rate ≤0.05, demonstrating the applicability of the method to genome-scale data.}, 
URL = {http://genome.cshlp.org/content/14/10a/1967.abstract}, 
eprint = {http://genome.cshlp.org/content/14/10a/1967.full.pdf+html}, 
journal = {Genome Research} 
}