@article{Linhart01072008,
author = {Linhart, Chaim and Halperin, Yonit and Shamir, Ron}, 
title = {Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets},
year = {2008}, 
doi = {10.1101/gr.076117.108}, 
abstract ={We present a threefold contribution to the computational task of motif discovery, a key component in the effort of delineating the regulatory map of a genome: (1) We constructed a comprehensive large-scale, publicly-available compendium of transcription factor and microRNA target gene sets derived from diverse high-throughput experiments in several metazoans. We used the compendium as a benchmark for motif discovery tools. (2) We developed Amadeus, a highly efficient, user-friendly software platform for genome-scale detection of novel motifs, applicable to a wide range of motif discovery tasks. Amadeus improves upon extant tools in terms of accuracy, running time, output information, and ease of use and is the only program that attained a high success rate on the metazoan compendium. (3) We demonstrate that by searching for motifs based on their genome-wide localization or chromosomal distributions (without using a predefined target set), Amadeus uncovers diverse known phenomena, as well as novel regulatory motifs.}, 
URL = {http://genome.cshlp.org/content/early/2008/06/03/gr.076117.108.abstract}, 
eprint = {http://genome.cshlp.org/content/early/2008/06/03/gr.076117.108.full.pdf+html}, 
journal = {Genome Research} 
}