References
[1] Kellis, M., et al., Sequencing and comparison of yeast species to identify genes and regulatory elements[J]. Nature, 2003. 423(6937): p. 241-54.
[2] Wang, T.a.G.D.S., Combining phylogenetic data with co-regulated genes to identify regulatory motifs[J]. Bioinformatics, 2003. 19(18): p. 2369-80.
[3] Stormo, G.D., DNA binding sites: representation and discovery[J]. Bioinformatics, 2000. 16(1): p. 16-23.
[4] Tompa, M., et al., Assessing computational tools for the discovery of transcription factor binding sites[J]. Nat Biotechnol, 2005. 23(1): p. 137-44.
[5] Das, M.K.a.H.K.D., A survey of DNA motif finding algorithms[J]. BMC Bioinformatics, 2007. 8 Suppl 7: p. S21.
[6] van Nimwegen, E., Finding regulatory elements and regulatory motifs: a general probabilistic framework[J]. BMC Bioinformatics, 2007. 8 Suppl 6: p. S4.
[7] Wasserman, W.W. and J.W. Fickett, Identification of regulatory regions which confer muscle-specific gene expression[J]. J Mol Biol, 1998. 278(1): p. 167-81.
[8] Krivan, W. and W.W. Wasserman, A predictive model for regulatory sequences directing liver-specific transcription[J]. Genome Res, 2001. 11(9): p. 1559-66.
[9 Klepper, K., et al., Assessment of composite motif discovery methods[J]. BMC Bioinformatics, 2008. 9: p. 123.
[10] Klepper, K., et al. Bioinformatics and Gene Regulation[EB/OL][cited; Available from: http://tare.medisin.ntnu.no/composite.
[11] Frith, M.C., U. Hansen, and Z. Weng, Detection of cis-element clusters in higher eukaryotic DNA[J]. Bioinformatics, 2001. 17(10): p. 878-89.
[12] Aerts, S., et al., Computational detection of cis -regulatory modules[J]. Bioinformatics, 2003. 19 Suppl 2: p. ii5-14.
[13] Sinha, S., E. van Nimwegen, and E.D. Siggia, A probabilistic method to detect regulatory modules[J]. Bioinformatics, 2003. 19 Suppl 1: p. i292-301.
[14] Johansson, O., et al., Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm[J]. Bioinformatics, 2003. 19 Suppl 1: p. i169-76.
[15] Frith, M.C., M.C. Li, and Z. Weng, Cluster-Buster: Finding dense clusters of motifs in DNA sequences[J]. Nucleic Acids Res, 2003. 31(13): p. 3666-8.
[16] Kel, A., et al., Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations[J]. Bioinformatics, 2006. 22(10): p. 1190-7.
[17] Matys, V., et al., TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes[J]. Nucleic Acids Res, 2006. 34(Database issue): p. D108-10.
[18] Boyer, L.A., et al., Core transcriptional regulatory circuitry in human embryonic stem cells[J]. Cell, 2005. 122(6): p. 947-56.