Project Key References:

 

Bailey TL, Elkan C (1995) The value of prior knowledge in discovering motifs with MEME. Proc Int Conf Intell Syst Mol Biol 3: 21-29

Crooks GE, Hon G, Chandonia J-M, Brenner S.E. (2004) WebLogo: a sequence logo generator, Genome Research, 14:1188-1190

Frith MC, Fu Y, Yu L, Chen JF, Hansen U, Weng Z (2004) Detection of functional DNA motifs via statistical over-representation, Nucleic Acids Research, 32: 1372-1381

Liseron-Monfils C, Lewis T, Ashlock D, McNicholas P, Fauteux F, Strömvik M, Raizada MN (2013) Promzea: A pipeline for discovery of co-regulatory motifs in maize and other plant species and its application to the anthocyanin and phlobaphene biosynthetic pathways and Maize Development Atlas Promzea in Review

Liu X, Brutlag D, Liu J (2001) BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. In RB Altman, AK Dunker, L Hunter, TE Klein, eds, Pacific Symposium on Biocomputing 2001, pp 127-138

Pavesi G, Zambelli F, Pesole G (2007) WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences. BMC Bioinformatics 8: 46

Zambelli F, Pesole G, Pavesi G (2009) Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes, Nucleic Acids Research, 37: W247-W252