Blanchette,M. and Tompa,M. (2002) Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res., 12, 739-748.
Blanchette,M. and Tompa,M. (2003) FootPrinter: A program designed for phylogenetic footprinting. Nucleic Acids Res., 31, 3840-3842.
Bockamp,E.O., McLaughlin,F., Murrell,A.M., Gottgens,B., Robb,L., Begley,C.G. and Green,A.R. (1995) Lineage-restricted regulation of the murine SCL/TAL-1 promoter. Blood, 86, 1502-1514.
Bray N, Dubchak I, Pachter L: AVID: A global alignment program. Genome Res 2003, 13:97-102.
Bray,N. and Pachter,L. (2003) MAVID multiple alignment server. Nucleic Acids Res., 31, 3525-3526.
Bray,N. and Pachter,L. (2004) MAVID: constrained ancestral alignment of multiple sequences. Genome Res., 14, 693-699.
Coessens B, Thijs G, Aerts S, Marchal K, De Smet F, Engelen K, Glenisson P, Moreau Y, Mathys J, De Moor B: INCLUSive: A web portal and service registry for microarray and regulatory sequence analysis. Nucleic Acids Res 2003, 31:3468-3470.
Davenne,M., Maconochie,M.K., Neun,R., Pattyn,A., Chambon,P., Krumlauf,R. and Rijli,F.M. (1999) Hoxa2 and Hoxb2 control dorsoventral patterns of neuronal development in the rostral hindbrain. Neuron, 22, 677-691.
Enright AJ, Van Dongen S, Ouzounis CA: An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 2002, 30:1575-1584.
Göttgens., Barton,L.M., Chapman,M.A., Sinclair,A.M., Knudsen,B., Grafham,D., Gilbert,J.G., Rogers,J., Bentley,D.R. and Green,A.R. (2002) Transcriptional regulation of the stem cell leukemia gene (SCL)--comparative analysis of five vertebrate SCL loci. Genome Res., 12, 749-759.
Jochum,W., Passegue,E. and Wagner,E.F. (2001) AP-1 in mouse development and tumorigenesis. Oncogene, 20, 2401-2412.
Kammandel,B., Chowdhury,K., Stoykova,A., Aparicio,S., Brenner,S. and Gruss,P. (1999) Distinct cis-essential modules direct the time-space pattern of the Pax6 gene activity. Dev. Biol., 205, 79-97.
Maconochie,M.K., Nonchev,S., Studer,M., Chan,S.K., Popperl,H., Sham,M.H., Mann,R.S. and Krumlauf,R. (1997) Cross-regulation in the mouse HoxB complex: the expression of Hoxb2 in rhombomere 4 is regulated by Hoxb1. Genes Dev., 11, 1885-1895.
Scemama,J.L., Hunter,M., McCallum,J., Prince,V. and Stellwag,E. (2002) Evolutionary divergence of vertebrate Hoxb2 expression patterns and transcriptional regulatory loci. J. Exp. Zool., 294, 285-299.
Sham,M.H., Vesque,C., Nonchev,S., Marshall,H., Frain,M., Gupta,R.D., Whiting,J., Wilkinson,D., Charnay,P. and Krumlauf,R. (1993) The zinc finger gene Krox20 regulates HoxB2 (Hox2.8) during hindbrain segmentation. Cell, 72, 183-196.
Sinclair,A.M., Gottgens,B., Barton,L.M., Stanley,M.L., Pardanaud,L., Klaine,M., Gering,M., Bahn,S., Sanchez,M., Bench,A.J. et al. (1999) Distinct 5' SCL enhancers direct transcription to developing brain, spinal cord, and endothelium: neural expression is mediated by GATA factor binding sites. Dev. Biol., 209, 128-142.
Thijs G, Moreau Y, De Smet F, Mathys J, Lescot M, Rombauts S, Rouze P, De Moor B, Marchal K: INCLUSive: integrated clustering, upstream sequence retrieval and motif sampling. Bioinformatics 2002, 18:331-332.
Vesque,C., Maconochie,M., Nonchev,S., Ariza-McNaughton,L., Kuroiwa,A., Charnay,P. and Krumlauf,R. (1996) Hoxb-2 transcriptional activation in rhombomeres 3 and 5 requires an evolutionarily conserved cis-acting element in addition to the Krox-20 binding site. EMBO J., 15, 5383-5396.
Vieille-Grosjean,I., Hunt,P., Gulisano,M., Boncinelli,E. and Thorogood,P. (1997) Branchial HOX gene expression and human craniofacial development. Dev. Biol., 183, 49-60.
Wingender,E., Chen,X., Fricke,E., Geffers,R., Hehl,R., Liebich,I., Krull,M., Matys,V., Michael,H., Ohnhauser,R. et al. (2001) The TRANSFAC system on gene expression regulation. Nucleic Acids Res., 29, 281-283.