View - ResearchGate

150 Davuluri44. Berezikov, E., Guryev, V., and Cuppen, E. (2005) CONREAL web server:identification and visualization of conserved transcription factor binding sites.Nucleic Acids Res. 33, W447–W450.45. Corcoran, D. L., Feingold, E., and Benos, P. V. (2005) FOOTER: a web tool forfinding mammalian DNA regulatory regions using phylogenetic footprinting.Nucleic Acids Res. 33, W442–W446.46. Das, D., Banerjee, N., and Zhang, M. Q. (2004) Interacting models of cooperativegene regulation. Proc. Natl. Acad. Sci. USA 101, 16,234–16,239.47. MacIsaac, K. D. and Fraenkel, E. (2006) Practical strategies for discoveringregulatory DNA sequence motifs. PLoS Comput. Biol. 2, E36.48. Vavouri, T. and Elgar, G. (2005) Prediction of cis-regulatory elements usingbinding site matrices—the successes, the failures and the reasons for both. Curr.Opin. Genet. Dev. 15, 395–402.49. Bulyk, M. L. (2003) Computational prediction of transcription-factor binding sitelocations. Genome Biol. 5, 201.50. Cartharius, K., Frech, K., Grote, K., et al. (2005) MatInspector and beyond:promoter analysis based on transcription factor binding sites. Bioinformatics21, 2933–2942.51. Chen, Q. K., Hertz, G. Z., and Stormo, G. D. (1995) MATRIX SEARCH 1.0: acomputer program that scans DNA sequences for transcriptional elements usinga database of weight matrices. Comput. Appl. Biosci. 11, 563–566.52. Wasserman, W. W. and Sandelin, A. (2004) Applied bioinformatics for theidentification of regulatory elements. Nat. Rev. Genet. 5, 276–287.53. Suzuki, Y., Yamashita, R., Shirota, M., et al. (2004) Sequence comparison ofhuman and mouse genes reveals a homologous block structure in the promoterregions. Genome Res. 14, 1711–1718.54. Iwama, H. and Gojobori, T. (2004) Highly conserved upstream sequences fortranscription factor genes and implications for the regulatory network. Proc. Natl.Acad. Sci. USA 101, 17,156–17,161.55. Wasserman, W. W., Palumbo, M., Thompson, W., Fickett, J. W., and Lawrence,C. E. (2000) Human-mouse genome comparisons to locate regulatory sites. Nat.Genet. 26, 225–228.56. Liu, Y., Liu, X. S., Wei, L., Altman, R. B., and Batzoglou, S. (2004) Eukaryoticregulatory element conservation analysis and identification using comparativegenomics. Genome Res. 14, 451–458.57. Loots, G. G. and Ovcharenko, I. (2004) rVISTA 2.0: evolutionary analysis oftranscription factor binding sites. Nucleic Acids Res. 32, W217–W221.58. Sandelin, A., Wasserman, W. W., and Lenhard, B. (2004) ConSite: web-basedprediction of regulatory elements using cross-species comparison. Nucleic AcidsRes. 32, W249–W252.59. Blanchette, M. and Tompa, M. (2003) FootPrinter: A program designed forphylogenetic footprinting. Nucleic Acids Res. 31, 3840–3842.60. Blanco, E., Messeguer, X., Smith, T. F., and Guigo, R. (2006) Transcription factormap alignment of promoter regions. PLoS Comput. Biol. 2, E49.