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Acknowledgements
The author thanks Mona Singh and the anonymous referees for their helpful sug-
gestions on the manuscript. E.Z. is supported by the NSF IGERT award DGE-
9972930 and the NIH award HHSN266200500021C.
References
[1]
Y. Barash, G. Elidan, N. Friedman, and T. Kaplan. Modeling dependencies in protein-
dna binding sites. In Proceedings of the Seventh Annual International Conference on
Research in Computational Molecular Biology , pages 28-37. ACM Press, 2003.
[2]
P. V. Benos, M. L. Bulyk, and G. D. Stormo. Additivity in protein-dna interactions:
how good an approximation is it? Nucleic Acids Research , 30(20):4442-4451, 2002.
[3]
M. Blanchette and M. Tompa. Discovery of regulatory elements by a computational
method for phylogenetic footprinting. Genome Res. , 12:739-748, 2002.
[4]
B. Boeckmann, A. Bairoch, R. Apweiler, M.-C. Blatter, A. Estreicher, E. Gasteiger,
M.J. Martin, K. Michoud, C. O'Donovan, I. Phan, S. Pilbout, and M. Schneider. The
swiss-prot protein knowledgebase and its supplement trembl in 2003. Nucleic Acids
Res. , 31:365-370, 2003.
[5]
J. Buhler and M. Tompa. Finding motifs using random projections. J. Comput. Biol. ,
9(2):225-242, 2002.
[6]
M. L. Bulyk, P. L. Johnson, and G. M. Church. Nucleotides of transcription factor
binding sites exert interdependent effects on the binding affinities of transcription
factors. Nucleic Acids Research , 30(5):1255—1261, 2002.
[7]
P. Cliften, P. Sundarsanam, A. Desikan, L. Fulton, B. Fulton, J. Majors, R. Water-
ston, B.A. Cohen, and M. Johnston. Finding functional features in Saccharomyces
genomes by phylogenetic footprinting. Science , 301(5629):71-76, 2003.
[8]
E. Fratkin, B. T. Naughton, D. L. Brutlag, and S. Batzoglou. Motifcut: regulatory
motifs finding with maximum density subgraphs. Bioinformatics , 22(14):e150-e157,
2006.
[9]
M. Grotschel, L. Lovasz, and A. Schrijver. Geometric Algorithms and Combinatorial
Optimization . Springer-Verlag, Berlin, Germany, 2nd edition, 1993.
[10]
D. GuhaThakurta. Computational identification of transcriptional regulatory ele-
ments in dna sequence. Nucleic Acids Res. , 34(12):3585-3598, 2006.
[11]
G. Hertz and G. Stormo. Identifying dna and protein patterns with statistically signif-
icant alignments of multiple sequences. Bioinformatics , 15:563-577, 1999.
[12]
L. S. Hon and A. N. Jain. A deterministic motif finding algorithm with application to
the human genome. Bioinformatics , 22(9):1047-1054, 2006.
[13]
J. Hu, B. Li, and D. Kihara. Limitations and potentials of current motif discovery
algorithms. Nucleic Acids Res. , 33(15):4899-4913, 2005.
[14]
J. Hughes, P. Estep, S. Tavazoie, and G. Church. Computational identification of
cis-regulatory elements associated with groups of functionally related genes in S.
cerevisiae . J. Mol. Biol. , 296:1205-1214, 2000.
[15]
U. Keich and P. Pevzner. Finding motifs in the twilight zone. Bioinformatics ,
18:1374-1381, 2002.
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