Biology Reference
In-Depth Information
tors with dna microarrays.
Nature Genetics
, 36(12):1331-1339, 2004.
[32]
B. T. Naughton, E. Fratkin, S. Batzoglou, and D. L. Brutlag. A graph-based motif
detection algorithm models complex nucleotide dependencies in transcription factor
binding sites.
Nucleic Acids Res.
, 34:5730-5739, 2006.
[33]
R. Osada, E. Zaslavsky, and M. Singh. Comparative analysis of methods for
representing and searching for transcription factor binding sites.
Bioinformatics
,
20(18):3516-3525, 2004.
[34]
G. Pavesi, P. Mereghetti, G. Mauri, and G. Pesole. Weeder web: discovery of tran-
scription factor binding sites in a set of sequences from co-regulated genes.
Nucleic
Acids Res.
, 32:W199-W203, 2004.
[35]
P. Pevzner and S. Sze. Combinatorial approaches to finding subtle signals in dna
sequences. In
Proceedings of the Eighth International Conference on Intelligent Sys-
tems for Molecular Biology
, pages 269-278. International Society for Computational
Biology, AAAI Press, 2000.
[36]
A. Price, S. Ramabhadran, and P. Pevzner. Finding subtle motifs by branching from
sample strings.
Bioinformatics
, 19 (Suppl 2):ii149-ii155, 2003.
[37]
K. Robison, A. M. McGuire, and G. M. Church. A comprehensive library of dna-
binding site matrices for 55 proteins applied to the complete
Escherichia coli
k-12
genome.
J. Mol. Biol.
, 284:241-254, 1998.
[38]
R. Siddharthan, E. D. Siggia, and E. van Nimwegen. Phylogibbs: a gibbs sampling
motif finder that incorporates phylogeny.
PLoS Computational Biology
, 1(7):e67,
2005.
[39]
S. Sinha and M. Tompa. A program for discovery of novel transcription factor binding
sites by statistical overrepresentation.
Nucleic Acids Res.
, 31(13):3586-3588, 2003.
[40]
P. T. Spellman, G. Sherlock, M. Q. Zhang, V. R. Iyer, K. Anders, M. B. Eisen,
P. O. Brown, D. Botstein, and B. Futcher. Comprehensive identification of cell cycle-
regulated genes of the yeast saccharomyces cerevisiae by microarray hybridization.
Molecular Biology of the Cell
, 9(12):3273-3297, 1998.
[41]
G. D. Stormo. Dna binding sites:
representation and discovery.
Bioinformatics
,
16:16-23, 2000.
[42]
S. H. Sze, S. Lu, and J. Chen. Integrating sample-driven and pattern-driven ap-
proaches in motif finding. In
WABI
, pages 438-449, 2004.
[43]
S. Tavazoie, J. D Hughes, M. J. Campbell, R. J. Cho, and G.M. Church. System-
atic determination of genetic network architecture.
Nature Genetics
, 22(3):281-285,
1999.
[44]
M. Tompa. An exact method for finding short motifs in sequences, with application to
the ribosome binding site problem. In
Proceedings of the Seventh International Con-
ference on Intelligent Systems for Molecular Biology
, pages 262-271. International
Society for Computational Biology, AAAI Press, 1999.
[45]
M. Tompa, N. Li, T. L. Bailey, G. M. Church, B. De Moor, E. Eskin, A. V. Favorov,
M. C. Frith, Y. Fu, W. J. Kent, V. J. Makeev, A. A. Mironov, W. S. Noble, G. Pavesi,
G. Pesole, M. Regnier, N. Simonis, S. Sinha, G. Thijs, J. van Helden, M. Vandenbo-
gaert, Z. Weng, C. Workman, C. Ye, and Z. Zhu. Assessing computational tools for
the discovery of transcription factor binding sites.
Nature Biotech.
, 23(1):137-144,
2005.
[46]
M. Vingron and P. Pevzner. Multiple sequence comparison and consistency on mul-
Search WWH ::
Custom Search