-
1
-
-
33750218960
-
-
Siddharthan, R., Siggia, E. D., and van Nimwegen, E. Phylogibbs: (2005) A gibbs sampling motif finder that incorporates phylogeny. PLoS Comput. Biol. 1, e67.
-
Siddharthan, R., Siggia, E. D., and van Nimwegen, E. Phylogibbs: (2005) A gibbs sampling motif finder that incorporates phylogeny. PLoS Comput. Biol. 1, e67.
-
-
-
-
2
-
-
0027912333
-
Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
-
Lawrence, C. E., Altschul. S. F., Boguski, M. S., Liu, J. S., Neuwald, A. F., and Wootton, J. C. (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 262, 208-214.
-
(1993)
Science
, vol.262
, pp. 208-214
-
-
Lawrence, C.E.1
Altschul, S.F.2
Boguski, M.S.3
Liu, J.S.4
Neuwald, A.F.5
Wootton, J.C.6
-
3
-
-
0028685490
-
Fitting a mixture model by expectation maximization to discover motifs in biopolymers
-
Bailey, T. L. and Elkan, C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. M. Conf. Intell. Syst. Mol. Biol. 2, 28-36.
-
(1994)
Proc. M. Conf. Intell. Syst. Mol. Biol
, vol.2
, pp. 28-36
-
-
Bailey, T.L.1
Elkan, C.2
-
4
-
-
2942576308
-
Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo
-
Rajewsky, N., Vergassola, M., Gaul, U., and Siggia, E. D. (2002) Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo. BMC Bioinformatics 3, 30.
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 30
-
-
Rajewsky, N.1
Vergassola, M.2
Gaul, U.3
Siggia, E.D.4
-
5
-
-
1042264827
-
A probabilistic method to detect regulatory modules
-
Sinha, S., van Nimwegen, E., and Siggia, E. D. (2003) A probabilistic method to detect regulatory modules. Bioinformatics 19, 292-301.
-
(2003)
Bioinformatics
, vol.19
, pp. 292-301
-
-
Sinha, S.1
van Nimwegen, E.2
Siggia, E.D.3
-
6
-
-
13244271362
-
Cross-species comparison significantly improves genome-wide prediction of cisregulatory modules in Drosophila
-
Sinha, S., Schroeder, M. D., Unnerstall, U., Gaul, U., and Siggia, E. D. (2004) Cross-species comparison significantly improves genome-wide prediction of cisregulatory modules in Drosophila. BMC Bioinformatics 5, 129.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 129
-
-
Sinha, S.1
Schroeder, M.D.2
Unnerstall, U.3
Gaul, U.4
Siggia, E.D.5
-
7
-
-
12744263842
-
Computational identification of developmental enhancers: Conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura
-
Berman, B. P., Pfeiffer, B. D., Laverty, T. R., et al. (2004) Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol. 5, R61.
-
(2004)
Genome Biol
, vol.5
-
-
Berman, B.P.1
Pfeiffer, B.D.2
Laverty, T.R.3
-
8
-
-
0037154273
-
Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome
-
Berman, B. P., Barret, Y. N., Pfeiffer, D., et al. (2002) Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc. Natl. Acad. Sci. USA 99, 757-762.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 757-762
-
-
Berman, B.P.1
Barret, Y.N.2
Pfeiffer, D.3
-
9
-
-
0041389077
-
Identification of functional clusters of transcription factor binding motifs in genome sequences: The MSCAN algorithm
-
Johansson, O., Alkema, W., Wasserman, W. W., and Lagergren, J. (2003) Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm. Bioinformatics 19, 169-176.
-
(2003)
Bioinformatics
, vol.19
, pp. 169-176
-
-
Johansson, O.1
Alkema, W.2
Wasserman, W.W.3
Lagergren, J.4
-
10
-
-
0035375137
-
Computational analysis of microarray data
-
Quackenbush, J. (2001) Computational analysis of microarray data. Nat. Rev. Genet. 2, 418-427.
-
(2001)
Nat. Rev. Genet
, vol.2
, pp. 418-427
-
-
Quackenbush, J.1
-
11
-
-
0041589546
-
FootPrinter: A program designed for phylogenetic footprinting
-
Blanchette, M. and Tompa, M. (2003) FootPrinter: a program designed for phylogenetic footprinting. Nucleic Acids Res. 31, 3840-3842.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3840-3842
-
-
Blanchette, M.1
Tompa, M.2
-
12
-
-
0036107903
-
Discovery of regulatory elements by a computational method for phylogenetic footprinting
-
Blanchette, M. and Tompa, M. (2002) Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res. 12, 739-748.
-
(2002)
Genome Res
, vol.12
, pp. 739-748
-
-
Blanchette, M.1
Tompa, M.2
-
13
-
-
0038032715
-
Tracing the evolutionary history of drosophila regulatory regions with models that identify transcription factor binding sites
-
Dermitzakis, E. T., Bergman, C. M., and Clark, A. G. (2003) Tracing the evolutionary history of drosophila regulatory regions with models that identify transcription factor binding sites. Mol. Biol. Evol. 20, 703-714.
-
(2003)
Mol. Biol. Evol
, vol.20
, pp. 703-714
-
-
Dermitzakis, E.T.1
Bergman, C.M.2
Clark, A.G.3
-
14
-
-
2942517986
-
Conservation of regulatory elements between two species of drosophila
-
Emberly, E., Rajewsky, N., and Siggia, E. D. (2003) Conservation of regulatory elements between two species of drosophila. BMC Bioinformatics 4, 57.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 57
-
-
Emberly, E.1
Rajewsky, N.2
Siggia, E.D.3
-
15
-
-
0032945593
-
DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment
-
Morgenstern, B. (1999) DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 15, 211-218.
-
(1999)
Bioinformatics
, vol.15
, pp. 211-218
-
-
Morgenstern, B.1
-
16
-
-
33646893879
-
Sigma: Multiple alignment of weakly-conserved non-coding dna sequences
-
Siddharthan, R. (2006) Sigma: multiple alignment of weakly-conserved non-coding dna sequences. BMC Bioinformatics 7, 143.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 143
-
-
Siddharthan, R.1
-
17
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
18
-
-
0037398368
-
LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA
-
Brudno, M., Do, C. B., Cooper, G. M., et al. (2003) LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13, 721-731.
-
(2003)
Genome Res
, vol.13
, pp. 721-731
-
-
Brudno, M.1
Do, C.B.2
Cooper, G.M.3
-
19
-
-
0037208166
-
TRANSFAC: Transcriptional regulation, from patterns to profiles
-
Matys, V., Fricke, E., Geffers, R., et al. (2003) TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 31, 374-378.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 374-378
-
-
Matys, V.1
Fricke, E.2
Geffers, R.3
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