-
1
-
-
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. Inter. Conf. Intell. Syst. Mol. Biol., 2, 28-36.
-
(1994)
Proc. Inter. Conf. Intell. Syst. Mol. Biol
, vol.2
, pp. 28-36
-
-
Bailey, T.L.1
Elkan, C.2
-
2
-
-
38849109559
-
TFBS identification based on genetic algorithm with combined representations and adaptive post-processing
-
Chan,T.-M. et al. (2008) TFBS identification based on genetic algorithm with combined representations and adaptive post-processing. Bioinformatics, 24, 341-349.
-
(2008)
Bioinformatics
, vol.24
, pp. 341-349
-
-
Chan, T.-M.1
-
3
-
-
2142738304
-
WebLogo: A sequence logo generator
-
Crooks,G.E. et al. (2004) WebLogo: A sequence logo generator. Genome Res., 14, 1188-1190.
-
(2004)
Genome Res
, vol.14
, pp. 1188-1190
-
-
Crooks, G.E.1
-
4
-
-
38549140094
-
-
Gama-Castro,S. et al, 2008 RegulonDB (version 6.0, Gene regulation model of Escherichia coli k-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res, 36, D120-D124
-
Gama-Castro,S. et al. (2008) RegulonDB (version 6.0): Gene regulation model of Escherichia coli k-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res., 36, D120-D124.
-
-
-
-
5
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
Harbison,C.T. et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature, 431, 99-104.
-
(2004)
Nature
, vol.431
, pp. 99-104
-
-
Harbison, C.T.1
-
6
-
-
0032826179
-
Identifying dna and protein patterns with statistically significant alignments of multiple sequences
-
Hertz,G.Z. and Stormo,G.D. (1999) Identifying dna and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15, 563-577.
-
(1999)
Bioinformatics
, vol.15
, pp. 563-577
-
-
Hertz, G.Z.1
Stormo, G.D.2
-
7
-
-
0025372992
-
Identification of consensus patterns in unaligned dna sequences known to be functionally related
-
Hertz,G.Z. et al. (1990) Identification of consensus patterns in unaligned dna sequences known to be functionally related. Comput. Appl. Biosci., 6, 81-92.
-
(1990)
Comput. Appl. Biosci
, vol.6
, pp. 81-92
-
-
Hertz, G.Z.1
-
8
-
-
0034628901
-
Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
-
Hughes,J.D. et al. (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol., 296, 1205-1214.
-
(2000)
J. Mol. Biol
, vol.296
, pp. 1205-1214
-
-
Hughes, J.D.1
-
9
-
-
0346490298
-
Computational discovery of gene regulatory binding motifs: A bayesian perspective
-
Jensen,S. et al. (2004) Computational discovery of gene regulatory binding motifs: A bayesian perspective. Stat. Sci., 19, 188-204.
-
(2004)
Stat. Sci
, vol.19
, pp. 188-204
-
-
Jensen, S.1
-
10
-
-
3242877502
-
Biooptimizer: A Bayesian scoring function approach to motif discovery
-
Jensen,S.T. and Liu,J.S. (2004) Biooptimizer: A Bayesian scoring function approach to motif discovery. Bioinformatics, 20, 1557-1564.
-
(2004)
Bioinformatics
, vol.20
, pp. 1557-1564
-
-
Jensen, S.T.1
Liu, J.S.2
-
11
-
-
0027912333
-
Detecting subtle sequence signals: A gibbs sampling strategy for multiple alignment
-
Lawrence,C.E. et al. (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
-
12
-
-
84950424966
-
Bayesian models for multiple local sequence alignment and Gibbs sampling strategies
-
Liu,J. et al. (1995) Bayesian models for multiple local sequence alignment and Gibbs sampling strategies. J. Am. Stat. Assoc., 90, 1156-1170.
-
(1995)
J. Am. Stat. Assoc
, vol.90
, pp. 1156-1170
-
-
Liu, J.1
-
13
-
-
0035228215
-
BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes
-
Liu,X. et al. (2001) BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. In Pacific Symposium on Biocomputing, 6, pp. 127-138.
-
(2001)
Pacific Symposium on Biocomputing
, vol.6
, pp. 127-138
-
-
Liu, X.1
-
14
-
-
0029144601
-
Gibbs motif sampling: Detection of bacterial outer membrane protein repeats
-
Neuwald,A.F. et al. (1995) Gibbs motif sampling: Detection of bacterial outer membrane protein repeats. Protein Sci., 4, 1618-1632.
-
(1995)
Protein Sci
, vol.4
, pp. 1618-1632
-
-
Neuwald, A.F.1
-
15
-
-
38849122853
-
Natural similarity measures between position frequency matrices with an application to clustering
-
Pape,U.J. et al. (2008) Natural similarity measures between position frequency matrices with an application to clustering. Bioinformatics, 24, 350-357.
-
(2008)
Bioinformatics
, vol.24
, pp. 350-357
-
-
Pape, U.J.1
-
16
-
-
0035224579
-
An algorithm for finding signals of unknown length in DNA sequences
-
Pavesi,G. et al. (2001) An algorithm for finding signals of unknown length in DNA sequences. Bioinformatics, 17 (Suppl. 1, S207-S214.
-
(2001)
Bioinformatics
, vol.17
, Issue.SUPPL. 1
-
-
Pavesi, G.1
-
17
-
-
0034565285
-
Combinatorial approaches to finding subtle signals in DNA sequences
-
Pevzner,P.A. and Sze,S.H. (2000) Combinatorial approaches to finding subtle signals in DNA sequences. Proc. Inter. Conf. Intell. Syst. Mol. Biol., 8, 269-278.
-
(2000)
Proc. Inter. Conf. Intell. Syst. Mol. Biol
, vol.8
, pp. 269-278
-
-
Pevzner, P.A.1
Sze, S.H.2
-
18
-
-
0031787969
-
Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation
-
Roth,F.P. et al. (1998) Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat. Biotechnol., 16, 939-945.
-
(1998)
Nat. Biotechnol
, vol.16
, pp. 939-945
-
-
Roth, F.P.1
-
19
-
-
0025008168
-
Sequence logos: A new way to display consensus sequences
-
Schneider,T.D. and Stephens,R.M. (1990) Sequence logos: A new way to display consensus sequences. Nucleic Acids Res., 18, 6097-6100.
-
(1990)
Nucleic Acids Res
, vol.18
, pp. 6097-6100
-
-
Schneider, T.D.1
Stephens, R.M.2
-
20
-
-
0023042012
-
Information content of binding sites on nucleotide sequences
-
Schneider,T.D. et al. (1986) Information content of binding sites on nucleotide sequences. J. Mol. Biol., 188, 415-431.
-
(1986)
J. Mol. Biol
, vol.188
, pp. 415-431
-
-
Schneider, T.D.1
-
21
-
-
33751251055
-
Gibbsst: A Gibbs sampling method for motif discovery with enhanced resistance to local optima
-
Shida,K. (2006a) Gibbsst: A Gibbs sampling method for motif discovery with enhanced resistance to local optima. BMC Bioinformatics, 7 486.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 486
-
-
Shida, K.1
-
22
-
-
34250180538
-
Hybrid Gibbs-sampling algorithm for challenging motif discovery: Gibbsdst
-
Shida,K. (2006b) Hybrid Gibbs-sampling algorithm for challenging motif discovery: Gibbsdst. Genome Inform., 17, 3-13.
-
(2006)
Genome Inform
, vol.17
, pp. 3-13
-
-
Shida, K.1
-
23
-
-
0037115891
-
Discovery of novel transcription factor binding sites by statistical overrepresentation
-
Sinha,S. and Tompa,M. (2002) Discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Res. 30, 5549-5560.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 5549-5560
-
-
Sinha, S.1
Tompa, M.2
-
24
-
-
0042905768
-
YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation
-
Sinha,S. and Tompa,M. (2003) YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Res., 31, 3586-3588.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3586-3588
-
-
Sinha, S.1
Tompa, M.2
-
25
-
-
0032494751
-
Information content and free energy in DNA-protein interactions
-
Stormo,G.D. (1998) Information content and free energy in DNA-protein interactions. J. Theor. Biol., 195, 135-137.
-
(1998)
J. Theor. Biol
, vol.195
, pp. 135-137
-
-
Stormo, G.D.1
-
26
-
-
0036137323
-
A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling
-
Thijs,G. et al. (2001) A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling. Bioinformatics, 17, 1113-1122.
-
(2001)
Bioinformatics
, vol.17
, pp. 1113-1122
-
-
Thijs, G.1
-
27
-
-
0036108622
-
A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes
-
Thijs,G. et al. (2002) A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. J. Comput. Biol., 9, 447-464.
-
(2002)
J. Comput. Biol
, vol.9
, pp. 447-464
-
-
Thijs, G.1
-
28
-
-
48449090922
-
RSAT: Regulatory sequence analysis tools
-
Thomas-Chollier,M. et al. (2008) RSAT: Regulatory sequence analysis tools. Nucleic Acids Res., 36, W119-W127.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Thomas-Chollier, M.1
-
29
-
-
21144439147
-
Assessing computational tools for the discovery of transcription factor binding sites
-
Tompa,M. et al. (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nat. Biotechnol., 23, 137-144.
-
(2005)
Nat. Biotechnol
, vol.23
, pp. 137-144
-
-
Tompa, M.1
-
30
-
-
0041620271
-
Regulatory sequence analysis tools
-
van Helden,J. (2003) Regulatory sequence analysis tools. Nucleic Acids Res., 31, 3593-3596.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3593-3596
-
-
van Helden, J.1
-
31
-
-
0032483307
-
Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies
-
van Helden,J. et al. (1998) Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Mol. Biol., 281, 827-842.
-
(1998)
J. Mol. Biol
, vol.281
, pp. 827-842
-
-
van Helden, J.1
-
32
-
-
0034656326
-
Discovering regulatory elements in non-coding sequences by analysis of spaced dyads
-
van Helden,J. et al. (2000) Discovering regulatory elements in non-coding sequences by analysis of spaced dyads. Nucleic Acids Res. 28, 1808-1818.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 1808-1818
-
-
van Helden, J.1
-
33
-
-
33745611139
-
Game: Detecting cis-regulatory elements using a genetic algorithm
-
Wei,Z. and Jensen,S.T. (2006) Game: Detecting cis-regulatory elements using a genetic algorithm. Bioinformatics, 22, 1577-1584.
-
(2006)
Bioinformatics
, vol.22
, pp. 1577-1584
-
-
Wei, Z.1
Jensen, S.T.2
-
34
-
-
0032861774
-
SCPD: A promoter database of the yeast Saccharomyces cerevisiae
-
Zhu,J. and Zhang,M.Q. (1999) SCPD: A promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics, 15, 607-611.
-
(1999)
Bioinformatics
, vol.15
, pp. 607-611
-
-
Zhu, J.1
Zhang, M.Q.2
|