-
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. Int. Conf. Intell. Syst. Mol. Biol. 2: 28-36.
-
(1994)
Proc. Int. Conf. Intell. Syst. Mol. Biol
, vol.2
, pp. 28-36
-
-
Bailey, T.L.1
Elkan, C.2
-
2
-
-
33747823564
-
MEME: Discovering and analyzing DNA and protein sequence motifs
-
Bailey, T.L., Williams, N., Misleh, C. and Li, W.W. (2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res. 34: W369-W373.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Bailey, T.L.1
Williams, N.2
Misleh, C.3
Li, W.W.4
-
3
-
-
39149108426
-
Gibberellin regulates pollen viability and pollen tube growth in rice
-
Chhun, T., Aya, K., Asano, K., Yamamoto, E., Morinaka, Y., Watanabe, M., et al. (2007) Gibberellin regulates pollen viability and pollen tube growth in rice. Plant Cell 19: 3876-3888.
-
(2007)
Plant Cell
, vol.19
, pp. 3876-3888
-
-
Chhun, T.1
Aya, K.2
Asano, K.3
Yamamoto, E.4
Morinaka, Y.5
Watanabe, M.6
-
4
-
-
2142738304
-
WebLogo: A sequence logo generator
-
Crooks, G.E., Hon, G., Chandonia, J.M. and Brenner, S.E. (2004) WebLogo: a sequence logo generator. Genome Res 14: 1188-1190.
-
(2004)
Genome Res
, vol.14
, pp. 1188-1190
-
-
Crooks, G.E.1
Hon, G.2
Chandonia, J.M.3
Brenner, S.E.4
-
5
-
-
33748805219
-
Predicting transcription factor binding sites using local over-representation and comparative genomics
-
Defrance, M. and Touzet, H. (2006) Predicting transcription factor binding sites using local over-representation and comparative genomics. BMC Bioinformatics 7: 396.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 396
-
-
Defrance, M.1
Touzet, H.2
-
6
-
-
0032441150
-
Cluster analysis and display of genome-wide expression patterns
-
Eisen, M.B., Spellman, P.T., Brown, P.O. and Botstein, D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA 95: 14863-14868.
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 14863-14868
-
-
Eisen, M.B.1
Spellman, P.T.2
Brown, P.O.3
Botstein, D.4
-
7
-
-
7944235892
-
Identification and molecular characterization of novel anther-specific genes in japonica rice, Oryza sativa L. by using cDNA microarray
-
Endo, M., Tsuchiya, T., Saito, H., Matsubara, H., Hakozaki, H., et al. (2004) Identification and molecular characterization of novel anther-specific genes in japonica rice, Oryza sativa L. by using cDNA microarray. Genes Genet. Syst. 79: 213-226.
-
(2004)
Genes Genet. Syst
, vol.79
, pp. 213-226
-
-
Endo, M.1
Tsuchiya, T.2
Saito, H.3
Matsubara, H.4
Hakozaki, H.5
-
8
-
-
0038806480
-
Sperm cells of Zea mays have a complex complement of mRNAs
-
Engel, M.L., Chaboud, A., Dumas, C. and McCormick, S. (2003) Sperm cells of Zea mays have a complex complement of mRNAs. Plant J. 34: 697-707.
-
(2003)
Plant J
, vol.34
, pp. 697-707
-
-
Engel, M.L.1
Chaboud, A.2
Dumas, C.3
McCormick, S.4
-
9
-
-
0027979295
-
Plant bZIP proteins gather at ACGT elements
-
Foster, R., Izawa, T. and Chua, N.H. (1994) Plant bZIP proteins gather at ACGT elements. FASEB J. 8: 192-200.
-
(1994)
FASEB J
, vol.8
, pp. 192-200
-
-
Foster, R.1
Izawa, T.2
Chua, N.H.3
-
10
-
-
33746592051
-
Transcriptional repression distinguishes somatic from germ cell lineages in a plant
-
Haerizadeh, F., Singh, M.B. and Bhalla, P.L. (2006) Transcriptional repression distinguishes somatic from germ cell lineages in a plant. Science 313: 496-499.
-
(2006)
Science
, vol.313
, pp. 496-499
-
-
Haerizadeh, F.1
Singh, M.B.2
Bhalla, P.L.3
-
11
-
-
0032918558
-
Plant cis-acting regulatory DNA elements (PLACE) database: 1999
-
Higo, K., Ugawa, Y., Iwamoto, M. and Korenaga, T. (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res. 27: 297-300.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 297-300
-
-
Higo, K.1
Ugawa, Y.2
Iwamoto, M.3
Korenaga, T.4
-
12
-
-
54149109965
-
Comprehensive transcriptome analysis of phytohormone biosynthesis and signaling genes in microspore/pollen and tapetum of rice
-
Hirano, K., Aya, K., Hobo, T., Sakakibara, H., Kojima, M., Shim, R.A., et al. (2008) Comprehensive transcriptome analysis of phytohormone biosynthesis and signaling genes in microspore/pollen and tapetum of rice. Plant Cell Physiol. 49: 1429-1450.
-
(2008)
Plant Cell Physiol
, vol.49
, pp. 1429-1450
-
-
Hirano, K.1
Aya, K.2
Hobo, T.3
Sakakibara, H.4
Kojima, M.5
Shim, R.A.6
-
13
-
-
54149084809
-
Various spatiotemporal expression profiles of anther-expressed genes in rice
-
Hobo, T., Suwabe, K., Aya, K., Suzuki, G., Yano, K., et al. (2008) Various spatiotemporal expression profiles of anther-expressed genes in rice. Plant Cell Physiol. 49: 1417-1428.
-
(2008)
Plant Cell Physiol
, vol.49
, pp. 1417-1428
-
-
Hobo, T.1
Suwabe, K.2
Aya, K.3
Suzuki, G.4
Yano, K.5
-
14
-
-
0034628901
-
Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
-
Hughes, J.D., Estep, P.W., Tavazoie, S. and Church, G.M. (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
Estep, P.W.2
Tavazoie, S.3
Church, G.M.4
-
15
-
-
84907150192
-
The map-based sequence of the rice genome
-
International Rice Genome Sequencing Project
-
International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436: 793-800.
-
(2005)
Nature
, vol.436
, pp. 793-800
-
-
-
16
-
-
0027263978
-
Plant bZIP protein DNA binding specificity
-
Izawa, T., Foster, R. and Chua, N.H. (1993) Plant bZIP protein DNA binding specificity. J. Mol. Biol. 230: 1131-1144.
-
(1993)
J. Mol. Biol
, vol.230
, pp. 1131-1144
-
-
Izawa, T.1
Foster, R.2
Chua, N.H.3
-
17
-
-
46149103439
-
Finding sequence motifs with Bayesian models incorporating positional information: An application to transcription factor binding sites
-
Kim, N.K., Tharakaraman, K., Marino-Ramirez, L. and Spouge, J.L. (2008) Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites. BMC Bioinformatics 9: 262.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 262
-
-
Kim, N.K.1
Tharakaraman, K.2
Marino-Ramirez, L.3
Spouge, J.L.4
-
18
-
-
33751373091
-
Adding sequence context to a Markov background model improves the identification of regulatory elements
-
Kim, N.K., Tharakaraman, K. and Spouge, J.L. (2006) Adding sequence context to a Markov background model improves the identification of regulatory elements. Bioinformatics 22: 2870-2875.
-
(2006)
Bioinformatics
, vol.22
, pp. 2870-2875
-
-
Kim, N.K.1
Tharakaraman, K.2
Spouge, J.L.3
-
19
-
-
0037343103
-
Laser-capture microdissection, a tool for the global analysis of gene expression in specific plant cell types: Identification of genes expressed differentially in epidermal cells or vascular tissues of maize
-
Nakazono, M., Qiu, F., Borsuk, L.A. and Schnable, P.S. (2003) Laser-capture microdissection, a tool for the global analysis of gene expression in specific plant cell types: identification of genes expressed differentially in epidermal cells or vascular tissues of maize. Plant Cell 15: 583-596.
-
(2003)
Plant Cell
, vol.15
, pp. 583-596
-
-
Nakazono, M.1
Qiu, F.2
Borsuk, L.A.3
Schnable, P.S.4
-
20
-
-
33745331251
-
Expressed sequence tag analysis of Lilium longiflorum generative cells
-
Okada, T., Bhalla, P.L. and Singh, M.B. (2006) Expressed sequence tag analysis of Lilium longiflorum generative cells. Plant Cell Physiol. 47: 698-705.
-
(2006)
Plant Cell Physiol
, vol.47
, pp. 698-705
-
-
Okada, T.1
Bhalla, P.L.2
Singh, M.B.3
-
21
-
-
26944493068
-
Gene family analysis of the Arabidopsis pollen transcriptome reveals biological implications for cell growth, division control, and gene expression regulation
-
Pina, C., Pinto, F., Feijo, J.A. and Becker, J.D. (2005) Gene family analysis of the Arabidopsis pollen transcriptome reveals biological implications for cell growth, division control, and gene expression regulation. Plant Physiol. 138: 744-756.
-
(2005)
Plant Physiol
, vol.138
, pp. 744-756
-
-
Pina, C.1
Pinto, F.2
Feijo, J.A.3
Becker, J.D.4
-
22
-
-
38549136871
-
-
Rice Annotation Project (2008) The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res. 36: D1028-D1033.
-
Rice Annotation Project (2008) The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res. 36: D1028-D1033.
-
-
-
-
23
-
-
35848948825
-
Control of male germ-cell development in flowering plants
-
Singh, M.B. and Bhalla, P.L. (2007) Control of male germ-cell development in flowering plants. Bioessays 29: 1124-1132.
-
(2007)
Bioessays
, vol.29
, pp. 1124-1132
-
-
Singh, M.B.1
Bhalla, P.L.2
-
24
-
-
54149088703
-
Separated transcriptomes of male gametophyte and tapetum in rice: Validity of a laser microdisection (LM) microarray
-
Suwabe, K., Suzuki, G., Takahashi, H., Shiono, K., Endo, M., et al. (2008) Separated transcriptomes of male gametophyte and tapetum in rice: validity of a laser microdisection (LM) microarray. Plant Cell Physiol. 49: 1407-1416.
-
(2008)
Plant Cell Physiol
, vol.49
, pp. 1407-1416
-
-
Suwabe, K.1
Suzuki, G.2
Takahashi, H.3
Shiono, K.4
Endo, M.5
-
25
-
-
0036137323
-
A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling
-
Thijs, G., Lescot, M., Marchal, K., Rombauts, S., De Moor, B., Rouze, P., 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
Lescot, M.2
Marchal, K.3
Rombauts, S.4
De Moor, B.5
Rouze, P.6
-
26
-
-
0036108622
-
A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes
-
Thijs, G., Marchal, K., Lescot, M., Rombauts, S., De Moor, B., Rouze, P., 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
Marchal, K.2
Lescot, M.3
Rombauts, S.4
De Moor, B.5
Rouze, P.6
-
27
-
-
0042697343
-
The evolution of transcriptional regulation in eukaryotes
-
Wray, G.A., Hahn, M.W., Abouheif, E., Balhoff, J.P., Pizer, M., Rockman, M.V., et al. (2003) The evolution of transcriptional regulation in eukaryotes. Mol. Biol. Evol. 20: 1377-1419.
-
(2003)
Mol. Biol. Evol
, vol.20
, pp. 1377-1419
-
-
Wray, G.A.1
Hahn, M.W.2
Abouheif, E.3
Balhoff, J.P.4
Pizer, M.5
Rockman, M.V.6
-
28
-
-
33947667480
-
Identification of plant promoter constituents by analysis of local distribution of short sequences
-
Yamamoto, Y.Y., Ichida, H., Matsui, M., Obokata, J., Sakurai, T., Satou, M., et al. (2007) Identification of plant promoter constituents by analysis of local distribution of short sequences. BMC Genomics 8: 67.
-
(2007)
BMC Genomics
, vol.8
, pp. 67
-
-
Yamamoto, Y.Y.1
Ichida, H.2
Matsui, M.3
Obokata, J.4
Sakurai, T.5
Satou, M.6
-
30
-
-
41049114729
-
In silico discovery of transcription regulatory elements in Plasmodium falciparum
-
Young, J.A., Johnson, J.R., Benner, C., Yan, S.F., Chen, K., Le Roch, K.G., et al. (2008) In silico discovery of transcription regulatory elements in Plasmodium falciparum. BMC Genomics 9: 70.
-
(2008)
BMC Genomics
, vol.9
, pp. 70
-
-
Young, J.A.1
Johnson, J.R.2
Benner, C.3
Yan, S.F.4
Chen, K.5
Le Roch, K.G.6
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