-
1
-
-
0034615580
-
Cell-cycle regulation of the DNA topoisomerase IIα promoter is mediated by proximal CCAAT boxes: possible involvement of acetylation
-
Adachi N., Nomoto M., Kohno K., Koyama H. Cell-cycle regulation of the DNA topoisomerase IIα promoter is mediated by proximal CCAAT boxes: possible involvement of acetylation. Gene 2000, 245:49-57.
-
(2000)
Gene
, vol.245
, pp. 49-57
-
-
Adachi, N.1
Nomoto, M.2
Kohno, K.3
Koyama, H.4
-
2
-
-
0034730140
-
Singular value decomposition for genome-wide expression data processing and modeling
-
Alter O., Brown P.O., Botstein D. Singular value decomposition for genome-wide expression data processing and modeling. Proc. Natl. Acad. Sci. U.S.A. 2000, 97:10101-10106.
-
(2000)
Proc. Natl. Acad. Sci. U.S.A.
, vol.97
, pp. 10101-10106
-
-
Alter, O.1
Brown, P.O.2
Botstein, D.3
-
3
-
-
38349129039
-
Revealing cell cycle control by combining model-based detection of periodic expression with novel cis-regulatory descriptors
-
Andersson C.R., Hvidsten T.R., Isaksson A., Gustafsson M.G., Komorowski J. Revealing cell cycle control by combining model-based detection of periodic expression with novel cis-regulatory descriptors. BMC Syst. Biol. 2007, 1:45.
-
(2007)
BMC Syst. Biol.
, vol.1
, pp. 45
-
-
Andersson, C.R.1
Hvidsten, T.R.2
Isaksson, A.3
Gustafsson, M.G.4
Komorowski, J.5
-
4
-
-
29444455715
-
Cell-cycle control of gene expression in budding and fission yeast
-
Bähler J. Cell-cycle control of gene expression in budding and fission yeast. Annu. Rev. Genet. 2005, 39:69-94.
-
(2005)
Annu. Rev. Genet.
, vol.39
, pp. 69-94
-
-
Bähler, J.1
-
6
-
-
78651307692
-
YPA: an integrated repository of promoter features in Saccharomyces cerevisiae
-
Chang D.T.H., Huang C.Y., Wu C.Y., Wu W.S. YPA: an integrated repository of promoter features in Saccharomyces cerevisiae. Nucleic Acids Res. 2011, 39(1):D647-D652.
-
(2011)
Nucleic Acids Res.
, vol.39
, Issue.1
-
-
Chang, D.T.H.1
Huang, C.Y.2
Wu, C.Y.3
Wu, W.S.4
-
7
-
-
42249094386
-
Systematic identification of cell cycle regulated transcription factors from microarray time series data
-
Cheng C., Li L.M. Systematic identification of cell cycle regulated transcription factors from microarray time series data. BMC Genomics 2008, 9:116.
-
(2008)
BMC Genomics
, vol.9
, pp. 116
-
-
Cheng, C.1
Li, L.M.2
-
8
-
-
0032112293
-
A genome-wide transcriptional analysis of the mitotic cell cycle
-
Cho R.J., Campbell M.J., Winzeler E.A., Steinmetz L., Conway A., Wodicka L., et al. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell 1998, 2(1):65-73.
-
(1998)
Mol. Cell
, vol.2
, Issue.1
, pp. 65-73
-
-
Cho, R.J.1
Campbell, M.J.2
Winzeler, E.A.3
Steinmetz, L.4
Conway, A.5
Wodicka, L.6
-
9
-
-
33748905107
-
Modelling the network of cell cycle transcription factors in the yeast saccharomyces cerevisiae
-
Cokus S., Rose S., Haynor D., Grønbech-Jensen N., Pellegrini M. Modelling the network of cell cycle transcription factors in the yeast saccharomyces cerevisiae. BMC Bioinformatics 2006, 7:381.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 381
-
-
Cokus, S.1
Rose, S.2
Haynor, D.3
Grønbech-Jensen, N.4
Pellegrini, M.5
-
10
-
-
14844285655
-
Comparison of computational methods for the identification of cell cycle-regulated genes
-
de Lichtenberg U., Jensen L.J., Fausbøll A., Jensen T.S., Bork P., Brunak S. Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics 2005, 21(7):1164-1171.
-
(2005)
Bioinformatics
, vol.21
, Issue.7
, pp. 1164-1171
-
-
de Lichtenberg, U.1
Jensen, L.J.2
Fausbøll, A.3
Jensen, T.S.4
Bork, P.5
Brunak, S.6
-
11
-
-
0035845501
-
Correspondence analysis applied to microarray data
-
Fellenberg K., Hauser N.C., Brors B., Neutzner A., Hoheisel J.D., Vingron M. Correspondence analysis applied to microarray data. Proc. Natl. Acad. Sci. U.S.A. 2001, 98:10781-10786.
-
(2001)
Proc. Natl. Acad. Sci. U.S.A.
, vol.98
, pp. 10781-10786
-
-
Fellenberg, K.1
Hauser, N.C.2
Brors, B.3
Neutzner, A.4
Hoheisel, J.D.5
Vingron, M.6
-
12
-
-
5044231636
-
Transcriptome of 3D7 and its gametocyte-less derivative F12 plasmodium falciparum clones during erythrocytic development using a gene-specific microarray assigned to gene regulation, cell cycle and transcription factors original research article
-
Gissot M., Refour P., Briquet S., Boschet C., Coupé S., Mazier D., et al. Transcriptome of 3D7 and its gametocyte-less derivative F12 plasmodium falciparum clones during erythrocytic development using a gene-specific microarray assigned to gene regulation, cell cycle and transcription factors original research article. Gene 2004, 341:267-277.
-
(2004)
Gene
, vol.341
, pp. 267-277
-
-
Gissot, M.1
Refour, P.2
Briquet, S.3
Boschet, C.4
Coupé, S.5
Mazier, D.6
-
13
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic denome
-
Harbison C.T., Gordon D.B., Lee T.I., Rinaldi N.J., Macisaac K.D., Danford T.W., et al. Transcriptional regulatory code of a eukaryotic denome. Nature 2004, 431:99-104.
-
(2004)
Nature
, vol.431
, pp. 99-104
-
-
Harbison, C.T.1
Gordon, D.B.2
Lee, T.I.3
Rinaldi, N.J.4
Macisaac, K.D.5
Danford, T.W.6
-
14
-
-
0032729435
-
Exploring expression data: identification and analysis of coexpressed genes
-
Heyer L.J., Kruglyak S., Yooseph S. Exploring expression data: identification and analysis of coexpressed genes. Genome Res. 1999, 9:1106-1115.
-
(1999)
Genome Res.
, vol.9
, pp. 1106-1115
-
-
Heyer, L.J.1
Kruglyak, S.2
Yooseph, S.3
-
15
-
-
80052165057
-
Human MicroRNA Target Identification by RRSM
-
in press.
-
Hsieh, W.J., Wang, H., in press. Human MicroRNA Target Identification by RRSM. J. Theor. Biol.
-
J. Theor. Biol.
-
-
Hsieh, W.J.1
Wang, H.2
-
16
-
-
0037343132
-
A multivariate approach applied to microarray data for identification of genes with cell-cycle coupled transcription
-
Johansson D., Lindgren P., Berglund A. A multivariate approach applied to microarray data for identification of genes with cell-cycle coupled transcription. Bioinformatics 2003, 19(4):467-473.
-
(2003)
Bioinformatics
, vol.19
, Issue.4
, pp. 467-473
-
-
Johansson, D.1
Lindgren, P.2
Berglund, A.3
-
17
-
-
14844293137
-
GCN5: a supervisor in all-inclusive control of vertebrate cell cycle progression through transcription regulation of various cell cycle-related genes
-
Kikuchi H., Takami Y., Nakayama T. GCN5: a supervisor in all-inclusive control of vertebrate cell cycle progression through transcription regulation of various cell cycle-related genes. Gene 2005, 347:83-97.
-
(2005)
Gene
, vol.347
, pp. 83-97
-
-
Kikuchi, H.1
Takami, Y.2
Nakayama, T.3
-
18
-
-
77957903560
-
The spatial distribution of cis regulatory elements in yeast promoters and its implications for transcription regulation
-
Lin Z., Wu W.S., Liang H., Yoo Y., Li W.H. The spatial distribution of cis regulatory elements in yeast promoters and its implications for transcription regulation. BMC Genomics 2010, 11:581.
-
(2010)
BMC Genomics
, vol.11
, pp. 581
-
-
Lin, Z.1
Wu, W.S.2
Liang, H.3
Yoo, Y.4
Li, W.H.5
-
19
-
-
0036081347
-
MIPS: a database for genomes and protein sequences
-
Mewes H.W., Frishman D., Guldener U., Mannhaupt G., Mayer K., Mokrejs M., et al. MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 2002, 30:31-34.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 31-34
-
-
Mewes, H.W.1
Frishman, D.2
Guldener, U.3
Mannhaupt, G.4
Mayer, K.5
Mokrejs, M.6
-
20
-
-
33747379083
-
The forkhead transcription factor hcm1 regulates chromosome segregation genes and fills the s-phase gap in the transcriptional circuitry of the cell cycle
-
Pramila T., Wu W., Miles S., Noble W.S., Breeden L.L. The forkhead transcription factor hcm1 regulates chromosome segregation genes and fills the s-phase gap in the transcriptional circuitry of the cell cycle. Genes Dev. 2006, 20(16):2266-2278.
-
(2006)
Genes Dev.
, vol.20
, Issue.16
, pp. 2266-2278
-
-
Pramila, T.1
Wu, W.2
Miles, S.3
Noble, W.S.4
Breeden, L.L.5
-
21
-
-
36749097895
-
High-resolution timing of cell cycle-regulated gene expression
-
Rowicka M., Kudlicki A., Tu B.P., Otwinowski Z. High-resolution timing of cell cycle-regulated gene expression. Proc. Natl. Acad. Sci. U.S.A. 2007, 104(43):16892-16897.
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.104
, Issue.43
, pp. 16892-16897
-
-
Rowicka, M.1
Kudlicki, A.2
Tu, B.P.3
Otwinowski, Z.4
-
22
-
-
18244384997
-
Comparisons of predicted genetic modules: identification of co- expressed genes through module gene flow
-
Shakhnovich B.E., Reddy T.E., Galinsky K., Mellor J., Delisi C. Comparisons of predicted genetic modules: identification of co- expressed genes through module gene flow. Genome Inform. 2004, 15(1):221-228.
-
(2004)
Genome Inform.
, vol.15
, Issue.1
, pp. 221-228
-
-
Shakhnovich, B.E.1
Reddy, T.E.2
Galinsky, K.3
Mellor, J.4
Delisi, C.5
-
23
-
-
0031742022
-
Comprehensive identification of cell cycle-regulated genes of the yeast saccharomyces cerevisiae by microarray hybridization
-
Spellman P.T., Sherlock G., Zhang M.Q., Iyer V.R., Anders K., Eisen M.B., et al. Comprehensive identification of cell cycle-regulated genes of the yeast saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 1998, 9:3273-3297.
-
(1998)
Mol. Biol. Cell
, vol.9
, pp. 3273-3297
-
-
Spellman, P.T.1
Sherlock, G.2
Zhang, M.Q.3
Iyer, V.R.4
Anders, K.5
Eisen, M.B.6
-
24
-
-
0033028596
-
Systematic determination of genetic network architecture
-
Tavazoie S., Hughes J.D., Campbell M.J., Cho R.J., Church G.M. Systematic determination of genetic network architecture. Nat. Genet. 1999, 22:281-285.
-
(1999)
Nat. Genet.
, vol.22
, pp. 281-285
-
-
Tavazoie, S.1
Hughes, J.D.2
Campbell, M.J.3
Cho, R.J.4
Church, G.M.5
-
25
-
-
33644873683
-
The YEASTRACT database: a tool for the analysis of transcription regulatory associations in saccharomyces cerevisiae
-
Teixeira M.C., Monteiro P., Jain P., Tenreiro S., Fernandes A.R., Mira N.P., et al. The YEASTRACT database: a tool for the analysis of transcription regulatory associations in saccharomyces cerevisiae. Nucleic Acids Res. 2006, 34:D446-D451.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Teixeira, M.C.1
Monteiro, P.2
Jain, P.3
Tenreiro, S.4
Fernandes, A.R.5
Mira, N.P.6
-
26
-
-
26444501081
-
Statistical methods for identifying yeast cell cycle transcription factors
-
13532-12537
-
Tsai H.K., Lu H.H., Li W.H. Statistical methods for identifying yeast cell cycle transcription factors. Proc. Natl. Acad. Sci. U.S.A. 2005, 102. 13532-12537.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
-
-
Tsai, H.K.1
Lu, H.H.2
Li, W.H.3
-
28
-
-
67650725491
-
Increasing microRNA target prediction confidence by the relative R-squared method
-
Wang H., Li W.H. Increasing microRNA target prediction confidence by the relative R-squared method. J. Theor. Biol. 2009, 259:793-798.
-
(2009)
J. Theor. Biol.
, vol.259
, pp. 793-798
-
-
Wang, H.1
Li, W.H.2
-
29
-
-
0035985177
-
Identification of gene periodically expressed in the human cell cycle and their expression in tumors
-
Whitfield M.L., Sherlock G., Saldanha A.J., Murray J.I., Ball C.A., Alexander K.E., et al. Identification of gene periodically expressed in the human cell cycle and their expression in tumors. Mol. Biol. Cell 2002, 13(6):1977-2000.
-
(2002)
Mol. Biol. Cell
, vol.13
, Issue.6
, pp. 1977-2000
-
-
Whitfield, M.L.1
Sherlock, G.2
Saldanha, A.J.3
Murray, J.I.4
Ball, C.A.5
Alexander, K.E.6
-
30
-
-
33751222851
-
Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle
-
Wu W.S., Li W.H., Chen B.S. Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics 2006, 7:421.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 421
-
-
Wu, W.S.1
Li, W.H.2
Chen, B.S.3
-
31
-
-
34447279700
-
Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data
-
Wu W.S., Li W.H., Chen B.S. Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data. BMC Bioinformatics 2007, 8:188.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 188
-
-
Wu, W.S.1
Li, W.H.2
Chen, B.S.3
-
32
-
-
55049118189
-
Identifying gene regulatory modules of heat shock response in yeast
-
Wu W.S., Li W.H. Identifying gene regulatory modules of heat shock response in yeast. BMC Genomics 2008, 9:439.
-
(2008)
BMC Genomics
, vol.9
, pp. 439
-
-
Wu, W.S.1
Li, W.H.2
-
33
-
-
58149333393
-
Systematic identification of yeast cell cycle transcription factors using multiple data sources
-
Wu W.S., Li W.H. Systematic identification of yeast cell cycle transcription factors using multiple data sources. BMC Bioinformatics 2008, 9:522.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 522
-
-
Wu, W.S.1
Li, W.H.2
-
34
-
-
33947409158
-
SPIDer: saccharomyces protein-protein interaction database
-
Wu X., Zhu L., Guo J., Fu C., Zhou H., Dong D., et al. SPIDer: saccharomyces protein-protein interaction database. BMC Bioinformatics 2006, 7:S16.
-
(2006)
BMC Bioinformatics
, vol.7
-
-
Wu, X.1
Zhu, L.2
Guo, J.3
Fu, C.4
Zhou, H.5
Dong, D.6
-
35
-
-
23744502897
-
Inferring yeast cell cycle regulators and interactions using transcription factor activities
-
Yang Y.L., Suen J., Brynildsen M.P., Galbraith S.J., Liao J.C. Inferring yeast cell cycle regulators and interactions using transcription factor activities. BMC Genomics 2005, 6(1):90.
-
(2005)
BMC Genomics
, vol.6
, Issue.1
, pp. 90
-
-
Yang, Y.L.1
Suen, J.2
Brynildsen, M.P.3
Galbraith, S.J.4
Liao, J.C.5
-
36
-
-
0035826942
-
Statistical modeling of large microarray data sets to identify stimulus response profiles
-
Zhao L.P., Prentice R., Breeden L. Statistical modeling of large microarray data sets to identify stimulus response profiles. Proc. Natl. Acad. Sci. U.S.A. 2001, 98:5631-5636.
-
(2001)
Proc. Natl. Acad. Sci. U.S.A.
, vol.98
, pp. 5631-5636
-
-
Zhao, L.P.1
Prentice, R.2
Breeden, L.3
|