-
1
-
-
0034730140
-
Singular value decomposition for genome-wide expression data processing and modeling
-
Alter, O., Brown, P., and Botstein, D. 2000. Singular value decomposition for genome-wide expression data processing and modeling. Proc. Natl. Acad. Sci. USA 97, 10101-10106.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 10101-10106
-
-
Alter, O.1
Brown, P.2
Botstein, D.3
-
2
-
-
35348872479
-
Analysis of time-series gene expression data: Methods, challenges, and opportunities
-
Androulakis, I., Yang, E., and Almon, R. 2007. Analysis of time-series gene expression data: methods, challenges, and opportunities. Annu. Rev. Biomed. Eng. 9, 205-228.
-
(2007)
Annu. Rev. Biomed. Eng
, vol.9
, pp. 205-228
-
-
Androulakis, I.1
Yang, E.2
Almon, R.3
-
3
-
-
16344369007
-
Clustering of gene expression data using a local shape-based similarity measure
-
Balasubramaniyan, R., Hullermeier, E., Weskamp, N., et al. 2005. Clustering of gene expression data using a local shape-based similarity measure. Bioinformatics 21, 1069-1077.
-
(2005)
Bioinformatics
, vol.21
, pp. 1069-1077
-
-
Balasubramaniyan, R.1
Hullermeier, E.2
Weskamp, N.3
-
4
-
-
0041346457
-
Continuous representations of time series gene expression data
-
Bar-Joseph, Z., Gerber, G., Gifford, D., et al. 2003. Continuous representations of time series gene expression data. J. Comput. Biol. 10, 241-256.
-
(2003)
J. Comput. Biol
, vol.10
, pp. 241-256
-
-
Bar-Joseph, Z.1
Gerber, G.2
Gifford, D.3
-
5
-
-
0035149551
-
Remodeling of yeast genome expression in response to environmental changes
-
Causton, H., Ren, B., Koh, S., et al. 2001. Remodeling of yeast genome expression in response to environmental changes. Mol. Biol. Cell 12, 323-337.
-
(2001)
Mol. Biol. Cell
, vol.12
, pp. 323-337
-
-
Causton, H.1
Ren, B.2
Koh, S.3
-
6
-
-
55749116150
-
Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network
-
Chechik, G., Oh, E., Rando, O., et al. 2008. Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network. Nature Biotechnology 26, 1251-1259.
-
(2008)
Nature Biotechnology
, vol.26
, pp. 1251-1259
-
-
Chechik, G.1
Oh, E.2
Rando, O.3
-
7
-
-
13244284551
-
Dynamic complex formation during the yeast cell cycle
-
de Lichtenberg, U., Jensen, L.J., Brunak, S., et al. 2005. Dynamic complex formation during the yeast cell cycle. Science 307, 724-727.
-
(2005)
Science
, vol.307
, pp. 724-727
-
-
de Lichtenberg, U.1
Jensen, L.J.2
Brunak, S.3
-
8
-
-
0030669030
-
Exploring the metabolic and genetic control of gene expression on a genomic scale
-
DeRisi, J., Iyer, V., and Brown, P. 1997. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680.
-
(1997)
Science
, vol.278
, pp. 680
-
-
DeRisi, J.1
Iyer, V.2
Brown, P.3
-
9
-
-
28644452470
-
Clustering short time series gene expression data
-
Ernst, J., Nau, G., and Bar-Joseph, Z. 2005. Clustering short time series gene expression data. Bioinformatics 21, i159-i168.
-
(2005)
Bioinformatics
, vol.21
-
-
Ernst, J.1
Nau, G.2
Bar-Joseph, Z.3
-
10
-
-
0035162698
-
Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog MEC1p
-
Gasch, A., Huang, M., Metzner, S., et al. 2001. Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog MEC1p. Mol. Biol. Cell 12, 2987-3003.
-
(2001)
Mol. Biol. Cell
, vol.12
, pp. 2987-3003
-
-
Gasch, A.1
Huang, M.2
Metzner, S.3
-
11
-
-
0033637153
-
Genomic expression programs in the response of yeast cells to environmental changes
-
Gasch, A., Spellman, P., Kao, C., et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11, 4241-4257.
-
(2000)
Mol. Biol. Cell
, vol.11
, pp. 4241-4257
-
-
Gasch, A.1
Spellman, P.2
Kao, C.3
-
12
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
Harbison, C.T., Gordon, D.B., Lee, T.I., 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
Gordon, D.B.2
Lee, T.I.3
-
13
-
-
0035852785
-
Dynamic modelling of gene expression data
-
Holter, N., Maritan, A., Cieplak, M., et al. 2001. Dynamic modelling of gene expression data. Proc. Natl. Acad. Sci. USA 98, 1693-1698.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 1693-1698
-
-
Holter, N.1
Maritan, A.2
Cieplak, M.3
-
14
-
-
0034682504
-
Fundamental patterns underlying gene expression profiles: Simplicity from complexity
-
Holter, N., Mitra, M., Maritan, A., et al. 2000. Fundamental patterns underlying gene expression profiles: simplicity from complexity. Proc. Natl. Acad. Sci. USA 97, 8409-8414.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 8409-8414
-
-
Holter, N.1
Mitra, M.2
Maritan, A.3
-
15
-
-
0035875010
-
Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria
-
Kalir, S., McClure, J., Pabbaraju, K., et al. 2001. Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria. Science 292, 2080-2083.
-
(2001)
Science
, vol.292
, pp. 2080-2083
-
-
Kalir, S.1
McClure, J.2
Pabbaraju, K.3
-
16
-
-
34250735674
-
RNA regulons: Coordination of post-transcriptional events
-
Keene, J. 2007. RNA regulons: coordination of post-transcriptional events. Nat. Rev. Genet. 8, 533-543.
-
(2007)
Nat. Rev. Genet
, vol.8
, pp. 533-543
-
-
Keene, J.1
-
17
-
-
29344439378
-
Effects of iodine on global gene expression in Saccharomyces cerevisiae
-
Kitagawa, E., Akama, K., and Iwahashi, H. 2005. Effects of iodine on global gene expression in Saccharomyces cerevisiae. Biosci. Biotechnol. Biochem. 69, 2285-2293.
-
(2005)
Biosci. Biotechnol. Biochem
, vol.69
, pp. 2285-2293
-
-
Kitagawa, E.1
Akama, K.2
Iwahashi, H.3
-
18
-
-
18144415477
-
Dynamical remodeling of the transcriptome during short-term anaerobiosis in Saccharomyces cerevisiae: Differential response and role of MSN2 and/or MSN4 and other factors in galactose and glucose media
-
Lai, L., Kosorukoff, A., Burke, P., et al. 2005. Dynamical remodeling of the transcriptome during short-term anaerobiosis in Saccharomyces cerevisiae: differential response and role of MSN2 and/or MSN4 and other factors in galactose and glucose media. Mol. Cell Biol. 25, 4075-4091.
-
(2005)
Mol. Cell Biol
, vol.25
, pp. 4075-4091
-
-
Lai, L.1
Kosorukoff, A.2
Burke, P.3
-
19
-
-
43449096915
-
Chromatin decouples promoter threshold from dynamic range
-
Lam, F., Steger, D., and O'Shea, E. 2008. Chromatin decouples promoter threshold from dynamic range. Nature 453, 246.
-
(2008)
Nature
, vol.453
, pp. 246
-
-
Lam, F.1
Steger, D.2
O'Shea, E.3
-
20
-
-
0037339264
-
Clustering of time-course gene expression data using a mixed-effects model with B-splines
-
Luan, Y., and Li, H. 2003. Clustering of time-course gene expression data using a mixed-effects model with B-splines. Bioinformatics 19, 474-482.
-
(2003)
Bioinformatics
, vol.19
, pp. 474-482
-
-
Luan, Y.1
Li, H.2
-
21
-
-
33644855951
-
A data-driven clustering method for time course gene expression data
-
Ma, P., Castillo-Davis, C., Zhong, W., et al. 2006. A data-driven clustering method for time course gene expression data. Nucleic Acids Res. 34, 1261.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 1261
-
-
Ma, P.1
Castillo-Davis, C.2
Zhong, W.3
-
22
-
-
29144446889
-
A haploid-specific transcriptional response to irradiation in Saccharomyces cerevisiae
-
Mercier, G., Berthault, N., Touleimat, N., et al. 2005. A haploid-specific transcriptional response to irradiation in Saccharomyces cerevisiae. Nucleic Acids Res. 33, 6635.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 6635
-
-
Mercier, G.1
Berthault, N.2
Touleimat, N.3
-
23
-
-
4143058645
-
Gene networks inference using dynamic Bayesian networks
-
Perrin, B., Ralaivola, L., Mazurie, A., et al. 2003. Gene networks inference using dynamic Bayesian networks. Bioinformatics 19, 138-148.
-
(2003)
Bioinformatics
, vol.19
, pp. 138-148
-
-
Perrin, B.1
Ralaivola, L.2
Mazurie, A.3
-
24
-
-
0035861975
-
Beyond synexpression relationships: Local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions
-
Qian, J., Dolled-Filhart, M., Lin, Y., et al. 2001. Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions. J. Mol. Biol. 314, 1053-1066.
-
(2001)
J. Mol. Biol
, vol.314
, pp. 1053-1066
-
-
Qian, J.1
Dolled-Filhart, M.2
Lin, Y.3
-
25
-
-
0037047161
-
Cluster analysis of gene expression dynamics
-
Ramoni, M., Sebastiani, P., and Kohane, I. 2002. Cluster analysis of gene expression dynamics. Proc. Natl. Acad. Sci. USA 99, 9121-9126.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 9121-9126
-
-
Ramoni, M.1
Sebastiani, P.2
Kohane, I.3
-
26
-
-
4944252468
-
Using hidden Markov models to analyze gene expression time course data
-
Schliep, A., Schonhuth, A., and Steinhoff, C. 2003. Using hidden Markov models to analyze gene expression time course data. Bioinformatics 19, 1264-1272.
-
(2003)
Bioinformatics
, vol.19
, pp. 1264-1272
-
-
Schliep, A.1
Schonhuth, A.2
Steinhoff, C.3
-
27
-
-
0037007033
-
Analysis of cell-cycle gene expression in human cells as determined by microarrays and double-thymidine block synchronization
-
Shedden, K., and Cooper, S. 2002. Analysis of cell-cycle gene expression in human cells as determined by microarrays and double-thymidine block synchronization. Proc. Natl. Acad. Sci. USA 99, 4379-4384.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 4379-4384
-
-
Shedden, K.1
Cooper, S.2
-
28
-
-
28644440465
-
Combined static and dynamic analysis for determining the quality of time-series expression profiles
-
Simon, I., Siegfried, Z., Ernst, J., et al. 2005. Combined static and dynamic analysis for determining the quality of time-series expression profiles. Nat. Biotechnol. 23, 1503-1508.
-
(2005)
Nat. Biotechnol
, vol.23
, pp. 1503-1508
-
-
Simon, I.1
Siegfried, Z.2
Ernst, J.3
-
29
-
-
0031742022
-
Comprehensive identification of cell cycle regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
-
Spellman, P., Sherlock, G., Zhang, M., et al. 1998. Comprehensive identification of cell cycle regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9, 3273-3297.
-
(1998)
Mol. Biol. Cell
, vol.9
, pp. 3273-3297
-
-
Spellman, P.1
Sherlock, G.2
Zhang, M.3
-
30
-
-
24644519314
-
Significance analysis of time course microarray experiments
-
Storey, J., Xiao, W., Leek, J., et al. 2005. Significance analysis of time course microarray experiments. Proc. Natl. Acad. Sci. USA 102, 12837.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 12837
-
-
Storey, J.1
Xiao, W.2
Leek, J.3
-
31
-
-
33746691336
-
Extensive low-affinity transcriptional interactions in the yeast genome
-
Tanay, A. 2006. Extensive low-affinity transcriptional interactions in the yeast genome. Genome Res. 16, 962.
-
(2006)
Genome Res
, vol.16
, pp. 962
-
-
Tanay, A.1
-
32
-
-
0034960264
-
Missing value estimation methods for DNA microarrays
-
Troyanskaya, O., Cantor, M., Sherlock, G., et al. 2001. Missing value estimation methods for DNA microarrays. Bioinformatics 17, 520-525.
-
(2001)
Bioinformatics
, vol.17
, pp. 520-525
-
-
Troyanskaya, O.1
Cantor, M.2
Sherlock, G.3
-
33
-
-
0031915896
-
Large-scale temporal gene expression mapping of central nervous system development
-
Wen, X., Fuhrman, S., Michaels, G., et al. 1998. Large-scale temporal gene expression mapping of central nervous system development. Proc. Natl. Acad. Sci. USA 95, 334.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 334
-
-
Wen, X.1
Fuhrman, S.2
Michaels, G.3
-
34
-
-
0347093600
-
Identifying periodically expressed transcripts in microarray time series data
-
Wichert, S., Fokianos, K., and Strimmer, K. 2004. Identifying periodically expressed transcripts in microarray time series data. Bioinformatics 20, 5-20.
-
(2004)
Bioinformatics
, vol.20
, pp. 5-20
-
-
Wichert, S.1
Fokianos, K.2
Strimmer, K.3
-
35
-
-
18044382523
-
Transcriptional response of Saccharomyces cerevisiae to the plasma membrane-perturbing compound chitosan
-
Zakrzewska, A., Boorsma, A., Brul, S., et al. 2004. Transcriptional response of Saccharomyces cerevisiae to the plasma membrane-perturbing compound chitosan. Eukaryotic Cell 4, 703-715.
-
(2004)
Eukaryotic Cell
, vol.4
, pp. 703-715
-
-
Zakrzewska, A.1
Boorsma, A.2
Brul, S.3
-
36
-
-
2442526837
-
Just-in-time transcription program in metabolic pathways
-
Zaslaver, A., Mayo, A., Rosenberg, R., et al. 2004. Just-in-time transcription program in metabolic pathways. Nat. Genet. 36, 486-491.
-
(2004)
Nat. Genet
, vol.36
, pp. 486-491
-
-
Zaslaver, A.1
Mayo, A.2
Rosenberg, R.3
-
37
-
-
0035826942
-
Statistical modeling of large microarray data sets to identify stimulus-response profiles
-
Zhao, L., Prentice, R., and Breeden, L. 2001. Statistical modeling of large microarray data sets to identify stimulus-response profiles. Proc. Natl. Acad. Sci. USA 98, 5631-5636.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 5631-5636
-
-
Zhao, L.1
Prentice, R.2
Breeden, L.3
-
38
-
-
12744261506
-
A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data
-
Zou, M., and Conzen, S. 2005. A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data. Bioinformatics 21, 71-79.
-
(2005)
Bioinformatics
, vol.21
, pp. 71-79
-
-
Zou, M.1
Conzen, S.2
|