-
1
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
T.I. Lee Transcriptional regulatory networks in Saccharomyces cerevisiae Science 298 2002 799 804
-
(2002)
Science
, vol.298
, pp. 799-804
-
-
Lee, T.I.1
-
2
-
-
0036500609
-
A genomic regulatory network for development
-
E.H. Davidson A genomic regulatory network for development Science 295 2002 1669 1678
-
(2002)
Science
, vol.295
, pp. 1669-1678
-
-
Davidson, E.H.1
-
3
-
-
0034644270
-
The segment polarity network is a robust developmental module
-
G. von Dassow, E. Meir, E.M. Munro, and G.M. Odell The segment polarity network is a robust developmental module Nature 406 2000 188 192
-
(2000)
Nature
, vol.406
, pp. 188-192
-
-
Von Dassow, G.1
Meir, E.2
Munro, E.M.3
Odell, G.M.4
-
4
-
-
0037208166
-
TRANSFAC: Transcriptional regulation, from patterns to profiles
-
V. Matys TRANSFAC: transcriptional regulation, from patterns to profiles Nucleic Acids Res. 31 2003 374 378
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 374-378
-
-
Matys, V.1
-
5
-
-
0034069495
-
Gene ontology: Tool for the unification of biology
-
M. Ashburner Gene ontology: tool for the unification of biology Gene Ontol. Consortium. Nat. Genet. 25 2000 25 29
-
(2000)
Gene Ontol. Consortium. Nat. Genet.
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
-
6
-
-
0037252718
-
The Proteome Analysis database: A tool for the in silico analysis of whole proteomes
-
M. Pruess The Proteome Analysis database: a tool for the in silico analysis of whole proteomes Nucleic Acids Res. 31 2003 414 417
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 414-417
-
-
Pruess, M.1
-
7
-
-
0037440734
-
Evolution of transcription factors and the gene regulatory network in Escherichia coli
-
M. Madan Babu, and S.A. Teichmann Evolution of transcription factors and the gene regulatory network in Escherichia coli Nucleic Acids Res. 31 2003 1234 1244
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 1234-1244
-
-
Madan Babu, M.1
Teichmann, S.A.2
-
8
-
-
0032413411
-
Predicting gene regulatory elements in silico on a genomic scale
-
A. Brazma, I. Jonassen, J. Vilo, and E. Ukkonen Predicting gene regulatory elements in silico on a genomic scale Genome Res. 8 1998 1202 1215
-
(1998)
Genome Res.
, vol.8
, pp. 1202-1215
-
-
Brazma, A.1
Jonassen, I.2
Vilo, J.3
Ukkonen, E.4
-
10
-
-
0037785111
-
Computer modeling of promoter organization as a tool to study transcriptional coregulation
-
T. Werner, S. Fessele, H. Maier, and P.J. Nelson Computer modeling of promoter organization as a tool to study transcriptional coregulation FASEB J. 17 2003 1228 1237
-
(2003)
FASEB J.
, vol.17
, pp. 1228-1237
-
-
Werner, T.1
Fessele, S.2
Maier, H.3
Nelson, P.J.4
-
11
-
-
14844313962
-
Functional inference from nonrandom distributions of conserved predicted transcription factor binding sites
-
C. Dieterich, S. Rahmann, and M. Vingron Functional inference from nonrandom distributions of conserved predicted transcription factor binding sites Bioinformatics 20 Suppl. 1 2004 I109 I115
-
(2004)
Bioinformatics
, vol.20
, Issue.SUPPL. 1
-
-
Dieterich, C.1
Rahmann, S.2
Vingron, M.3
-
12
-
-
0032562789
-
Identification of regulatory regions which confer muscle-specific gene expression
-
W.W. Wasserman, and J.W. Fickett Identification of regulatory regions which confer muscle-specific gene expression J. Mol. Biol. 278 1998 167 181
-
(1998)
J. Mol. Biol.
, vol.278
, pp. 167-181
-
-
Wasserman, W.W.1
Fickett, J.W.2
-
13
-
-
0038349948
-
Sequencing and comparison of yeast species to identify genes and regulatory elements
-
M. Kellis, N. Patterson, M. Endrizzi, B. Birren, and E.S. Lander Sequencing and comparison of yeast species to identify genes and regulatory elements Nature 423 2003 241 254
-
(2003)
Nature
, vol.423
, pp. 241-254
-
-
Kellis, M.1
Patterson, N.2
Endrizzi, M.3
Birren, B.4
Lander, E.S.5
-
14
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
C.T. Harbison Transcriptional regulatory code of a eukaryotic genome Nature 431 2004 99 104
-
(2004)
Nature
, vol.431
, pp. 99-104
-
-
Harbison, C.T.1
-
15
-
-
0036940469
-
Learning about gene regulatory networks from gene deletion experiments
-
T. Schlitt, and A. Brazma Learning about gene regulatory networks from gene deletion experiments Comp. Funct. Genom. 3 2002 499 503
-
(2002)
Comp. Funct. Genom.
, vol.3
, pp. 499-503
-
-
Schlitt, T.1
Brazma, A.2
-
16
-
-
0034616930
-
Functional discovery via a compendium of expression profiles
-
T.R. Hughes Functional discovery via a compendium of expression profiles Cell 102 2000 109 126
-
(2000)
Cell
, vol.102
, pp. 109-126
-
-
Hughes, T.R.1
-
18
-
-
0345928693
-
Building and analysing genome-wide gene disruption networks
-
J. Rung, T. Schlitt, A. Brazma, K. Freivalds, and J. Vilo Building and analysing genome-wide gene disruption networks Bioinformatics 18 2002 S202 S210
-
(2002)
Bioinformatics
, vol.18
-
-
Rung, J.1
Schlitt, T.2
Brazma, A.3
Freivalds, K.4
Vilo, J.5
-
20
-
-
0037941585
-
Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data
-
E. Segal, M. Shapira, A. Regev, D. Pe'er, D. Botstein, D. Koller, and N. Friedman Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data Nat. Genet. 34 2003 166 176
-
(2003)
Nat. Genet.
, vol.34
, pp. 166-176
-
-
Segal, E.1
Shapira, M.2
Regev, A.3
Pe'Er, D.4
Botstein, D.5
Koller, D.6
Friedman, N.7
-
21
-
-
0036699526
-
Revealing modular organization in the yeast transcriptional network
-
J. Ihmels, G. Friedlander, S. Bergmann, O. Sarig, Y. Ziv, and N. Barkai Revealing modular organization in the yeast transcriptional network Nat. Genet. 31 2002 370 377
-
(2002)
Nat. Genet.
, vol.31
, pp. 370-377
-
-
Ihmels, J.1
Friedlander, G.2
Bergmann, S.3
Sarig, O.4
Ziv, Y.5
Barkai, N.6
-
22
-
-
0037676107
-
Motifs, modules and games in bacteria
-
D.M. Wolf, and A.P. Arkin Motifs, modules and games in bacteria Curr. Opin. Microbiol. 6 2003 125 134
-
(2003)
Curr. Opin. Microbiol.
, vol.6
, pp. 125-134
-
-
Wolf, D.M.1
Arkin, A.P.2
-
23
-
-
1542286745
-
Quantifying modularity in the evolution of biomolecular systems
-
B. Snel, and M.A. Huynen Quantifying modularity in the evolution of biomolecular systems Genome Res. 14 2004 391 397
-
(2004)
Genome Res.
, vol.14
, pp. 391-397
-
-
Snel, B.1
Huynen, M.A.2
-
24
-
-
0034704248
-
Genome-wide location and function of DNA binding proteins
-
B. Ren Genome-wide location and function of DNA binding proteins Science 290 2000 2306 2309
-
(2000)
Science
, vol.290
, pp. 2306-2309
-
-
Ren, B.1
-
25
-
-
17944372930
-
Serial regulation of transcriptional regulators in the yeast cell cycle
-
I. Simon Serial regulation of transcriptional regulators in the yeast cell cycle Cell 106 2001 697 708
-
(2001)
Cell
, vol.106
, pp. 697-708
-
-
Simon, I.1
-
26
-
-
0037722938
-
Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling
-
J. Zeitlinger, I. Simon, C.T. Harbison, N.M. Hannett, T.L. Volkert, G.R. Fink, and R.A. Young Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling Cell 113 2003 395 404
-
(2003)
Cell
, vol.113
, pp. 395-404
-
-
Zeitlinger, J.1
Simon, I.2
Harbison, C.T.3
Hannett, N.M.4
Volkert, T.L.5
Fink, G.R.6
Young, R.A.7
-
27
-
-
4644326931
-
Genomic analysis of regulatory network dynamics reveals large topological changes
-
N.M. Luscombe, M.M. Babu, H. Yu, M. Snyder, S.A. Teichmann, and M. Gerstein Genomic analysis of regulatory network dynamics reveals large topological changes Nature 431 2004 308 312
-
(2004)
Nature
, vol.431
, pp. 308-312
-
-
Luscombe, N.M.1
Babu, M.M.2
Yu, H.3
Snyder, M.4
Teichmann, S.A.5
Gerstein, M.6
-
28
-
-
3042848952
-
Evidence for dynamically organized modularity in the yeast protein-protein interaction network
-
J.D. Han Evidence for dynamically organized modularity in the yeast protein-protein interaction network Nature 430 2004 88 93
-
(2004)
Nature
, vol.430
, pp. 88-93
-
-
Han, J.D.1
-
29
-
-
0346752107
-
From gene networks to gene function
-
T. Schlitt, K. Palin, J. Rung, S. Dietmann, M. Lappe, E. Ukkonen, and A. Brazma From gene networks to gene function Genome Res. 13 2003 2568 2576
-
(2003)
Genome Res.
, vol.13
, pp. 2568-2576
-
-
Schlitt, T.1
Palin, K.2
Rung, J.3
Dietmann, S.4
Lappe, M.5
Ukkonen, E.6
Brazma, A.7
-
30
-
-
0141792394
-
Correlating protein-DNA and protein-protein interaction networks
-
T. Manke, R. Bringas, and M. Vingron Correlating protein-DNA and protein-protein interaction networks J. Mol. Biol. 333 2003 75 85
-
(2003)
J. Mol. Biol.
, vol.333
, pp. 75-85
-
-
Manke, T.1
Bringas, R.2
Vingron, M.3
-
31
-
-
0034721164
-
Error and attack tolerance of complex networks
-
R. Albert, H. Jeong, and A.L. Barabasi Error and attack tolerance of complex networks Nature 406 2000 378 382
-
(2000)
Nature
, vol.406
, pp. 378-382
-
-
Albert, R.1
Jeong, H.2
Barabasi, A.L.3
-
32
-
-
0035945558
-
Correction: Error and attack tolerance of complex networks
-
R. Albert, H. Jeong, and A.L. Barabasi Correction: error and attack tolerance of complex networks Nature 409 2001 542
-
(2001)
Nature
, vol.409
, pp. 542
-
-
Albert, R.1
Jeong, H.2
Barabasi, A.L.3
-
33
-
-
0037174670
-
Network motifs: Simple building blocks of complex networks
-
R. Milo, S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, and U. Alon Network motifs: simple building blocks of complex networks Science 298 2002 824 827
-
(2002)
Science
, vol.298
, pp. 824-827
-
-
Milo, R.1
Shen-Orr, S.2
Itzkovitz, S.3
Kashtan, N.4
Chklovskii, D.5
Alon, U.6
-
34
-
-
2442537233
-
Gene regulatory network growth by duplication
-
S.A. Teichmann, and M.M. Babu Gene regulatory network growth by duplication Nat. Genet. 36 2004 492 496
-
(2004)
Nat. Genet.
, vol.36
, pp. 492-496
-
-
Teichmann, S.A.1
Babu, M.M.2
-
35
-
-
0003737454
-
-
Oxford University Press Inc USA
-
S.A. Kauffman Investigations 2002 Oxford University Press Inc USA
-
(2002)
Investigations
-
-
Kauffman, S.A.1
-
36
-
-
0000842724
-
Formalization of regulatory networks: A logical method and its automation
-
D. Thieffry, M. Colet, and R. Thomas Formalization of regulatory networks: a logical method and its automation Math. Model. Sci. Comput. 55 1993 144 151
-
(1993)
Math. Model. Sci. Comput.
, vol.55
, pp. 144-151
-
-
Thieffry, D.1
Colet, M.2
Thomas, R.3
-
37
-
-
0037270514
-
Towards reconstruction of gene networks from expression data by supervised learning
-
L.A. Soinov, M.A. Krestyaninova, and A. Brazma Towards reconstruction of gene networks from expression data by supervised learning Genome Biol. 4 2003 R6
-
(2003)
Genome Biol.
, vol.4
, pp. 6
-
-
Soinov, L.A.1
Krestyaninova, M.A.2
Brazma, A.3
-
38
-
-
0842288337
-
Inferring cellular networks using probabilistic graphical models
-
N. Friedman Inferring cellular networks using probabilistic graphical models Science 303 2004 799 805
-
(2004)
Science
, vol.303
, pp. 799-805
-
-
Friedman, N.1
-
39
-
-
0032549745
-
Genomic cis-regulatory logic: Experimental and computational analysis of a sea urchin gene
-
C.H. Yuh, H. Bolouri, and E.H. Davidson Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene Science 279 1998 1896 1902
-
(1998)
Science
, vol.279
, pp. 1896-1902
-
-
Yuh, C.H.1
Bolouri, H.2
Davidson, E.H.3
-
40
-
-
0036607698
-
A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo
-
E.H. Davidson A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo Dev Biol 246 2002 162 190
-
(2002)
Dev Biol
, vol.246
, pp. 162-190
-
-
Davidson, E.H.1
-
41
-
-
0032616683
-
Identification of genetic networks from a small number of gene expression patterns under the Boolean network model
-
T. Akutsu, S. Miyano, and S. Kuhara Identification of genetic networks from a small number of gene expression patterns under the Boolean network model Pac. Symp. Biocomput. 1999 17 28
-
(1999)
Pac. Symp. Biocomput.
, pp. 17-28
-
-
Akutsu, T.1
Miyano, S.2
Kuhara, S.3
-
42
-
-
0015823097
-
Boolean formalization of genetic control circuits
-
R. Thomas Boolean formalization of genetic control circuits J. Theor. Biol. 42 1973 563 585
-
(1973)
J. Theor. Biol.
, vol.42
, pp. 563-585
-
-
Thomas, R.1
-
43
-
-
0014671878
-
Homeostasis and differentiation in random genetic control networks
-
S. Kauffman Homeostasis and differentiation in random genetic control networks Nature 224 1969 177 178
-
(1969)
Nature
, vol.224
, pp. 177-178
-
-
Kauffman, S.1
-
46
-
-
2342578714
-
Spatiotemporal control of gene expression with pulse-generating networks
-
S. Basu, R. Mehreja, S. Thiberge, M.T. Chen, and R. Weiss Spatiotemporal control of gene expression with pulse-generating networks Proc. Natl. Acad. Sci. USA 101 2004 6355 6360
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 6355-6360
-
-
Basu, S.1
Mehreja, R.2
Thiberge, S.3
Chen, M.T.4
Weiss, R.5
-
47
-
-
0034212551
-
Engineering stability in gene networks by autoregulation
-
A. Becskei, and L. Serrano Engineering stability in gene networks by autoregulation Nature 405 2000 590 593
-
(2000)
Nature
, vol.405
, pp. 590-593
-
-
Becskei, A.1
Serrano, L.2
-
48
-
-
0034688173
-
A synthetic oscillatory network of transcriptional regulators
-
M.B. Elowitz, and S. Leibler A synthetic oscillatory network of transcriptional regulators Nature 403 2000 335 338
-
(2000)
Nature
, vol.403
, pp. 335-338
-
-
Elowitz, M.B.1
Leibler, S.2
-
49
-
-
0034688174
-
Construction of a genetic toggle switch in Escherichia coli
-
T.S. Gardner, C.R. Cantor, and J.J. Collins Construction of a genetic toggle switch in Escherichia coli Nature 403 2000 339 342
-
(2000)
Nature
, vol.403
, pp. 339-342
-
-
Gardner, T.S.1
Cantor, C.R.2
Collins, J.J.3
-
50
-
-
17144456808
-
Positive feedback in eukaryotic gene networks: Cell differentiation by graded to binary response conversion
-
A. Becskei, B. Seraphin, and L. Serrano Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion EMBO J. 20 2001 2528 2535
-
(2001)
EMBO J.
, vol.20
, pp. 2528-2535
-
-
Becskei, A.1
Seraphin, B.2
Serrano, L.3
-
51
-
-
0029028963
-
Circuit simulation of genetic networks
-
H.H. McAdams, and L. Shapiro Circuit simulation of genetic networks Science 269 1995 650 656
-
(1995)
Science
, vol.269
, pp. 650-656
-
-
McAdams, H.H.1
Shapiro, L.2
-
52
-
-
2942572373
-
Reverse engineering of gene regulatory networks: A finite state linear model
-
A. Brazma, and T. Schlitt Reverse engineering of gene regulatory networks: a finite state linear model Genome Biol. 4 2003 P5
-
(2003)
Genome Biol.
, vol.4
, pp. 5
-
-
Brazma, A.1
Schlitt, T.2
-
53
-
-
0032567081
-
Dissecting the regulatory circuitry of a eukaryotic genome
-
F.C. Holstege Dissecting the regulatory circuitry of a eukaryotic genome Cell 95 1998 717 728
-
(1998)
Cell
, vol.95
, pp. 717-728
-
-
Holstege, F.C.1
-
55
-
-
2942718723
-
Control of stochasticity in eukaryotic gene expression
-
J.M. Raser, and E.K. O'Shea Control of stochasticity in eukaryotic gene expression Science 304 2004 1811 1814
-
(2004)
Science
, vol.304
, pp. 1811-1814
-
-
Raser, J.M.1
O'Shea, E.K.2
-
56
-
-
0842285841
-
Summing up the noise in gene networks
-
J. Paulsson Summing up the noise in gene networks Nature 427 2004 415 418
-
(2004)
Nature
, vol.427
, pp. 415-418
-
-
Paulsson, J.1
-
57
-
-
0032112293
-
A genome-wide transcriptional analysis of the mitotic cell cycle
-
R.J. Cho A genome-wide transcriptional analysis of the mitotic cell cycle Mol Cell. 2 1998 65 73
-
(1998)
Mol Cell.
, vol.2
, pp. 65-73
-
-
Cho, R.J.1
-
58
-
-
0031742022
-
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
-
P.T. Spellman Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization Mol. Biol. Cell 9 1998 3273 3297
-
(1998)
Mol. Biol. Cell
, vol.9
, pp. 3273-3297
-
-
Spellman, P.T.1
-
59
-
-
3543042493
-
Periodic gene expression program of the fission yeast cell cycle
-
G. Rustici Periodic gene expression program of the fission yeast cell cycle Nat. Genet. 36 2004 809 817
-
(2004)
Nat. Genet.
, vol.36
, pp. 809-817
-
-
Rustici, G.1
-
60
-
-
12244267727
-
Global transcriptional responses of fission yeast to environmental stress
-
D. Chen Global transcriptional responses of fission yeast to environmental stress Mol. Biol. Cell 14 2003 214 229
-
(2003)
Mol. Biol. Cell
, vol.14
, pp. 214-229
-
-
Chen, D.1
-
61
-
-
0033637153
-
Genomic expression programs in the response of yeast cells to environmental changes
-
A.P. Gasch, P.T. Spellman, C.M. Kao, O. Carmel-Harel, M.B. Eisen, G. Storz, D. Botstein, and P.O. Brown Genomic expression programs in the response of yeast cells to environmental changes Mol. Biol. Cell 11 2000 4241 4257
-
(2000)
Mol. Biol. Cell
, vol.11
, pp. 4241-4257
-
-
Gasch, A.P.1
Spellman, P.T.2
Kao, C.M.3
Carmel-Harel, O.4
Eisen, M.B.5
Storz, G.6
Botstein, D.7
Brown, P.O.8
-
62
-
-
0035805255
-
Integrated genomic and proteomic analyses of a systematically perturbed metabolic network
-
T. Ideker Integrated genomic and proteomic analyses of a systematically perturbed metabolic network Science 292 2001 929 934
-
(2001)
Science
, vol.292
, pp. 929-934
-
-
Ideker, T.1
-
63
-
-
0037135134
-
Systematic identification of pathways that couple cell growth and division in yeast
-
P. Jorgensen, J.L. Nishikawa, B.J. Breitkreutz, and M. Tyers Systematic identification of pathways that couple cell growth and division in yeast Science 297 2002 395 400
-
(2002)
Science
, vol.297
, pp. 395-400
-
-
Jorgensen, P.1
Nishikawa, J.L.2
Breitkreutz, B.J.3
Tyers, M.4
|