-
1
-
-
14644396645
-
Functional cartography of complex metabolic networks
-
Guimera R, Nunes Amaral LA (2005) Functional cartography of complex metabolic networks. Nature 433: 895-900.
-
(2005)
Nature
, vol.433
, pp. 895-900
-
-
Guimera, R.1
Nunes Amaral, L.A.2
-
2
-
-
0034943378
-
The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes
-
Wagner A (2001) The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol Biol Evol 18: 1283-1292.
-
(2001)
Mol Biol Evol
, vol.18
, pp. 1283-1292
-
-
Wagner, A.1
-
3
-
-
0036578795
-
Network motifs in the transcriptional regulation network of Escherichia coli
-
Shen-Orr SS, Milo R, Mangan S, Alon U (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 31: 64-68.
-
(2002)
Nat Genet
, vol.31
, pp. 64-68
-
-
Shen-Orr, S.S.1
Milo, R.2
Mangan, S.3
Alon, U.4
-
4
-
-
0034029892
-
Robustness against mutations in genetic networks of yeast
-
Wagner A (2000) Robustness against mutations in genetic networks of yeast. Nat Genet 24: 355-361.
-
(2000)
Nat Genet
, vol.24
, pp. 355-361
-
-
Wagner, A.1
-
5
-
-
0036500993
-
Systems biology: A brief overview
-
Kitano H (2002) Systems biology: A brief overview. Science 295: 1662-1664.
-
(2002)
Science
, vol.295
, pp. 1662-1664
-
-
Kitano, H.1
-
7
-
-
25444448797
-
Spontaneous evolution of modularity and network motifs
-
Kashtan N, Alon U (2005) Spontaneous evolution of modularity and network motifs. Proc Natl Acad Sci U S A 102: 13773-13778.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 13773-13778
-
-
Kashtan, N.1
Alon, U.2
-
8
-
-
1942469444
-
Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction
-
Yeger-Lotem E, Sattath S, Kashtan N, Itzkovitz S, Milo R, et al. (2004) Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. Proc Natl Acad Sci U S A 101: 5934-5939.
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 5934-5939
-
-
Yeger-Lotem, E.1
Sattath, S.2
Kashtan, N.3
Itzkovitz, S.4
Milo, R.5
-
9
-
-
0034688174
-
Construction of a genetic toggle switch in Escherichia coli
-
Gardner TS, Cantor CR, Collins JJ (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403: 339-342.
-
(2000)
Nature
, vol.403
, pp. 339-342
-
-
Gardner, T.S.1
Cantor, C.R.2
Collins, J.J.3
-
10
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, 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
Rinaldi, N.J.4
Macisaac, K.D.5
-
11
-
-
2442537233
-
Gene regulatory network growth by duplication
-
Teichmann SA, Babu MM (2004) Gene regulatory network growth by duplication. Nat Genet 36: 492-496.
-
(2004)
Nat Genet
, vol.36
, pp. 492-496
-
-
Teichmann, S.A.1
Babu, M.M.2
-
12
-
-
3042722019
-
Evolutionary changes in cis and trans gene regulation
-
Wittkopp PJ, Haerum BK, Clark AG (2004) Evolutionary changes in cis and trans gene regulation. Nature 430: 85-88.
-
(2004)
Nature
, vol.430
, pp. 85-88
-
-
Wittkopp, P.J.1
Haerum, B.K.2
Clark, A.G.3
-
13
-
-
48949094754
-
Local regulatory variation in Saccharomyces cerevisiae
-
doi:10.1371/journal.pgen.0010025
-
Ronald J, Brem RB, Whittle J, Kruglyak L (2005) Local regulatory variation in Saccharomyces cerevisiae. PLoS Genet 1: e25. doi:10.1371/journal.pgen.0010025
-
(2005)
PLoS Genet
, vol.1
-
-
Ronald, J.1
Brem, R.B.2
Whittle, J.3
Kruglyak, L.4
-
14
-
-
0030947344
-
Molecular evidence for an ancient duplication of the entire yeast genome
-
Wolfe KH, Shields DC (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387: 708-713.
-
(1997)
Nature
, vol.387
, pp. 708-713
-
-
Wolfe, K.H.1
Shields, D.C.2
-
15
-
-
1942452749
-
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
-
Kellis M, Birren BW, Lander ES (2004) Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428: 617-624.
-
(2004)
Nature
, vol.428
, pp. 617-624
-
-
Kellis, M.1
Birren, B.W.2
Lander, E.S.3
-
16
-
-
2942552376
-
Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network
-
Dobrin R, Beg QK, Barabasi AL, Oltvai ZN (2004) Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network. BMC Bioinformatics 5: 10.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 10
-
-
Dobrin, R.1
Beg, Q.K.2
Barabasi, A.L.3
Oltvai, Z.N.4
-
17
-
-
8844244033
-
Very low gene duplication rate in the yeast genome
-
Gao LZ, Innan H (2004) Very low gene duplication rate in the yeast genome. Science 306: 1367-1370.
-
(2004)
Science
, vol.306
, pp. 1367-1370
-
-
Gao, L.Z.1
Innan, H.2
-
18
-
-
0036613237
-
Extensive genomic duplication during early chordate evolution
-
McLysaght A, Hokamp K, Wolfe KH (2002) Extensive genomic duplication during early chordate evolution. Nat Genet 31: 200-204.
-
(2002)
Nat Genet
, vol.31
, pp. 200-204
-
-
McLysaght, A.1
Hokamp, K.2
Wolfe, K.H.3
-
19
-
-
0035081235
-
Gene duplication and the structure of eukaryotic genomes
-
Friedman R, Hughes AL (2001) Gene duplication and the structure of eukaryotic genomes. Genome Res 11: 373-381.
-
(2001)
Genome Res
, vol.11
, pp. 373-381
-
-
Friedman, R.1
Hughes, A.L.2
-
20
-
-
33644876020
-
Pfam: Clans, web tools and services
-
Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, et al. (2006) Pfam: Clans, web tools and services. Nucleic Acids Res 34: 247-251.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 247-251
-
-
Finn, R.D.1
Mistry, J.2
Schuster-Bockler, B.3
Griffiths-Jones, S.4
Hollich, V.5
-
21
-
-
0036578654
-
Topological and causal structure of the yeast transcriptional regulatory network
-
Guelzim N, Bottani S, Bourgine P, Kepes F (2002) Topological and causal structure of the yeast transcriptional regulatory network. Nat Genet 31: 60-63.
-
(2002)
Nat Genet
, vol.31
, pp. 60-63
-
-
Guelzim, N.1
Bottani, S.2
Bourgine, P.3
Kepes, F.4
-
22
-
-
9244257298
-
Interacting models of cooperative gene regulation
-
Das D, Banerjee N, Zhang M (2004) Interacting models of cooperative gene regulation. Proc Natl Acad Sci U S A 101: 16234-16239.
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 16234-16239
-
-
Das, D.1
Banerjee, N.2
Zhang, M.3
-
23
-
-
0032499071
-
Evidence for two modes of cooperative DNA binding in vivo that do not involve direct protein-protein interactions
-
Vashee S, Melcher K, Ding WV, Johnston SA, Kodadek T (1998) Evidence for two modes of cooperative DNA binding in vivo that do not involve direct protein-protein interactions. Curr Biol 8: 452-458.
-
(1998)
Curr Biol
, vol.8
, pp. 452-458
-
-
Vashee, S.1
Melcher, K.2
Ding, W.V.3
Johnston, S.A.4
Kodadek, T.5
-
24
-
-
33746611519
-
Activated signal transduction kinases frequently occupy target genes
-
Pokholok DK, Zeitlinger J, Hannett NM, Reynolds DB, Young RA (2006) Activated signal transduction kinases frequently occupy target genes. Science 313: 533-536.
-
(2006)
Science
, vol.313
, pp. 533-536
-
-
Pokholok, D.K.1
Zeitlinger, J.2
Hannett, N.M.3
Reynolds, D.B.4
Young, R.A.5
-
25
-
-
0029879360
-
The Saccharomyces cerevisiae zinc finger proteins Msn2p and Msn4p are required for transcriptional induction through the stress response element (STRE)
-
Martinez-Pastor MT, Marchler G, Schuller C, Marchler-Bauer A, Ruis H, et al. (1996) The Saccharomyces cerevisiae zinc finger proteins Msn2p and Msn4p are required for transcriptional induction through the stress response element (STRE). EMBO J 15: 2227-2235.
-
(1996)
EMBO J
, vol.15
, pp. 2227-2235
-
-
Martinez-Pastor, M.T.1
Marchler, G.2
Schuller, C.3
Marchler-Bauer, A.4
Ruis, H.5
-
26
-
-
33646167129
-
Plasticity of the cis-regulatory input function of a gene
-
doi:10.1371/journal.pbio.0040045
-
Mayo AE, Setty Y, Shavit S, Zaslaver A, Alon U (2006) Plasticity of the cis-regulatory input function of a gene. PLoS Biol 4: e45. doi:10.1371/journal.pbio.0040045
-
(2006)
PLoS Biol
, vol.4
-
-
Mayo, A.E.1
Setty, Y.2
Shavit, S.3
Zaslaver, A.4
Alon, U.5
-
27
-
-
0035883741
-
Mechanisms controlling differential promoter-occupancy by the yeast forkhead proteins Fkh1p and Fkh2p: Implications for regulating the cell cycle and differentiation
-
Hollenhorst PC, Pietz G, Fox CA (2001) Mechanisms controlling differential promoter-occupancy by the yeast forkhead proteins Fkh1p and Fkh2p: Implications for regulating the cell cycle and differentiation. Genes Dev 15: 2445-2456.
-
(2001)
Genes Dev
, vol.15
, pp. 2445-2456
-
-
Hollenhorst, P.C.1
Pietz, G.2
Fox, C.A.3
-
28
-
-
0033972072
-
The probability of duplicate gene preservation by subfunctionalization
-
Lynch M, Force A (2000) The probability of duplicate gene preservation by subfunctionalization. Genetics 154: 459-473.
-
(2000)
Genetics
, vol.154
, pp. 459-473
-
-
Lynch, M.1
Force, A.2
-
29
-
-
0035697435
-
The probability of preservation of a newly arisen gene duplicate
-
Lynch M, O'Hely M, Walsh B, Force A (2001) The probability of preservation of a newly arisen gene duplicate. Genetics 159: 1789-1804.
-
(2001)
Genetics
, vol.159
, pp. 1789-1804
-
-
Lynch, M.1
O'Hely, M.2
Walsh, B.3
Force, A.4
-
30
-
-
0036792156
-
Asymmetric functional divergence of duplicate genes in yeast
-
Wagner A (2002) Asymmetric functional divergence of duplicate genes in yeast. Mol Biol Evol 19: 1760-1768.
-
(2002)
Mol Biol Evol
, vol.19
, pp. 1760-1768
-
-
Wagner, A.1
-
32
-
-
0142027814
-
Structure and function of the feed-forward loop network motif
-
Mangan S, Alon U (2003) Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci U S A 100: 11980-11985.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 11980-11985
-
-
Mangan, S.1
Alon, U.2
-
34
-
-
33745012299
-
Modularity and community structure in networks
-
Newman MEJ (2006) Modularity and community structure in networks. Proc Natl Acad Sci U S A 103: 8577-8582.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 8577-8582
-
-
Newman, M.E.J.1
-
35
-
-
33746207758
-
Bacterial regulatory networks are extremely flexible in evolution
-
Lozada-Chavez I, Janga SC, Collado-Vides J (2006) Bacterial regulatory networks are extremely flexible in evolution. Nucleic Acids Res 34: 3434-3445.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 3434-3445
-
-
Lozada-Chavez, I.1
Janga, S.C.2
Collado-Vides, J.3
-
36
-
-
0038157152
-
Dosage sensitivity and the evolution of gene families in yeast
-
Papp B, Pal C, Hurst LD (2003) Dosage sensitivity and the evolution of gene families in yeast. Nature 424: 194-197.
-
(2003)
Nature
, vol.424
, pp. 194-197
-
-
Papp, B.1
Pal, C.2
Hurst, L.D.3
-
38
-
-
19544389317
-
Energy constraints on the evolution of gene expression
-
Wagner A (2005) Energy constraints on the evolution of gene expression. Mol Biol Evol 22: 1365-1374.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 1365-1374
-
-
Wagner, A.1
-
39
-
-
0041704531
-
Evolution of cis-regulatory elements in duplicated genes of yeast
-
Papp B, Pal C, Hurst LD (2003) Evolution of cis-regulatory elements in duplicated genes of yeast. Trends Genet 19: 417-422.
-
(2003)
Trends Genet
, vol.19
, pp. 417-422
-
-
Papp, B.1
Pal, C.2
Hurst, L.D.3
-
40
-
-
2942615357
-
Upstream plasticity and downstream robustness in evolution of molecular networks
-
Maslov S, Sneppen K, Eriksen KA, Yan KK (2004) Upstream plasticity and downstream robustness in evolution of molecular networks. BMC Evol Biol 4: 9.
-
(2004)
BMC Evol Biol
, vol.4
, pp. 9
-
-
Maslov, S.1
Sneppen, K.2
Eriksen, K.A.3
Yan, K.K.4
-
41
-
-
28844434073
-
An evolutionary and functional assessment of regulatory network motifs
-
Mazurie A, Bottani S, Vergassola M (2005) An evolutionary and functional assessment of regulatory network motifs. Genome Biol 6: R35.
-
(2005)
Genome Biol
, vol.6
-
-
Mazurie, A.1
Bottani, S.2
Vergassola, M.3
-
42
-
-
25144525014
-
Core transcriptional regulatory circuitry in human embryonic stem cells
-
Boyer LA, Lee TI, Cole MF, Johnstone SE, Levine SS, et al. (2005) Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122: 947-956.
-
(2005)
Cell
, vol.122
, pp. 947-956
-
-
Boyer, L.A.1
Lee, T.I.2
Cole, M.F.3
Johnstone, S.E.4
Levine, S.S.5
-
43
-
-
25844471721
-
The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species
-
Byrne KP, Wolfe KH (2005) The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res 15: 1456-1461.
-
(2005)
Genome Res
, vol.15
, pp. 1456-1461
-
-
Byrne, K.P.1
Wolfe, K.H.2
-
44
-
-
0036074510
-
Protein-DNA interactions: Amino acid conservation and the effects of mutations on binding specificity
-
Luscombe NM, Thornton JM (2002) Protein-DNA interactions: Amino acid conservation and the effects of mutations on binding specificity. J Mol Biol 320: 991-1009.
-
(2002)
J Mol Biol
, vol.320
, pp. 991-1009
-
-
Luscombe, N.M.1
Thornton, J.M.2
-
45
-
-
1842505125
-
Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics
-
Sandelin A, Wasserman WW (2004) Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics. J Mol Biol 338: 207-215.
-
(2004)
J Mol Biol
, vol.338
, pp. 207-215
-
-
Sandelin, A.1
Wasserman, W.W.2
-
46
-
-
0037743679
-
Convergent evolution of gene circuits
-
Conant GC, Wagner A (2003) Convergent evolution of gene circuits. Nat Genet 34: 264-266.
-
(2003)
Nat Genet
, vol.34
, pp. 264-266
-
-
Conant, G.C.1
Wagner, A.2
-
48
-
-
0030712874
-
Yap, a novel family of eight bZIP proteins in Saccharomyces cerevisiae with distinct biological functions
-
Fernandes L, Rodrigues-Pousada C, Struhl K (1997) Yap, a novel family of eight bZIP proteins in Saccharomyces cerevisiae with distinct biological functions. Mol Cell Biol 17: 6982-6993.
-
(1997)
Mol Cell Biol
, vol.17
, pp. 6982-6993
-
-
Fernandes, L.1
Rodrigues-Pousada, C.2
Struhl, K.3
-
49
-
-
0027994717
-
Toward a code for the interactions of zinc fingers with DNA: Selection of randomized fingers displayed on phage
-
Choo Y, Klug A (1994) Toward a code for the interactions of zinc fingers with DNA: Selection of randomized fingers displayed on phage. Proc Natl Acad Sci U S A 91: 11163-11167.
-
(1994)
Proc Natl Acad Sci U S A
, vol.91
, pp. 11163-11167
-
-
Choo, Y.1
Klug, A.2
-
50
-
-
0027331505
-
How do "Zn2 cys6" proteins distinguish between similar upstream activation sites? Comparison of the DNA-binding specificity of the GAL4 protein in vitro and in vivo
-
Vashee S, Xu H, Johnston SA, Kodadek T (1993) How do "Zn2 cys6" proteins distinguish between similar upstream activation sites? Comparison of the DNA-binding specificity of the GAL4 protein in vitro and in vivo. J Biol Chem 268: 24699-24706.
-
(1993)
J Biol Chem
, vol.268
, pp. 24699-24706
-
-
Vashee, S.1
Xu, H.2
Johnston, S.A.3
Kodadek, T.4
|