-
2
-
-
0037316239
-
Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms
-
Ma HW, Zeng AP: Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics 2003, 19:270-277.
-
(2003)
Bioinformatics
, vol.19
, pp. 270-277
-
-
Ma, H.W.1
Zeng, A.P.2
-
3
-
-
0037313750
-
Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network
-
Forster J, Famili I, Fu P, Palsson BO, Nielsen J: Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 2003, 13:244-253.
-
(2003)
Genome Res.
, vol.13
, pp. 244-253
-
-
Forster, J.1
Famili, I.2
Fu, P.3
Palsson, B.O.4
Nielsen, J.5
-
4
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA: Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 2002, 298:799-804.
-
(2002)
Science
, vol.298
, pp. 799-804
-
-
Lee, T.I.1
Rinaldi, N.J.2
Robert, F.3
Odom, D.T.4
Bar-Joseph, Z.5
Gerber, G.K.6
Hannett, N.M.7
Harbison, C.T.8
Thompson, C.M.9
Simon, I.10
Zeitlinger, J.11
Jennings, E.G.12
Murray, H.L.13
Gordon, D.B.14
Ren, B.15
Wyrick, J.J.16
Tagne, J.B.17
Volkert, T.L.18
Fraenkel, E.19
Gifford, D.K.20
Young, R.A.21
more..
-
5
-
-
9144270496
-
RegulonDB (version 4.0): Transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12
-
Database issue:D303-D306
-
Salgado H, Gama-Castro S, Martinez-Antonio A, Diaz-Peredo E, Sanchez-Solano F, Peralta-Gil M, Garcia-Alonso D, Jimenez-Jacinto V, Santos-Zavaleta A, Bonavides-Martinez C, Collado-Vides J: RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucleic Acids Res 2004, 32 Database issue:D303-D306.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Salgado, H.1
Gama-Castro, S.2
Martinez-Antonio, A.3
Diaz-Peredo, E.4
Sanchez-Solano, F.5
Peralta-Gil, M.6
Garcia-Alonso, D.7
Jimenez-Jacinto, V.8
Santos-Zavaleta, A.9
Bonavides-Martinez, C.10
Collado-Vides, J.11
-
6
-
-
0037208166
-
TRANSFAC: Transcriptional regulation, from patterns to profiles
-
Matys V, Fricke E, Geffers R, Gossling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, Kloos DU, Land S, Lewicki-Potapov B, Michael H, Munch R, Reuter I, Rotert S, Saxel H, Scheer M, Thiele S, Wingender E: TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res 2003, 31: 74-378.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 374-378
-
-
Matys, V.1
Fricke, E.2
Geffers, R.3
Gossling, E.4
Haubrock, M.5
Hehl, R.6
Hornischer, K.7
Karas, D.8
Kel, A.E.9
Kel-Margoulis, O.V.10
Kloos, D.U.11
Land, S.12
Lewicki-Potapov, B.13
Michael, H.14
Munch, R.15
Reuter, I.16
Rotert, S.17
Saxel, H.18
Scheer, M.19
Thiele, S.20
Wingender, E.21
more..
-
7
-
-
0036578795
-
Network motifs in the transcriptional regulation network of Escherichia coli
-
Shen-Orr SS, Milo R, Mangan S, Alon U: Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 2002, 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
-
8
-
-
0036578654
-
Topological and causal structure of the yeast transcriptional regulatory network
-
Guelzim N, Bottani S, Bourgine P, Kepes F: Topological and causal structure of the yeast transcriptional regulatory network. Nat Genet 2002, 31:60-63.
-
(2002)
Nat. Genet.
, vol.31
, pp. 60-63
-
-
Guelzim, N.1
Bottani, S.2
Bourgine, P.3
Kepes, F.4
-
9
-
-
2942552376
-
Aggregation of topological motifs in the escherichia coli transcriptional regulatory network
-
Dobrin R, Beg QK, Barabasi AL, Oltvai ZN: aggregation of topological motifs in the escherichia coli transcriptional regulatory network. BMC Bioinformatics 2004, 5:10.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 10
-
-
Dobrin, R.1
Beg, Q.K.2
Barabasi, A.L.3
Oltvai, Z.N.4
-
10
-
-
0242386460
-
Identifying global regulators in transcriptional regulatory networks in bacteria
-
Martinez-Antonio A, Collado-Vides J: Identifying global regulators in transcriptional regulatory networks in bacteria. Curr Opin Microbiol 2003, 6:482-489.
-
(2003)
Curr. Opin. Microbiol.
, vol.6
, pp. 482-489
-
-
Martinez-Antonio, A.1
Collado-Vides, J.2
-
11
-
-
0037440734
-
Evolution of transcription factors and the gene regulatory network in Escherichia coli
-
Madan BM, Teichmann SA: Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucleic Acids Res 2003, 31:1234-1244.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 1234-1244
-
-
Madan, B.M.1
Teichmann, S.A.2
-
12
-
-
0242574985
-
Reconciling gene expression data with known genome-scale regulatory network structures
-
Herrgard MJ, Covert MW, Palsson BO: Reconciling gene expression data with known genome-scale regulatory network structures. Genome Res 2003, 13:2423-2434.
-
(2003)
Genome Res.
, vol.13
, pp. 2423-2434
-
-
Herrgard, M.J.1
Covert, M.W.2
Palsson, B.O.3
-
13
-
-
0242407438
-
Regulatory network of Escherichia coli: Consistency between literature knowledge and microarray profiles
-
Gutierrez-Rios RM, Rosenblueth DA, Loza JA, Huerta AM, Glasner JD, Blattner FR, Collado-Vides J: Regulatory network of Escherichia coli: consistency between literature knowledge and microarray profiles. Genome Res 2003, 13:2435-2443.
-
(2003)
Genome Res.
, vol.13
, pp. 2435-2443
-
-
Gutierrez-Rios, R.M.1
Rosenblueth, D.A.2
Loza, J.A.3
Huerta, A.M.4
Glasner, J.D.5
Blattner, F.R.6
Collado-Vides, J.7
-
14
-
-
2942606066
-
Structure and evolution of transcriptional regulatory networks
-
Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA: Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol 2004, 14:283-291.
-
(2004)
Curr. Opin. Struct. Biol.
, vol.14
, pp. 283-291
-
-
Babu, M.M.1
Luscombe, N.M.2
Aravind, L.3
Gerstein, M.4
Teichmann, S.A.5
-
15
-
-
0037743679
-
Convergent evolution of gene circuits
-
Conant GC, Wagner A: Convergent evolution of gene circuits. Nat Genet 2003, 34:264-266.
-
(2003)
Nat. Genet.
, vol.34
, pp. 264-266
-
-
Conant, G.C.1
Wagner, A.2
-
17
-
-
0037174670
-
Network motifs: Simple building blocks of complex networks
-
Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U: Network motifs: simple building blocks of complex networks. Science 2002, 298:824-827.
-
(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
-
18
-
-
0141596113
-
Molecular networks: The top-down view
-
Bray D: Molecular networks: the top-down view. Science 2003, 301:1864-1865.
-
(2003)
Science
, vol.301
, pp. 1864-1865
-
-
Bray, D.1
-
19
-
-
18744422155
-
The modular era of functional genomics
-
Segal E, Kim SK: The modular era of functional genomics. Genome Biol 2003, 4:317.
-
(2003)
Genome Biol.
, vol.4
, pp. 317
-
-
Segal, E.1
Kim, S.K.2
-
20
-
-
0037941585
-
Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data
-
Segal E, Shapira M, Regev A, Pe'er D, Botstein D, Koller D, Friedman N: Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet 2003, 34:166-176.
-
(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
-
-
0037199968
-
Hierarchical Organization of Modularity in Metabolic Networks
-
Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL: Hierarchical Organization of Modularity in Metabolic Networks. Science 2002, 297:1551-1555.
-
(2002)
Science
, vol.297
, pp. 1551-1555
-
-
Ravasz, E.1
Somera, A.L.2
Mongru, D.A.3
Oltvai, Z.N.4
Barabasi, A.L.5
-
23
-
-
10744226222
-
Computational discovery of gene modules and regulatory networks
-
Bar-Joseph Z, Gerber GK, Lee TI, Rinaldi NJ, Yoo JY, Robert F, Gordon DB, Fraenkel E, Jaakkola TS, Young RA, Gifford DK: Computational discovery of gene modules and regulatory networks. Nat Biotechnol 2003, 21:1337-1342.
-
(2003)
Nat. Biotechnol.
, vol.21
, pp. 1337-1342
-
-
Bar-Joseph, Z.1
Gerber, G.K.2
Lee, T.I.3
Rinaldi, N.J.4
Yoo, J.Y.5
Robert, F.6
Gordon, D.B.7
Fraenkel, E.8
Jaakkola, T.S.9
Young, R.A.10
Gifford, D.K.11
-
24
-
-
0742305866
-
Network biology: Understanding the cell's functional organization
-
Barabasi AL, Oltvai ZN: Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5: 01-113.
-
(2004)
Nat. Rev. Genet.
, vol.5
, pp. 101-113
-
-
Barabasi, A.L.1
Oltvai, Z.N.2
-
25
-
-
1542286745
-
Quantifying modularity in the evolution of biomolecular systems
-
Snel B, Huynen MA: Quantifying modularity in the evolution of biomolecular systems. Genome Res 2004, 14:391-397.
-
(2004)
Genome Res.
, vol.14
, pp. 391-397
-
-
Snel, B.1
Huynen, M.A.2
-
26
-
-
0345305369
-
Functional modules by relating protein interaction networks and gene expression
-
Tornow S, Mewes HW: Functional modules by relating protein interaction networks and gene expression. Nucleic Acids Res 2003, 31:6283-6289.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 6283-6289
-
-
Tornow, S.1
Mewes, H.W.2
-
27
-
-
4444234772
-
Decomposition of metabolic network based on the global connectivity structure of reaction graph
-
Ma HW, Zhao XM, Yuan YJ, Zeng AP: Decomposition of metabolic network based on the global connectivity structure of reaction graph. Bioinformatics 2004, 20:1870-1876.
-
(2004)
Bioinformatics
, vol.20
, pp. 1870-1876
-
-
Ma, H.W.1
Zhao, X.M.2
Yuan, Y.J.3
Zeng, A.P.4
-
28
-
-
0036188159
-
Exploring the pathway structure of metabolism: Decomposition into subnetworks and application to Mycoplasma pneumoniae
-
Schuster S, Pfeiffer T, Moldenhauer F, Koch I, Dandekar T: Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae. Bioinformatics 2002, 18:351-361.
-
(2002)
Bioinformatics
, vol.18
, pp. 351-361
-
-
Schuster, S.1
Pfeiffer, T.2
Moldenhauer, F.3
Koch, I.4
Dandekar, T.5
-
29
-
-
1542357674
-
Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data
-
Tanay A, Sharan R, Kupiec M, Shamir R: Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data. Proc Natl Acad Sci U S A 2004, 101:2981-2986.
-
(2004)
Proc. Natl. Acad. Sci. U. S. A.
, vol.101
, pp. 2981-2986
-
-
Tanay, A.1
Sharan, R.2
Kupiec, M.3
Shamir, R.4
-
30
-
-
0346156102
-
Detection of functional modules from protein interaction networks
-
Pereira-Leal JB, Enright AJ, Ouzounis CA: Detection of functional modules from protein interaction networks. Proteins 2004, 54:49-57.
-
(2004)
Proteins
, vol.54
, pp. 49-57
-
-
Pereira-Leal, J.B.1
Enright, A.J.2
Ouzounis, C.A.3
-
31
-
-
0002226683
-
Pajek - Program for Large Network Analysis
-
Batagelj V, Mrvar A: Pajek - Program for Large Network Analysis. connections 1998, 21:47-57.
-
(1998)
Connections
, vol.21
, pp. 47-57
-
-
Batagelj, V.1
Mrvar, A.2
-
32
-
-
0042093610
-
The connectivity structure, giant strong component and centrality of metabolic networks
-
Ma HW, Zeng AP: The connectivity structure, giant strong component and centrality of metabolic networks. Bioinformatics 2003, 19:1423-1430.
-
(2003)
Bioinformatics
, vol.19
, pp. 1423-1430
-
-
Ma, H.W.1
Zeng, A.P.2
-
33
-
-
0033971754
-
EcoGene: A genome sequence database for Escherichia coli K-12
-
Rudd KE: EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 2000, 28:60-64.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 60-64
-
-
Rudd, K.E.1
-
34
-
-
84885682472
-
-
2004 [http://www.weizmann.ac.il/mcb/UriAlon].
-
(2004)
-
-
-
35
-
-
0033912262
-
The bacterial enhancer-dependent sigma(54) (sigma(N)) transcription factor
-
Buck M, Gallegos MT, Studholme DJ, Guo Y, Gralla JD: The bacterial enhancer-dependent sigma(54) (sigma(N)) transcription factor. J Bacteriol 2000, 182:4129-4136.
-
(2000)
J. Bacteriol.
, vol.182
, pp. 4129-4136
-
-
Buck, M.1
Gallegos, M.T.2
Studholme, D.J.3
Guo, Y.4
Gralla, J.D.5
|