-
4
-
-
77951044336
-
Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels
-
Bhardwaj N, Yan KK, Gerstein M (2010) Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels. Proc Natl Acad Sci USA 107:6841-6846.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 6841-6846
-
-
Bhardwaj, N.1
Yan, K.K.2
Gerstein, M.3
-
5
-
-
0019058442
-
Programs, life cycles, and laws of software evolution
-
Lehman MM (1980) Programs, life cycles, and laws of software evolution. Proc IEEE 68:1060-1076.
-
(1980)
Proc IEEE
, vol.68
, pp. 1060-1076
-
-
Lehman, M.M.1
-
6
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
Lee TI, et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298:799-804.
-
(2002)
Science
, vol.298
, pp. 799-804
-
-
Lee, T.I.1
-
7
-
-
0036901602
-
Modeling transcriptional regulatory networks
-
Bolouri H, Davidson EH (2002) Modeling transcriptional regulatory networks. Bioessays 24:1118-1129.
-
(2002)
Bioessays
, vol.24
, pp. 1118-1129
-
-
Bolouri, H.1
Davidson, E.H.2
-
8
-
-
0742305866
-
Network biology: Understanding the cell's functional organization
-
Barabási A, Oltvai ZN (2004) Network biology: Understanding the cell's functional organization. Nat Rev Genet 5:101-113.
-
(2004)
Nat Rev Genet
, vol.5
, pp. 101-113
-
-
Barabási, A.1
Oltvai, Z.N.2
-
9
-
-
2942606066
-
Structure and evolution of transcriptional regulatory networks
-
Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA (2004) Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol 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
-
10
-
-
4644326931
-
Genomic analysis of regulatory network dynamics reveals large topological changes
-
Luscombe NM, et al. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431:308-312.
-
(2004)
Nature
, vol.431
, pp. 308-312
-
-
Luscombe, N.M.1
-
11
-
-
0032077377
-
From specific gene regulation to genomic networks: A global analysis of transcriptional regulation in Escherichia coli
-
Thieffry D, Huerta AM, Perez-Rueda E, Collado-Vides J (1998) From specific gene regulation to genomic networks: A global analysis of transcriptional regulation in Escherichia coli. Bioessays 20:433-440.
-
(1998)
Bioessays
, vol.20
, pp. 433-440
-
-
Thieffry, D.1
Huerta, A.M.2
Perez-Rueda, E.3
Collado-Vides, J.4
-
12
-
-
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
-
13
-
-
13544269611
-
An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs
-
DOI 10.1093/nar/gkh1009
-
Ma H, et al. (2004) An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs. Nucleic Acids Res 32:6643-6649. (Pubitemid 40220376)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.22
, pp. 6643-6649
-
-
Ma, H.-W.1
Kumar, B.2
Ditges, U.3
Gunzer, F.4
Buer, J.5
Zeng, A.-P.6
-
14
-
-
61449254451
-
Principles of transcriptional regulation and evolution of the metabolic system in E. coli
-
Seshasayee AS, Fraser GM, Babu MM, Luscombe NM (2009) Principles of transcriptional regulation and evolution of the metabolic system in E. coli. Genome Res 19:79-91.
-
(2009)
Genome Res
, vol.19
, pp. 79-91
-
-
Seshasayee, A.S.1
Fraser, G.M.2
Babu, M.M.3
Luscombe, N.M.4
-
15
-
-
38549140094
-
RegulonDB (version 6.0): Gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation
-
Gama-Castro S, et al. (2008) RegulonDB (version 6.0): Gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res 36:D120-124.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Gama-Castro, S.1
-
16
-
-
27744547023
-
Computational architecture of the yeast regulatory network
-
Maslov S, Sneppen K (2005) Computational architecture of the yeast regulatory network. Phys Biol 2:S94-100.
-
(2005)
Phys Biol
, vol.2
-
-
Maslov, S.1
Sneppen, K.2
-
17
-
-
0038483826
-
Emergence scaling in random networks
-
Barabasi AL, Albert R (1999) Emergence scaling in random networks. Science 286:509-512.
-
(1999)
Science
, vol.286
, pp. 509-512
-
-
Barabasi, A.L.1
Albert, R.2
-
18
-
-
0346280179
-
Software systems as complex networks: Structure, function, and evolvability of software collaboration graphs
-
Myers CR (2003) Software systems as complex networks: Structure, function, and evolvability of software collaboration graphs. Phys Rev E 68:046116.
-
(2003)
Phys Rev E
, vol.68
, pp. 046116
-
-
Myers, C.R.1
-
19
-
-
0141484562
-
Biological networks: The tinkerer as an engineer
-
Alon U (2003) Biological networks: The tinkerer as an engineer. Science 301:1866-1867.
-
(2003)
Science
, vol.301
, pp. 1866-1867
-
-
Alon, U.1
-
20
-
-
0015482049
-
On the criteria to be used in decomposing systems into modules
-
Parnas DL (1972) On the criteria to be used in decomposing systems into modules. Commun ACM 15:1053-1058.
-
(1972)
Commun ACM
, vol.15
, pp. 1053-1058
-
-
Parnas, D.L.1
-
21
-
-
20344379457
-
Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli
-
Balazsi G, Barabasi A, Oltvai ZN (2005) Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli. Proc Natl Acad Sci USA 102:7841-7846.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 7841-7846
-
-
Balazsi, G.1
Barabasi, A.2
Oltvai, Z.N.3
-
22
-
-
39549098697
-
Persistence drives gene clustering in bacterial genomes
-
DOI 10.1186/1471-2164-9-4
-
Fang G, Rocha EPC, Danchin A (2008) Persistence drives gene clustering in bacterial genomes. BMC Genomics 9:4. (Pubitemid 351659652)
-
(2008)
BMC Genomics
, vol.9
, pp. 4
-
-
Fang, G.1
Rocha, E.P.C.2
Danchin, A.3
-
23
-
-
57549101206
-
Bacteria as computers making computers
-
Danchin A (2009) Bacteria as computers making computers. FEMS Microbiol Rev 33:3-26.
-
(2009)
FEMS Microbiol Rev
, vol.33
, pp. 3-26
-
-
Danchin, A.1
-
24
-
-
0037177560
-
Evolutionary rate in the protein interaction network
-
Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW (2002) Evolutionary rate in the protein interaction network. Science 296:750-752.
-
(2002)
Science
, vol.296
, pp. 750-752
-
-
Fraser, H.B.1
Hirsh, A.E.2
Steinmetz, L.M.3
Scharfe, C.4
Feldman, M.W.5
-
25
-
-
38049138722
-
Positive selection at the protein network periphery: Evaluation in terms of structural constraints and cellular context
-
Kim PM, Korbel JO, Gerstein MB (2007) Positive selection at the protein network periphery: Evaluation in terms of structural constraints and cellular context. Proc Natl Acad Sci USA 104:20274-20279.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 20274-20279
-
-
Kim, P.M.1
Korbel, J.O.2
Gerstein, M.B.3
-
26
-
-
34247622363
-
The importance of bottlenecks in protein networks: Correlation with gene essentiality and expression dynamics
-
Yu H, Kim PM, Sprecher E, Trifonov V, Gerstein M (2007) The importance of bottlenecks in protein networks: Correlation with gene essentiality and expression dynamics. PLoS Comput Biol 3:e59.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Yu, H.1
Kim, P.M.2
Sprecher, E.3
Trifonov, V.4
Gerstein, M.5
-
27
-
-
67649872627
-
Toolbox model of evolution of prokaryotic metabolic networks and their regulation
-
Maslov S, Krishna S, Pang TY, Sneppen K (2009) Toolbox model of evolution of prokaryotic metabolic networks and their regulation. Proc Natl Acad Sci USA 106:9743-9748.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 9743-9748
-
-
Maslov, S.1
Krishna, S.2
Pang, T.Y.3
Sneppen, K.4
-
28
-
-
0036078078
-
Essential genes are more evolutionarily conserved than are nonessential genes in bacteria
-
Jordan IK, Rogozin IB, Wolf YI, Koonin EV (2002) Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res 12:962-968.
-
(2002)
Genome Res
, vol.12
, pp. 962-968
-
-
Jordan, I.K.1
Rogozin, I.B.2
Wolf, Y.I.3
Koonin, E.V.4
-
29
-
-
58149179978
-
ATGC: A database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes
-
Novichkov PS, Ratnere I, Wolf YI, Koonin EV, Dubchak I (2009) ATGC: A database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes. Nucleic Acids Res 37:D448-454.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Novichkov, P.S.1
Ratnere, I.2
Wolf, Y.I.3
Koonin, E.V.4
Dubchak, I.5
-
30
-
-
33747847779
-
PAL2NAL: Robust conversion of protein sequence alignments into the corresponding codon alignments
-
Suyama M, Torrents D, Bork P (2006) PAL2NAL: Robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res 34:W609-612.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Suyama, M.1
Torrents, D.2
Bork, P.3
-
31
-
-
34547803197
-
PAML 4: Phylogenetic analysis by maximum likelihood
-
Yang Z (2007) PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586-1591.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 1586-1591
-
-
Yang, Z.1
|