-
5
-
-
41349086001
-
Growing scale-free networks with small-world behavior
-
10.1103/PhysRevE.65.036123
-
Klemm K Eguiluz VM Growing scale-free networks with small-world behavior Physical Review E 2002, 65:036123. 10.1103/PhysRevE.65.036123
-
(2002)
Physical Review E
, vol.65
, pp. 036123
-
-
Klemm, K.K.1
Eguiluz, V.M.2
-
6
-
-
0032482432
-
Collective dynamics of 'small-world' networks
-
10.1038/30918 9623998
-
Watts DJ Strogatz SH Collective dynamics of 'small-world' networks Nature 1998, 393(6684):440-442. 10.1038/30918 9623998
-
(1998)
Nature
, vol.393
, Issue.6684
, pp. 440-442
-
-
Watts, D.J.1
Strogatz, S.H.2
-
7
-
-
0742305866
-
Network biology: Understanding the cell's functional organization
-
10.1038/nrg1272 14735121
-
Barabasi AL Oltvai ZN Network biology: Understanding the cell's functional organization Nature Reviews Genetics 2004, 5:101-113. 10.1038/ nrg1272 14735121
-
(2004)
Nature Reviews Genetics
, vol.5
, pp. 101-113
-
-
Barabasi, A.L.1
Oltvai, Z.N.2
-
8
-
-
0038483826
-
Emergence of scaling in random networks
-
10.1126/science.286.5439.509 10521342
-
Barabasi AL Albert R Emergence of scaling in random networks Science 1999, 286(5439):509-512. 10.1126/science.286.5439.509 10521342
-
(1999)
Science
, vol.286
, Issue.5439
, pp. 509-512
-
-
Barabasi, A.L.1
Albert, R.2
-
9
-
-
0642285840
-
Preferential attachment in the protein network evolution
-
10.1103/PhysRevLett.91.138701 14525344
-
Eisenberg E Levanon EY Preferential attachment in the protein network evolution Physical Review Letters 2003, 91:138701. 10.1103/ PhysRevLett.91.138701 14525344
-
(2003)
Physical Review Letters
, vol.91
, pp. 138701
-
-
Eisenberg, E.1
Levanon, E.Y.2
-
10
-
-
27944470116
-
Preferential attachment in the evolution of metabolic networks
-
1316878 16281983 10.1186/1471-2164-6-159
-
Light S Kraulis P Elofsson A Preferential attachment in the evolution of metabolic networks BMC Genomics 2005, 6:159. 1316878 16281983 10.1186/ 1471-2164-6-159
-
(2005)
BMC Genomics
, vol.6
, pp. 159
-
-
Light, S.1
Kraulis, P.2
Elofsson, A.3
-
11
-
-
0037423828
-
How the global structure of protein interaction networks evolves
-
10.1098/rspb.2002.2269
-
Wagner A How the global structure of protein interaction networks evolves Proceedings Biological Sciences, The Royal Society 2003, 270:457-466. 10.1098/rspb.2002.2269
-
(2003)
Proceedings Biological Sciences, The Royal Society
, vol.270
, pp. 457-466
-
-
Wagner, A.1
-
12
-
-
33845875196
-
Relating three-dimensional structures to protein networks provides evolutionary insights
-
10.1126/science.1136174 17185604
-
Kim PM Lu LJ Xia Y Gerstein MB Relating three-dimensional structures to protein networks provides evolutionary insights Science 2006, 314(5807):1938-1941. 10.1126/science.1136174 17185604
-
(2006)
Science
, vol.314
, Issue.5807
, pp. 1938-1941
-
-
Kim, P.M.1
Lu, L.J.2
Xia, Y.3
Gerstein, M.B.4
-
13
-
-
2442537233
-
Gene regulatory network growth by duplication
-
10.1038/ng1340 15107850
-
Teichmann SA Babu MM Gene regulatory network growth by duplication Nature Genetics 2004, 36(5):492-496. 10.1038/ng1340 15107850
-
(2004)
Nature Genetics
, vol.36
, Issue.5
, pp. 492-496
-
-
Teichmann, S.A.1
Babu, M.M.2
-
14
-
-
2442477788
-
Genomic analysis of essentiality within protein networks
-
10.1016/j.tig.2004.04.008 15145574
-
Yu H Greenbaum D Lu HX Zhu X Gerstein M Genomic analysis of essentiality within protein networks Trends in Genetics 2004, 20:227-231. 10.1016/ j.tig.2004.04.008 15145574
-
(2004)
Trends in Genetics
, vol.20
, pp. 227-231
-
-
Yu, H.1
Greenbaum, D.2
Lu, H.X.3
Zhu, X.4
Gerstein, M.5
-
15
-
-
33745242506
-
Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networks
-
10.1016/j.jmb.2006.04.026 16730024
-
Balaji S Iyer LM Aravind L Babu MM Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networks Journal of Molecular Biology 2006, 360:204-212. 10.1016/ j.jmb.2006.04.026 16730024
-
(2006)
Journal of Molecular Biology
, vol.360
, pp. 204-212
-
-
Balaji, S.1
Iyer, L.M.2
Aravind, L.3
Babu, M.M.4
-
16
-
-
11244333081
-
Properties of metabolic networks: Structure versus function
-
1305059 15574705 10.1529/biophysj.104.055723
-
Mahadevan R Palsson BO Properties of metabolic networks: Structure versus function Biophysical Journal 2005, 88:L07-09. 1305059 15574705 10.1529/biophysj.104.055723
-
(2005)
Biophysical Journal
, vol.88
-
-
Mahadevan, R.1
Palsson, B.O.2
-
17
-
-
26444469935
-
A system of counteracting feedback loops regulates Cdc42p activity during spontaneous cell polarization
-
10.1016/j.devcel.2005.08.014 16198298
-
Ozbudak EM Becskei A van Oudenaarden A A system of counteracting feedback loops regulates Cdc42p activity during spontaneous cell polarization Developmental Cell 2005, 9:565-571. 10.1016/ j.devcel.2005.08.014 16198298
-
(2005)
Developmental Cell
, vol.9
, pp. 565-571
-
-
Ozbudak, E.M.1
Becskei, A.2
van Oudenaarden, A.3
-
20
-
-
33846694082
-
Coupled positive and negative feedback circuits form an essential building block of cellular signaling pathways
-
10.1002/bies.20511 17187378
-
Kim D Kwon YK Cho KH Coupled positive and negative feedback circuits form an essential building block of cellular signaling pathways BioEssays 2007, 29:85-90. 10.1002/bies.20511 17187378
-
(2007)
BioEssays
, vol.29
, pp. 85-90
-
-
Kim, D.1
Kwon, Y.K.2
Cho, K.H.3
-
21
-
-
0029807944
-
How proteolysis drives the cell cycle
-
10.1126/science.274.5293.1652 8939846
-
King RW Deshaies RJ Peters JM Kirschner MW How proteolysis drives the cell cycle Science 1996, 274:1652-1659. 10.1126/science.274.5293.1652 8939846
-
(1996)
Science
, vol.274
, pp. 1652-1659
-
-
King, R.W.1
Deshaies, R.J.2
Peters, J.M.3
Kirschner, M.W.4
-
22
-
-
1842788016
-
Multiple feedback loops are key to a robust dynamic performance of tryptophan regulation in Escherichia coli
-
10.1016/S0014-5793(04)00310-2 15063755
-
Venkatesh KV Bhartiya S Ruhela A Multiple feedback loops are key to a robust dynamic performance of tryptophan regulation in Escherichia coli FEBS Letters 2004, 563(1-3):234. 10.1016/S0014-5793(04)00310-2 15063755
-
(2004)
FEBS Letters
, vol.563
, Issue.1-3
, pp. 234
-
-
Venkatesh, K.V.1
Bhartiya, S.2
Ruhela, A.3
-
24
-
-
0034644270
-
The segment polarity network is a robust developmental module
-
10.1038/35018085 10910359
-
von Dassow G Meir E Munro EM Odell GM The segment polarity network is a robust developmental module Nature 2000, 406:188-192. 10.1038/35018085 10910359
-
(2000)
Nature
, vol.406
, pp. 188-192
-
-
von Dassow, G.1
Meir, E.2
Munro, E.M.3
Odell, G.M.4
-
25
-
-
0032496358
-
The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes
-
10.1126/science.280.5365.895 9572732
-
Ferrell JE Jr Machleder EM The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes Science 1998, 280:895-898. 10.1126/ science.280.5365.895 9572732
-
(1998)
Science
, vol.280
, pp. 895-898
-
-
Ferrell Jr., J.E.1
Machleder, E.M.2
-
26
-
-
0037047611
-
MAP kinase phosphatase as a locus of fexibility in a mitogen-activated protein kinase signaling network
-
10.1126/science.1068873 12169734
-
Bhalla US Ram PT Iyengar R MAP kinase phosphatase as a locus of fexibility in a mitogen-activated protein kinase signaling network Science 2002, 297:1018-1023. 10.1126/science.1068873 12169734
-
(2002)
Science
, vol.297
, pp. 1018-1023
-
-
Bhalla, U.S.1
Ram, P.T.2
Iyengar, R.3
-
27
-
-
0345700833
-
Building a cell cycle oscillator: Hysteresis and bistability in the activation of Cdc2
-
10.1038/ncb954 12629549
-
Pomerening JR Sontag ED Ferrell JE Jr Building a cell cycle oscillator: hysteresis and bistability in the activation of Cdc2 Nature Cell Biology 2003, 5:346-351. 10.1038/ncb954 12629549
-
(2003)
Nature Cell Biology
, vol.5
, pp. 346-351
-
-
Pomerening, J.R.1
Sontag, E.D.2
Ferrell Jr., J.E.3
-
28
-
-
33645073688
-
Phenotypic variation in bacteria: The role of feedback regulation
-
W VJ 10.1038/nrmicro1381 16541134
-
Smits WK Kuipers OP W VJ Phenotypic variation in bacteria: The role of feedback regulation Nature Reviews Microbiology 2006, 4:259-271. 10.1038/ nrmicro1381 16541134
-
(2006)
Nature Reviews Microbiology
, vol.4
, pp. 259-271
-
-
Smits, W.K.1
Kuipers, O.P.2
-
29
-
-
0037417803
-
Hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts
-
10.1073/pnas.0235349100
-
Sha W Moore J Chen K Lassaletta AD Yi CS Tyson JJ Sible JC Hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts Proceedings of the National Academy of Sciences, USA 2003, 100(3):975-980. 10.1073/ pnas.0235349100
-
(2003)
Proceedings of the National Academy of Sciences, USA
, vol.100
, Issue.3
, pp. 975-980
-
-
Sha, W.1
Moore, J.2
Chen, K.3
Lassaletta, A.D.4
Yi, C.S.5
Tyson, J.J.6
Sible, J.C.7
-
30
-
-
0037174669
-
Oscillatory expression of the bHLH factor Hes1 regulated by a negative feedback loop
-
10.1126/science.1074560 12399594
-
Hirata H Yoshiura S Ohtsuka T Bessho Y Harada T Yoshikawa K Kageyama R Oscillatory expression of the bHLH factor Hes1 regulated by a negative feedback loop Science 2002, 298:840-843. 10.1126/science.1074560 12399594
-
(2002)
Science
, vol.298
, pp. 840-843
-
-
Hirata, H.1
Yoshiura, S.2
Ohtsuka, T.3
Bessho, Y.4
Harada, T.5
Yoshikawa, K.6
Kageyama, R.7
-
31
-
-
1842687878
-
The yeast cell-cycle network is robustly designed
-
10.1073/pnas.0305937101
-
Li F Long T Lu Y Ouyang Q Tang C The yeast cell-cycle network is robustly designed Proceedings of the National Academy of Sciences, USA 2004, 101:4781-4786. 10.1073/pnas.0305937101
-
(2004)
Proceedings of the National Academy of Sciences, USA
, vol.101
, pp. 4781-4786
-
-
Li, F.1
Long, T.2
Lu, Y.3
Ouyang, Q.4
Tang, C.5
-
32
-
-
7644238181
-
Biological robustness
-
10.1038/nrg1471 15520792
-
Kitano H Biological robustness Nature Reviews Genetics 2004, 5(11):826-837. 10.1038/nrg1471 15520792
-
(2004)
Nature Reviews Genetics
, vol.5
, Issue.11
, pp. 826-837
-
-
Kitano, H.1
-
33
-
-
33847268619
-
Robustness can evolve gradually in complex regulatory gene networks with varying topology
-
1794322 17274682 10.1371/journal.pcbi.0030015
-
Ciliberti S Martin OC Wagner A Robustness can evolve gradually in complex regulatory gene networks with varying topology PLoS Computational Biology 2007, 3(2):e15. 1794322 17274682 10.1371/ journal.pcbi.0030015
-
(2007)
PLoS Computational Biology
, vol.3
, Issue.2
-
-
Ciliberti, S.1
Martin, O.C.2
Wagner, A.3
-
34
-
-
18144408736
-
Cell fates as high-dimensional attractor states of a complex gene regulatory network
-
10.1103/PhysRevLett.94.128701 15903968
-
Huang S Eichler G Bar-Yam Y Ingber DE Cell fates as high-dimensional attractor states of a complex gene regulatory network Physical Review Letters 2005, 94(12):128701. 10.1103/PhysRevLett.94.128701 15903968
-
(2005)
Physical Review Letters
, vol.94
, Issue.12
, pp. 128701
-
-
Huang, S.1
Eichler, G.2
Bar-Yam, Y.3
Ingber, D.E.4
-
35
-
-
0034564982
-
Regulation of the L-arabinose operon of Escherichia coli
-
10.1016/S0168-9525(00)02153-3 11102706
-
Schleif R Regulation of the L-arabinose operon of Escherichia coli Trends in Genetics 2000, 16(12):559. 10.1016/S0168-9525(00)02153-3 11102706
-
(2000)
Trends in Genetics
, vol.16
, Issue.12
, pp. 559
-
-
Schleif, R.1
-
36
-
-
0035805255
-
Integrated genomic and proteomic analyses of a systematically perturbed metabolic network
-
10.1126/science.292.5518.929 11340206
-
Ideker T Thorsson V Ranish JA Christmas R Buhler J Eng JK Bumgarner R Goodlett DR Aebersold R Hood L Integrated genomic and proteomic analyses of a systematically perturbed metabolic network Science 2001, 292(5518):929. 10.1126/science.292.5518.929 11340206
-
(2001)
Science
, vol.292
, Issue.5518
, pp. 929
-
-
Ideker, T.1
Thorsson, V.2
Ranish, J.A.3
Christmas, R.4
Buhler, J.5
Eng, J.K.6
Bumgarner, R.7
Goodlett, D.R.8
Aebersold, R.9
Hood, L.10
-
37
-
-
0036282743
-
Osmotic stress signaling and osmoadaptation in yeasts
-
10.1128/MMBR.66.2.300-372.2002
-
Hohmann S Osmotic stress signaling and osmoadaptation in yeasts Microbiology and Molecular Biology Reviews 2002, 66(2):300. 10.1128/ MMBR.66.2.300-372.2002
-
(2002)
Microbiology and Molecular Biology Reviews
, vol.66
, Issue.2
, pp. 300
-
-
Hohmann, S.1
-
39
-
-
0035912804
-
Interlocked feedback loops contribute to the robustness of the Neurospora circadian clock
-
10.1073/pnas.121170298
-
Cheng P Yang Y Liu Y Interlocked feedback loops contribute to the robustness of the Neurospora circadian clock Proceedings of the National Academy of Sciences, USA 2001, 98(13):7408. 10.1073/pnas.121170298
-
(2001)
Proceedings of the National Academy of Sciences, USA
, vol.98
, Issue.13
, pp. 7408
-
-
Cheng, P.1
Yang, Y.2
Liu, Y.3
-
40
-
-
0037423224
-
vrille, Pdp1, and dClock form a second feedback loop in the Drosophila circadian clock
-
10.1016/S0092-8674(03)00074-6 12581523
-
Cyran SA Buchsbaum AM Reddy KL Lin MC Glossop NR Hardin PE Young MW Storti RV Blau J vrille, Pdp1, and dClock form a second feedback loop in the Drosophila circadian clock Cell 2003, 112(3):329. 10.1016/ S0092-8674(03)00074-6 12581523
-
(2003)
Cell
, vol.112
, Issue.3
, pp. 329
-
-
Cyran, S.A.1
Buchsbaum, A.M.2
Reddy, K.L.3
Lin, M.C.4
Glossop, N.R.5
Hardin, P.E.6
Young, J.M.W.7
Storti, R.V.8
Blau9
-
41
-
-
3142517462
-
Topology and robustness in the Drosophila segment polarity network
-
423129 15208707 10.1371/journal.pbio.0020123
-
Ingolia NT Topology and robustness in the Drosophila segment polarity network PLoS Biology 2004, 2(6):e123. 423129 15208707 10.1371/ journal.pbio.0020123
-
(2004)
PLoS Biology
, vol.2
, Issue.6
-
-
Ingolia, N.T.1
-
42
-
-
19344376625
-
Design and diversity in bacterial chemotaxis: A comparative study in Escherichia coli and Bacillus subtilis
-
340952 14966542 10.1371/journal.pbio.0020049
-
Rao CV Kirby JR Arkin AP Design and diversity in bacterial chemotaxis: A comparative study in Escherichia coli and Bacillus subtilis PLoS Biology 2004, 2(2):e49. 340952 14966542 10.1371/journal.pbio.0020049
-
(2004)
PLoS Biology
, vol.2
, Issue.2
-
-
Rao, C.V.1
Kirby, J.R.2
Arkin, A.P.3
-
43
-
-
1542619848
-
Cancer as a robust system: Implications for anticancer therapy
-
10.1038/nrc1300 14993904
-
Kitano H Cancer as a robust system: Implications for anticancer therapy Nature Reviews Cancer 2004, 4(3):227-235. 10.1038/nrc1300 14993904
-
(2004)
Nature Reviews Cancer
, vol.4
, Issue.3
, pp. 227-235
-
-
Kitano, H.1
-
44
-
-
0036500834
-
Reverse engineering of biological complexity
-
1669 10.1126/science.1069981 11872830
-
Csete ME Doyle JC Reverse engineering of biological complexity Science 2002, 295:5560-1664. 1669 10.1126/science.1069981 11872830
-
(2002)
Science
, vol.295
, pp. 1664-1669
-
-
Csete, M.E.1
Doyle, J.C.2
-
45
-
-
23644437498
-
Formation of regulatory patterns during signal propagation in a Mammalian cellular network
-
1083 10.1126/science.1108876 16099987
-
Ma'ayan A Jenkins S Neves S Hasseldine A Grace E Dubin-Thaler B Eungdamrong N Weng G Ram P Rice J Kershenbaum A Stolovitzky G Blitzer R Iyengar R Formation of regulatory patterns during signal propagation in a Mammalian cellular network Science 2005, (309):5737-1078. 1083 10.1126/ science.1108876 16099987
-
(2005)
Science
, vol.309
, Issue.309
, pp. 1078-1083
-
-
Ma'ayan, A.1
Jenkins, S.2
Neves, S.3
Hasseldine, A.4
Grace, E.5
Dubin-Thaler, B.6
Eungdamrong, N.7
Weng, G.8
Ram, P.9
Rice, J.10
Kershenbaum, A.11
Stolovitzky, G.12
Blitzer, R.13
Iyengar, R.14
-
46
-
-
34147097353
-
Boolean dynamics of biological networks with multiple coupled feedback loops
-
10.1529/biophysj.106.097097 17259267
-
Kwon YK Cho KH Boolean dynamics of biological networks with multiple coupled feedback loops Biophysical Journal 2007, 92:2975-2981. 10.1529/ biophysj.106.097097 17259267
-
(2007)
Biophysical Journal
, vol.92
, pp. 2975-2981
-
-
Kwon, Y.K.1
Cho, K.H.2
-
47
-
-
39749142711
-
Boolean Modeling of Genetic Regulatory Networks
-
Albert R Boolean Modeling of Genetic Regulatory Networks Lecture Notes in Physics 2004, 650:459-481.
-
(2004)
Lecture Notes in Physics
, vol.650
, pp. 459-481
-
-
Albert, R.1
-
48
-
-
33747874092
-
Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle
-
10.1093/bioinformatics/btl210 16873462
-
Faure A Naldi A Chaouiya C Thieffry D Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle Bioinformatics 2006, 22:e124-131. 10.1093/bioinformatics/btl210 16873462
-
(2006)
Bioinformatics
, vol.22
-
-
Faure, A.1
Naldi, A.2
Chaouiya, C.3
Thieffry, D.4
-
49
-
-
0034715919
-
Shape-dependent control of cell growth, differentiation, and apoptosis: Switching between attractors and in cell regulatory networks
-
10.1006/excr.2000.5044 11082279
-
Huang S Ingber EE Shape-dependent control of cell growth, differentiation, and apoptosis: Switching between attractors and in cell regulatory networks Experimental Cell Research 2000, 261:91-103. 10.1006/ excr.2000.5044 11082279
-
(2000)
Experimental Cell Research
, vol.261
, pp. 91-103
-
-
Huang, S.1
Ingber, E.E.2
-
50
-
-
13444256478
-
Inparanoid: A comprehensive database of eukaryotic orthologs
-
540061 15608241 10.1093/nar/gki107
-
O'Brien KP Remm M Sonnhammer EL Inparanoid: A comprehensive database of eukaryotic orthologs Nucleic Acids Research 2005, 33:D476-480. 540061 15608241 10.1093/nar/gki107
-
(2005)
Nucleic Acids Research
, vol.33
-
-
O'Brien, K.P.1
Remm, M.2
Sonnhammer, E.L.3
|