-
1
-
-
7444253428
-
Systems biology and new technologies enable predictive and preventative medicine
-
Hood L, Heath JR, Phelps ME, Lin B, (2004) Systems biology and new technologies enable predictive and preventative medicine. Science 306: 640-643.
-
(2004)
Science
, vol.306
, pp. 640-643
-
-
Hood, L.1
Heath, J.R.2
Phelps, M.E.3
Lin, B.4
-
2
-
-
33644555054
-
Proteome survey reveals modularity of the yeast cell machinery
-
Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440: 631-636.
-
(2006)
Nature
, vol.440
, pp. 631-636
-
-
Gavin, A.C.1
Aloy, P.2
Grandi, P.3
Krause, R.4
Boesche, M.5
-
3
-
-
25444448797
-
Spontaneous evolution of modularity and network motifs
-
Kashtan N, Alon U, (2005) Spontaneous evolution of modularity and network motifs. Proc Natl Acad Sci USA 102: 13773-13778.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 13773-13778
-
-
Kashtan, N.1
Alon, U.2
-
4
-
-
55549117151
-
Hepatitis C virus infection protein network
-
de Chassey B, Navratil V, Tafforeau L, Hiet MS, Aublin-Gex A, et al. (2008) Hepatitis C virus infection protein network. Mol Syst Biol 4: 230.
-
(2008)
Mol Syst Biol
, vol.4
, pp. 230
-
-
de Chassey, B.1
Navratil, V.2
Tafforeau, L.3
Hiet, M.S.4
Aublin-Gex, A.5
-
5
-
-
33746866355
-
From systems biology to synthetic biology
-
Church GM, (2005) From systems biology to synthetic biology. Mol Syst Biol 1: 0032.
-
(2005)
Mol Syst Biol
, vol.1
, pp. 0032
-
-
Church, G.M.1
-
6
-
-
27844497945
-
FoxO transcription factors at the interface between longevity and tumor suppression
-
Greer EL, Brunet A, (2005) FoxO transcription factors at the interface between longevity and tumor suppression. Oncogene 24: 7410-7425.
-
(2005)
Oncogene
, vol.24
, pp. 7410-7425
-
-
Greer, E.L.1
Brunet, A.2
-
7
-
-
34547660196
-
FoxO transcription factors and stem cell homeostasis: Insights from the hematopoietic system
-
Tothova Z, Gilliland DG, (2007) FoxO transcription factors and stem cell homeostasis: Insights from the hematopoietic system. Cell Stem Cell 1: 140-152.
-
(2007)
Cell Stem Cell
, vol.1
, pp. 140-152
-
-
Tothova, Z.1
Gilliland, D.G.2
-
8
-
-
0030467846
-
Osmotic regulation of gene expression
-
Burg MB, Kwon ED, Kultz D, (1996) Osmotic regulation of gene expression. FASEB J 10: 1598-1606.
-
(1996)
FASEB J
, vol.10
, pp. 1598-1606
-
-
Burg, M.B.1
Kwon, E.D.2
Kultz, D.3
-
9
-
-
84984933073
-
Structure and function of a transcriptional network activated by the MAPK Hog1
-
Capaldi AP, Kaplan T, Liu Y, Habib N, Regev A, et al. (2008) Structure and function of a transcriptional network activated by the MAPK Hog1. Nature Genetics 40: 1300-1306.
-
(2008)
Nature Genetics
, vol.40
, pp. 1300-1306
-
-
Capaldi, A.P.1
Kaplan, T.2
Liu, Y.3
Habib, N.4
Regev, A.5
-
10
-
-
17744372861
-
Roles of the heat shock transcription factors in regulation of the heat shock response and beyond
-
Pirkkala L, Nykanen P, Sistonen L, (2001) Roles of the heat shock transcription factors in regulation of the heat shock response and beyond. FASEB J 15: 1118-1131.
-
(2001)
FASEB J
, vol.15
, pp. 1118-1131
-
-
Pirkkala, L.1
Nykanen, P.2
Sistonen, L.3
-
11
-
-
1942453302
-
Predicting gene expression from sequence
-
Beer MA, Tavazoie S, (2004) Predicting gene expression from sequence. Cell 117: 185-198.
-
(2004)
Cell
, vol.117
, pp. 185-198
-
-
Beer, M.A.1
Tavazoie, S.2
-
12
-
-
9244257298
-
Interacting models of cooperative gene regulation
-
Das D, Banerjee N, Zhang MQ, (2004) Interacting models of cooperative gene regulation. Proc Natl Acad Sci USA 101: 16234-16239.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 16234-16239
-
-
Das, D.1
Banerjee, N.2
Zhang, M.Q.3
-
13
-
-
58149354385
-
Analysis of combinatorial cis-regulation in synthetic and genomic promoters
-
Gertz J, Siggia ED, Cohen BA, (2009) Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Nature 457: 215-218.
-
(2009)
Nature
, vol.457
, pp. 215-218
-
-
Gertz, J.1
Siggia, E.D.2
Cohen, B.A.3
-
14
-
-
53549125545
-
A genome-scale analysis of the cis-regulatory circuitry underlying sonic hedgehog-mediated patterning of the mammalian limb
-
Vokes SA, Ji H, Wong WH, McMahon AP, (2008) A genome-scale analysis of the cis-regulatory circuitry underlying sonic hedgehog-mediated patterning of the mammalian limb. Genes and Development 22: 2651-2663.
-
(2008)
Genes and Development
, vol.22
, pp. 2651-2663
-
-
Vokes, S.A.1
Ji, H.2
Wong, W.H.3
McMahon, A.P.4
-
15
-
-
60149091656
-
ChIP-seq accurately predicts tissue-specific activity of enhancers
-
Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, et al. (2009) ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457: 854-858.
-
(2009)
Nature
, vol.457
, pp. 854-858
-
-
Visel, A.1
Blow, M.J.2
Li, Z.3
Zhang, T.4
Akiyama, J.A.5
-
16
-
-
70449132583
-
Combinatorial binding predicts spatio-temporal cis-regulatory activity
-
Zinzen RP, Girardot C, Gagneur J, Braun M, Furlong EEM, (2009) Combinatorial binding predicts spatio-temporal cis-regulatory activity. Nature 462: 65-70.
-
(2009)
Nature
, vol.462
, pp. 65-70
-
-
Zinzen, R.P.1
Girardot, C.2
Gagneur, J.3
Braun, M.4
Furlong, E.E.M.5
-
17
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 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
-
18
-
-
0037165942
-
Combinatorial synthesis of genetic networks
-
Guet CC, Elowitz MB, Hsing W, Leibler S, (2002) Combinatorial synthesis of genetic networks. Science 296: 1466-1470.
-
(2002)
Science
, vol.296
, pp. 1466-1470
-
-
Guet, C.C.1
Elowitz, M.B.2
Hsing, W.3
Leibler, S.4
-
19
-
-
0037079054
-
Computational systems biology
-
Kitano H, (2002) Computational systems biology. Nature 420: 206-210.
-
(2002)
Nature
, vol.420
, pp. 206-210
-
-
Kitano, H.1
-
20
-
-
33750203381
-
Genetic regulation of fluxes: iron homeostasis of Escherichia coli
-
Semsey S, Andersson AM, Krishna S, Jensen MH, Massé E, et al. (2006) Genetic regulation of fluxes: iron homeostasis of Escherichia coli. Nucl Acids Res 34: 4960-4967.
-
(2006)
Nucl Acids Res
, vol.34
, pp. 4960-4967
-
-
Semsey, S.1
Andersson, A.M.2
Krishna, S.3
Jensen, M.H.4
Massé, E.5
-
21
-
-
1442354192
-
Multistability in the lactose utilization network of Escherichia coli
-
Ozbudak EM, Thattai M, Lim HN, Shraiman BI, van Oudenaarden A, (2004) Multistability in the lactose utilization network of Escherichia coli. Letters to Nature 427: 237-240.
-
(2004)
Letters to Nature
, vol.427
, pp. 237-240
-
-
Ozbudak, E.M.1
Thattai, M.2
Lim, H.N.3
Shraiman, B.I.4
van Oudenaarden, A.5
-
22
-
-
0031935932
-
Frequency selectivity, multistability, and oscillations emerge from models of genetic regulatory systems
-
Smolen P, Baxter DA, Byrne JH, (1998) Frequency selectivity, multistability, and oscillations emerge from models of genetic regulatory systems. Am J Physiol Cell Physiol 274: C531-C542.
-
(1998)
Am J Physiol Cell Physiol
, vol.274
-
-
Smolen, P.1
Baxter, D.A.2
Byrne, J.H.3
-
23
-
-
0034724292
-
Differential regulation of circadian pacemaker output by separate clock genes in Drosophila
-
Park JH, Helfrich-Förster C, Lee G, Liu L, Rosbash M, et al. (2000) Differential regulation of circadian pacemaker output by separate clock genes in Drosophila. Proc Natl Acad Sci USA 97: 3608-3613.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 3608-3613
-
-
Park, J.H.1
Helfrich-Förster, C.2
Lee, G.3
Liu, L.4
Rosbash, M.5
-
24
-
-
0037044575
-
The IκB-NκB signaling module: Temporal control and selective gene activation
-
Hoffmann A, Levchenko A, Scott ML, Baltimore D, (2002) The IκB-NκB signaling module: Temporal control and selective gene activation. Science 298: 1241-1245.
-
(2002)
Science
, vol.298
, pp. 1241-1245
-
-
Hoffmann, A.1
Levchenko, A.2
Scott, M.L.3
Baltimore, D.4
-
25
-
-
2642544592
-
Estrogen receptor-α directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter
-
Métivier R, Penot G, Hübner MR, Reid G, Brand H, et al. (2003) Estrogen receptor-α directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell 115: 751-763.
-
(2003)
Cell
, vol.115
, pp. 751-763
-
-
Métivier, R.1
Penot, G.2
Hübner, M.R.3
Reid, G.4
Brand, H.5
-
26
-
-
20844451181
-
Transcriptional complexes engaged by apo-estrogen receptor-α isoforms have divergent outcomes
-
Métivier R, Penot G, Carmouche RP, Hubner MR, Reid G, et al. (2004) Transcriptional complexes engaged by apo-estrogen receptor-α isoforms have divergent outcomes. EMBO J 23: 3653-3666.
-
(2004)
EMBO J
, vol.23
, pp. 3653-3666
-
-
Métivier, R.1
Penot, G.2
Carmouche, R.P.3
Hubner, M.R.4
Reid, G.5
-
27
-
-
4644326931
-
Genomic analysis of regulatory network dynamics reveals large topological changes
-
Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, et al. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Letters to Nature 413: 308-312.
-
(2004)
Letters to Nature
, vol.413
, pp. 308-312
-
-
Luscombe, N.M.1
Babu, M.M.2
Yu, H.3
Snyder, M.4
Teichmann, S.A.5
-
28
-
-
77953281765
-
Global coordination of transcriptional control and mRNA decay during cellular differentiation
-
Amorim MJ, Cotobal C, Duncan C, Mata J, (2010) Global coordination of transcriptional control and mRNA decay during cellular differentiation. Mol Syst Biol 6: 380.
-
(2010)
Mol Syst Biol
, vol.6
, pp. 380
-
-
Amorim, M.J.1
Cotobal, C.2
Duncan, C.3
Mata, J.4
-
29
-
-
77955291454
-
Systematic analysis of Cis-elements in unstable mRNAs demonstrates that CUGBP1 is a key regulator of mRNA decay in muscle cells
-
Lee JE, Lee JY, Wilusz J, Tian B, Wilusz CJ, (2010) Systematic analysis of Cis-elements in unstable mRNAs demonstrates that CUGBP1 is a key regulator of mRNA decay in muscle cells. PLoS ONE 5: e11201.
-
(2010)
PLoS ONE
, vol.5
-
-
Lee, J.E.1
Lee, J.Y.2
Wilusz, J.3
Tian, B.4
Wilusz, C.J.5
-
30
-
-
33745879143
-
Intracellular protein degradation: from a vague idea thru the lysosome and the ubiquitin-proteasome system and onto human diseases and drug targeting
-
Ciechanover A, (2006) Intracellular protein degradation: from a vague idea thru the lysosome and the ubiquitin-proteasome system and onto human diseases and drug targeting. Exp Biol Med 231: 1197-1211.
-
(2006)
Exp Biol Med
, vol.231
, pp. 1197-1211
-
-
Ciechanover, A.1
-
31
-
-
57149116929
-
Tight regulation of unstructured proteins: From transcript synthesis to protein degradation
-
Gsponer J, Futschik ME, Teichmann SA, Babu MM, (2008) Tight regulation of unstructured proteins: From transcript synthesis to protein degradation. Science 322: 1365-1368.
-
(2008)
Science
, vol.322
, pp. 1365-1368
-
-
Gsponer, J.1
Futschik, M.E.2
Teichmann, S.A.3
Babu, M.M.4
-
32
-
-
64349094767
-
Tissue specificity and the human protein interaction network
-
Bossi A, Lehner B, (2009) Tissue specificity and the human protein interaction network. Mol Syst Biol 5: 260.
-
(2009)
Mol Syst Biol
, vol.5
, pp. 260
-
-
Bossi, A.1
Lehner, B.2
-
33
-
-
79251573543
-
Initial characterization of the human central proteome
-
Burkard TR, Planyavsky M, Kaupe I, Breitwieser FP, Bürckstümmer T, et al. (2011) Initial characterization of the human central proteome. BMC Syst Biol 5: 17.
-
(2011)
BMC Syst Biol
, vol.5
, pp. 17
-
-
Burkard, T.R.1
Planyavsky, M.2
Kaupe, I.3
Breitwieser, F.P.4
Bürckstümmer, T.5
-
35
-
-
26844581913
-
Delay-induced stochastic oscillations in gene regulation
-
Bratsun D, Volfson D, Tsimring LS, Hasty J, (2005) Delay-induced stochastic oscillations in gene regulation. Proc Natl Acad Sci USA 102: 14593-14598.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 14593-14598
-
-
Bratsun, D.1
Volfson, D.2
Tsimring, L.S.3
Hasty, J.4
-
36
-
-
0034691214
-
Stochastic focusing: Fluctuation-enhanced sensitivity of intracellular regulation
-
Paulsson J, Berg OG, Ehrenberg M, (2000) Stochastic focusing: Fluctuation-enhanced sensitivity of intracellular regulation. Proc Natl Acad Sci USA 97: 7148-7153.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 7148-7153
-
-
Paulsson, J.1
Berg, O.G.2
Ehrenberg, M.3
-
37
-
-
45149138762
-
Computation at the edge of chaos
-
Langton CG, (1990) Computation at the edge of chaos. Physica D 42: 12-37.
-
(1990)
Physica D
, vol.42
, pp. 12-37
-
-
Langton, C.G.1
-
38
-
-
0002082980
-
Revisiting the edge of chaos: Evolving cellular automata to perform computations
-
Mitchell M, Hraber PT, Crutchfield JP, (1993) Revisiting the edge of chaos: Evolving cellular automata to perform computations. Complex Systems 7: 89-130.
-
(1993)
Complex Systems
, vol.7
, pp. 89-130
-
-
Mitchell, M.1
Hraber, P.T.2
Crutchfield, J.P.3
-
40
-
-
0000629105
-
Power-law distributions in some random Boolean networks
-
Bhattacharjya A, Liang S, (1996) Power-law distributions in some random Boolean networks. Phys Rev Lett 77: 1644-1647.
-
(1996)
Phys Rev Lett
, vol.77
, pp. 1644-1647
-
-
Bhattacharjya, A.1
Liang, S.2
-
41
-
-
0032520557
-
Ordered and disordered dynamics in random networks
-
Glass L, Hill C, (1998) Ordered and disordered dynamics in random networks. Europhys Lett 41: 599-604.
-
(1998)
Europhys Lett
, vol.41
, pp. 599-604
-
-
Glass, L.1
Hill, C.2
-
42
-
-
0141480040
-
The role of certain Post classes in Boolean network models of genetic networks
-
Shmulevich I, Lähdesmäki H, Dougherty ER, Astola J, Zhang W, (2003) The role of certain Post classes in Boolean network models of genetic networks. Proc Natl Acad Sci USA 100: 10734-10739.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 10734-10739
-
-
Shmulevich, I.1
Lähdesmäki, H.2
Dougherty, E.R.3
Astola, J.4
Zhang, W.5
-
43
-
-
45849122105
-
Inflation of the edge of chaos in a simple model of gene interaction networks
-
Stokić D, Hanel R, Thurner S, (2008) Inflation of the edge of chaos in a simple model of gene interaction networks. Phys Rev E 77: 061917.
-
(2008)
Phys Rev E
, vol.77
, pp. 061917
-
-
Stokić, D.1
Hanel, R.2
Thurner, S.3
-
44
-
-
78650467651
-
Living on the edge of chaos: minimally nonlinear models of genetic regulatory dynamics
-
Hanel R, Pöchacker M, Thurner S, (2010) Living on the edge of chaos: minimally nonlinear models of genetic regulatory dynamics. Phil Trans Roy Acad Sci A 368: 5583-5596.
-
(2010)
Phil Trans Roy Acad Sci A
, vol.368
, pp. 5583-5596
-
-
Hanel, R.1
Pöchacker, M.2
Thurner, S.3
-
45
-
-
0015609281
-
The logical analysis of continuous non-linear biochemical control networks
-
Glass L, Kauffman SA, (1973) The logical analysis of continuous non-linear biochemical control networks. J Theor Biol 39: 103-129.
-
(1973)
J Theor Biol
, vol.39
, pp. 103-129
-
-
Glass, L.1
Kauffman, S.A.2
-
46
-
-
79951757406
-
State reduction for network intervention in probabilistic Boolean networks
-
Qian X, Ghaffari N, Ivanov I, Dougherty ER, (2010) State reduction for network intervention in probabilistic Boolean networks. Bioinformatics 26: 3098-3104.
-
(2010)
Bioinformatics
, vol.26
, pp. 3098-3104
-
-
Qian, X.1
Ghaffari, N.2
Ivanov, I.3
Dougherty, E.R.4
-
47
-
-
0345269975
-
Genetic network analyzer: qualitative simulation of genetic regulatory networks
-
de Jong H, Geiselmann J, Hernandez C, Page M, (2003) Genetic network analyzer: qualitative simulation of genetic regulatory networks. Bioinformatics 19: 336-344.
-
(2003)
Bioinformatics
, vol.19
, pp. 336-344
-
-
de Jong, H.1
Geiselmann, J.2
Hernandez, C.3
Page, M.4
-
48
-
-
2942750479
-
Modeling the quorum sensing regulatory network of human-pathogenic Pseudomonas aeruginosa
-
Viretta AU, Fussenegger M, (2004) Modeling the quorum sensing regulatory network of human-pathogenic Pseudomonas aeruginosa. Biotech Prog 20: 670-678.
-
(2004)
Biotech Prog
, vol.20
, pp. 670-678
-
-
Viretta, A.U.1
Fussenegger, M.2
-
49
-
-
33646377419
-
Qualitative simulation of the carbon starvation response in Escherichia coli
-
Ropers D, de Jong H, Page M, Schneider D, Geiselmann J, (2006) Qualitative simulation of the carbon starvation response in Escherichia coli. Biosystems 84: 124-152.
-
(2006)
Biosystems
, vol.84
, pp. 124-152
-
-
Ropers, D.1
de Jong, H.2
Page, M.3
Schneider, D.4
Geiselmann, J.5
-
50
-
-
0035212532
-
A trajectory piecewise-linear approach to model order reduction and fast simulation of nonlinear circuits and micromachined devices
-
Rewieński M, White J, (2003) A trajectory piecewise-linear approach to model order reduction and fast simulation of nonlinear circuits and micromachined devices. IEEE/ACM Trans Comp Aided Design pp. 252-257.
-
(2003)
IEEE/ACM Trans Comp Aided Design
, pp. 252-257
-
-
Rewieński, M.1
White, J.2
-
51
-
-
0014974440
-
On the relation between effector concentration and the rate of induced enzyme synthesis
-
Yagil G, Yagil E, (1971) On the relation between effector concentration and the rate of induced enzyme synthesis. Biophys J 11: 11-27.
-
(1971)
Biophys J
, vol.11
, pp. 11-27
-
-
Yagil, G.1
Yagil, E.2
-
53
-
-
29244452623
-
Piecewise-linear models of genetic regulatory networks: Equilibria and their stability
-
Casey R, de Jong H, Gouzé JL, (2006) Piecewise-linear models of genetic regulatory networks: Equilibria and their stability. J Math Biol 52: 27-56.
-
(2006)
J Math Biol
, vol.52
, pp. 27-56
-
-
Casey, R.1
de Jong, H.2
Gouzé, J.L.3
-
54
-
-
62549097283
-
Symbolic dynamics of biological feedback networks
-
Pigolotti S, Krishna S, Jensen MH, (2009) Symbolic dynamics of biological feedback networks. Phys Rev Lett 102: 088701.
-
(2009)
Phys Rev Lett
, vol.102
, pp. 088701
-
-
Pigolotti, S.1
Krishna, S.2
Jensen, M.H.3
-
55
-
-
69249127529
-
Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture
-
Jothi R, Balaji S, Wuster A, Grochow JA, Gsponer J, et al. (2009) Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol 5: 294.
-
(2009)
Mol Syst Biol
, vol.5
, pp. 294
-
-
Jothi, R.1
Balaji, S.2
Wuster, A.3
Grochow, J.A.4
Gsponer, J.5
-
56
-
-
79956322553
-
Global quantification of mammalian gene expression control
-
Schwanhäusser B, Busse D, Li N, Dittmar G, Schuchhardt J, et al. (2011) Global quantification of mammalian gene expression control. Nature 473: 337-342.
-
(2011)
Nature
, vol.473
, pp. 337-342
-
-
Schwanhäusser, B.1
Busse, D.2
Li, N.3
Dittmar, G.4
Schuchhardt, J.5
|