-
1
-
-
0014489272
-
Metabolic stability and epigenesis in randomly constructed genetic nets
-
Kauffman SA, (1969) Metabolic stability and epigenesis in randomly constructed genetic nets. J Theor Biol 22: 437-467.
-
(1969)
J Theor Biol
, vol.22
, pp. 437-467
-
-
Kauffman, S.A.1
-
2
-
-
0025948178
-
Regulatory networks seen as asynchronous automata: A logical description
-
Thomas R, (1991) Regulatory networks seen as asynchronous automata: A logical description. J Theor Biol 153: 1-23.
-
(1991)
J Theor Biol
, vol.153
, pp. 1-23
-
-
Thomas, R.1
-
3
-
-
0029267491
-
Dynamical behaviour of biological regulatory networks-i. biological role of feedback loops and practical use of the concept of the loop-characteristic state
-
Thomas R, Thieffry D, Kaufman M, (1995) Dynamical behaviour of biological regulatory networks-i. biological role of feedback loops and practical use of the concept of the loop-characteristic state. Bull Math Biol 57: 247-76.
-
(1995)
Bull Math Biol
, vol.57
, pp. 247-276
-
-
Thomas, R.1
Thieffry, D.2
Kaufman, M.3
-
4
-
-
0036207347
-
Modeling and simulation of genetic regulatory systems: a literature review
-
de Jong H, (2002) Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol 9: 67-103.
-
(2002)
J Comput Biol
, vol.9
, pp. 67-103
-
-
de Jong, H.1
-
5
-
-
34548451679
-
A Markovian approach to the control of genetic regulatory networks
-
Chen PCY, Chen JW, (2007) A Markovian approach to the control of genetic regulatory networks. Biosystems 90: 535-545.
-
(2007)
Biosystems
, vol.90
, pp. 535-545
-
-
Chen, P.C.Y.1
Chen, J.W.2
-
6
-
-
0842285841
-
Summing up the noise in gene networks
-
Paulsson J, (2004) Summing up the noise in gene networks. Nature 427: 415-418.
-
(2004)
Nature
, vol.427
, pp. 415-418
-
-
Paulsson, J.1
-
7
-
-
0036184629
-
Probabilistic boolean networks: a rule-based uncertainty model for gene regulatory networks
-
Shmulevich I, Dougherty ER, Kim S, Zhang W, (2002) Probabilistic boolean networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics 18: 261-74.
-
(2002)
Bioinformatics
, vol.18
, pp. 261-274
-
-
Shmulevich, I.1
Dougherty, E.R.2
Kim, S.3
Zhang, W.4
-
8
-
-
0346505356
-
Steady-state analysis of genetic regulatory networks modelled by probabilistic boolean networks
-
Shmulevich I, Gluhovsky I, Hashimoto RF, Dougherty ER, Zhang W, (2003) Steady-state analysis of genetic regulatory networks modelled by probabilistic boolean networks. Comp Funct Genom 4: 601-608.
-
(2003)
Comp Funct Genom
, vol.4
, pp. 601-608
-
-
Shmulevich, I.1
Gluhovsky, I.2
Hashimoto, R.F.3
Dougherty, E.R.4
Zhang, W.5
-
9
-
-
0037551723
-
Can Markov Chain Models Mimic Biological Regulation?
-
Kim S, Li H, Dougherty ER, Cao N, Chen Y, et al. (2003) Can Markov Chain Models Mimic Biological Regulation? J Biol Syst 10: 337-357.
-
(2003)
J Biol Syst
, vol.10
, pp. 337-357
-
-
Kim, S.1
Li, H.2
Dougherty, E.R.3
Cao, N.4
Chen, Y.5
-
10
-
-
34250793514
-
Inference of a probabilistic Boolean network from a single observed temporal sequence
-
Marshall S, Yu L, Xiao Y, Dougherty ER, (2007) Inference of a probabilistic Boolean network from a single observed temporal sequence. EURASIP J Bioinf Syst Biol pp. 32454.
-
(2007)
EURASIP J Bioinf Syst Biol
, pp. 32454
-
-
Marshall, S.1
Yu, L.2
Xiao, Y.3
Dougherty, E.R.4
-
11
-
-
33947131109
-
Design of probabilistic Boolean networks under the requirement of contextual data consistency
-
Dougherty E, (2006) Design of probabilistic Boolean networks under the requirement of contextual data consistency. IEEE T Signal Proces 54: 3603-3613.
-
(2006)
IEEE T Signal Proces
, vol.54
, pp. 3603-3613
-
-
Dougherty, E.1
-
12
-
-
34547825448
-
Simulation study in Probabilistic Boolean Network models for genetic regulatory networks
-
Zhang SQ, Ching WK, Ng MK, Akutsu T, (2007) Simulation study in Probabilistic Boolean Network models for genetic regulatory networks. Int J Data Min Bioin 1: 217-240.
-
(2007)
Int J Data Min Bioin
, vol.1
, pp. 217-240
-
-
Zhang, S.Q.1
Ching, W.K.2
Ng, M.K.3
Akutsu, T.4
-
13
-
-
2342444140
-
External control in Markovian genetic regulatory networks: the imperfect information case
-
Datta A, Choudhary A, Bittner ML, Dougherty ER, (2004) External control in Markovian genetic regulatory networks: the imperfect information case. Bioinformatics 20: 924-930.
-
(2004)
Bioinformatics
, vol.20
, pp. 924-930
-
-
Datta, A.1
Choudhary, A.2
Bittner, M.L.3
Dougherty, E.R.4
-
14
-
-
30344473639
-
Systematic intervention of transcription for identifying network response to disease and cellular phenotypes
-
Li H, Zhan M, (2006) Systematic intervention of transcription for identifying network response to disease and cellular phenotypes. Bioinformatics 22: 96-102.
-
(2006)
Bioinformatics
, vol.22
, pp. 96-102
-
-
Li, H.1
Zhan, M.2
-
15
-
-
77958183488
-
Piecewise Affine Models of Regulatory Genetic Networks: Review and Probabilistic Interpretation
-
In: Lévine J, Müllhaupt P, editors, Advances in the Theory of Control, Signals and Systems with Physical Modeling, vol 407
-
Chaves M, Gouzé JL, (2010) Piecewise Affine Models of Regulatory Genetic Networks: Review and Probabilistic Interpretation. In: Lévine J, Müllhaupt P, editors. pp. 241-253 Advances in the Theory of Control, Signals and Systems with Physical Modeling, vol 407.
-
(2010)
, pp. 241-253
-
-
Chaves, M.1
Gouzé, J.L.2
-
16
-
-
84859951572
-
Transition probabilities for piecewise affine models of genetic networks
-
In: Proc. Int. Symp. Mathematical Theory of Networks and Systems (MTNS 10), Budapest, Hungary, Jul. 2010
-
Chaves M, Farcot E, Gouzé JL, (2010) Transition probabilities for piecewise affine models of genetic networks. pp. 1-8 In: Proc. Int. Symp. Mathematical Theory of Networks and Systems (MTNS 10), Budapest, Hungary, Jul. 2010.
-
(2010)
, pp. 1-8
-
-
Chaves, M.1
Farcot, E.2
Gouzé, J.L.3
-
18
-
-
33745588542
-
Pattern matching statistics on correlated sources
-
In: Proc. of LATIN'06. Number 3887 in Lect. Notes Comput. Sci
-
Bourdon J, Vallée B, (2006) Pattern matching statistics on correlated sources. pp. 224-237 In: Proc. of LATIN'06. Number 3887 in Lect. Notes Comput. Sci.
-
(2006)
, pp. 224-237
-
-
Bourdon, J.1
Vallée, B.2
-
19
-
-
47649132170
-
The environmental contribution to gene expression profiles
-
Gibson G, (2008) The environmental contribution to gene expression profiles. Nat Rev Genet 9: 575-81.
-
(2008)
Nat Rev Genet
, vol.9
, pp. 575-581
-
-
Gibson, G.1
-
20
-
-
33645027986
-
Stochastic protein expression in individual cells at the single molecule level
-
Cai L, Friedman N, Xie XS, (2006) Stochastic protein expression in individual cells at the single molecule level. Nature 440: 358-362.
-
(2006)
Nature
, vol.440
, pp. 358-362
-
-
Cai, L.1
Friedman, N.2
Xie, X.S.3
-
21
-
-
77955102352
-
Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells
-
Taniguchi Y, Choi PJ, Li GW, Chen H, Babu M, et al. (2010) Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 329: 533-538.
-
(2010)
Science
, vol.329
, pp. 533-538
-
-
Taniguchi, Y.1
Choi, P.J.2
Li, G.W.3
Chen, H.4
Babu, M.5
-
22
-
-
33645033645
-
Probing gene expression in live cells, one protein molecule at a time
-
Yu J, Xiao J, Ren X, Lao K, Xie XS, (2006) Probing gene expression in live cells, one protein molecule at a time. Science 311: 1600-1603.
-
(2006)
Science
, vol.311
, pp. 1600-1603
-
-
Yu, J.1
Xiao, J.2
Ren, X.3
Lao, K.4
Xie, X.S.5
-
23
-
-
79961194517
-
Connecting protein and mRNA burst distributions for stochastic models of gene expression
-
Elgart V, Jia T, Fenley AT, Kulkarni R, (2011) Connecting protein and mRNA burst distributions for stochastic models of gene expression. Phys Biol 8: 046001.
-
(2011)
Phys Biol
, vol.8
, pp. 046001
-
-
Elgart, V.1
Jia, T.2
Fenley, A.T.3
Kulkarni, R.4
-
24
-
-
25444532704
-
Stochastic Local Search: Foundations & Applications (The Morgan Kaufmann Series in Artificial Intelligence)
-
Morgan Kaufmann, 1 edition
-
Hoos HH, Stützle T, (2004) Stochastic Local Search: Foundations & Applications (The Morgan Kaufmann Series in Artificial Intelligence). Morgan Kaufmann, 1 edition.
-
(2004)
-
-
Hoos, H.H.1
Stützle, T.2
-
25
-
-
49649117268
-
Critical dynamics in genetic regulatory networks: examples from four kingdoms
-
Balleza E, Alvarez-Buylla ER, Chaos A, Kauffman S, Shmulevich I, et al. (2008) Critical dynamics in genetic regulatory networks: examples from four kingdoms. PLoS One 3: e2456.
-
(2008)
PLoS One
, vol.3
-
-
Balleza, E.1
Alvarez-Buylla, E.R.2
Chaos, A.3
Kauffman, S.4
Shmulevich, I.5
-
26
-
-
1242333310
-
Qualitative simulation of genetic regulatory networks using piecewise-linear models
-
de Jong H, Gouzé JL, Hernandez C, Page M, Sari T, et al. (2004) Qualitative simulation of genetic regulatory networks using piecewise-linear models. Bull Math Biol 66: 301-40.
-
(2004)
Bull Math Biol
, vol.66
, pp. 301-340
-
-
de Jong, H.1
Gouzé, J.L.2
Hernandez, C.3
Page, M.4
Sari, T.5
-
27
-
-
25444489027
-
Phenotypic diversity, population growth, and information in fluctuating environments
-
Kussell E, Leibler S, (2005) Phenotypic diversity, population growth, and information in fluctuating environments. Science 309: 2075-8.
-
(2005)
Science
, vol.309
, pp. 2075-2078
-
-
Kussell, E.1
Leibler, S.2
-
28
-
-
0030632048
-
The N-end rule pathway of protein degradation
-
Varshavsky A, (1997) The N-end rule pathway of protein degradation. Genes Cells 2: 13-28.
-
(1997)
Genes Cells
, vol.2
, pp. 13-28
-
-
Varshavsky, A.1
-
29
-
-
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: 124-52.
-
(2006)
Biosystems
, vol.84
, pp. 124-152
-
-
Ropers, D.1
de Jong, H.2
Page, M.3
Schneider, D.4
Geiselmann, J.5
-
30
-
-
0026620949
-
Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli
-
Ball CA, Osuna R, Ferguson KC, Johnson RC, (1992) Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli. J Bacteriol 174: 8043-56.
-
(1992)
J Bacteriol
, vol.174
, pp. 8043-8056
-
-
Ball, C.A.1
Osuna, R.2
Ferguson, K.C.3
Johnson, R.C.4
-
31
-
-
0030839962
-
The relationship between external glucose concentration and cAMP levels inside Escherichia coli: implications for models of phosphotransferasemediated regulation of adenylate cyclase
-
Notley-McRobb L, Death A, Ferenci T, (1997) The relationship between external glucose concentration and cAMP levels inside Escherichia coli: implications for models of phosphotransferasemediated regulation of adenylate cyclase. Microbiology+ 143: 1909-1918.
-
(1997)
Microbiology+
, vol.143
, pp. 1909-1918
-
-
Notley-McRobb, L.1
Death, A.2
Ferenci, T.3
-
32
-
-
0035810698
-
Allosteric regulation of the cAMP receptor protein
-
Harman JG, (2001) Allosteric regulation of the cAMP receptor protein. Biochim Biophys Acta 1547: 1-17.
-
(2001)
Biochim Biophys Acta
, vol.1547
, pp. 1-17
-
-
Harman, J.G.1
-
33
-
-
0037582107
-
Regulation of crp transcription by oscillation between distinct nucleoprotein complexes
-
González-Gil G, Kahmann R, Muskhelishvili G, (1998) Regulation of crp transcription by oscillation between distinct nucleoprotein complexes. EMBO J 17: 2877-85.
-
(1998)
EMBO J
, vol.17
, pp. 2877-2885
-
-
González-Gil, G.1
Kahmann, R.2
Muskhelishvili, G.3
-
34
-
-
0028298782
-
Mechanism of the down-regulation of cAMP receptor protein by glucose in Escherichia coli: role of autoregulation of the crp gene
-
Ishizuka H, Hanamura A, Inada T, Aiba H, (1994) Mechanism of the down-regulation of cAMP receptor protein by glucose in Escherichia coli: role of autoregulation of the crp gene. EMBO J 13: 3077-82.
-
(1994)
EMBO J
, vol.13
, pp. 3077-3082
-
-
Ishizuka, H.1
Hanamura, A.2
Inada, T.3
Aiba, H.4
-
35
-
-
0033814887
-
The expression of the Escherichia coli fis gene is strongly dependent on the superhelical density of DNA
-
Schneider R, Travers A, Muskhelishvili G, (2000) The expression of the Escherichia coli fis gene is strongly dependent on the superhelical density of DNA. Mol Microbiol 38: 167-75.
-
(2000)
Mol Microbiol
, vol.38
, pp. 167-175
-
-
Schneider, R.1
Travers, A.2
Muskhelishvili, G.3
-
36
-
-
10244239406
-
A bayesian connectivity-based approach to constructing probabilistic gene regulatory networks
-
Zhou X, Wang X, Pal R, Ivanov I, Bittner M, et al. (2004) A bayesian connectivity-based approach to constructing probabilistic gene regulatory networks. Bioinformatics 20: 2918-2927.
-
(2004)
Bioinformatics
, vol.20
, pp. 2918-2927
-
-
Zhou, X.1
Wang, X.2
Pal, R.3
Ivanov, I.4
Bittner, M.5
-
37
-
-
0036227648
-
DNA supercoiling in Escherichia coli is under tight and subtle homeostatic control, involving gene-expression and metabolic regulation of both topoisomerase I and DNA gyrase
-
Snoep JL, van der Weijden CC, Andersen HW, Westerhoff HV, Jensen PR, (2002) DNA supercoiling in Escherichia coli is under tight and subtle homeostatic control, involving gene-expression and metabolic regulation of both topoisomerase I and DNA gyrase. Eur J Biochem 269: 1662-9.
-
(2002)
Eur J Biochem
, vol.269
, pp. 1662-1669
-
-
Snoep, J.L.1
van der Weijden, C.C.2
Andersen, H.W.3
Westerhoff, H.V.4
Jensen, P.R.5
-
38
-
-
0034065133
-
Escherichia coli response to hydrogen peroxide: a role for DNA supercoiling, topoisomerase I and Fis
-
Weinstein-Fischer D, Elgrably-Weiss M, Altuvia S, (2000) Escherichia coli response to hydrogen peroxide: a role for DNA supercoiling, topoisomerase I and Fis. Mol Microbiol 35: 1413-20.
-
(2000)
Mol Microbiol
, vol.35
, pp. 1413-1420
-
-
Weinstein-Fischer, D.1
Elgrably-Weiss, M.2
Altuvia, S.3
-
39
-
-
0035082155
-
DNA supercoiling and transcription in Escherichia coli: The FIS connection
-
Travers A, Schneider R, Muskhelishvili G, (2001) DNA supercoiling and transcription in Escherichia coli: The FIS connection. Biochimie 83: 213-7.
-
(2001)
Biochimie
, vol.83
, pp. 213-217
-
-
Travers, A.1
Schneider, R.2
Muskhelishvili, G.3
|