-
2
-
-
0015609281
-
The logical analysis of continuous, non-linear biochemical control networks
-
Glass, L. & Kauffman, S. A. The logical analysis of continuous, non-linear biochemical control networks. J. Theor. Biol. 39, 103-129 (1973).
-
(1973)
J. Theor. Biol
, vol.39
, pp. 103-129
-
-
Glass, L.1
Kauffman, S.A.2
-
3
-
-
0015823097
-
Boolean formalization of genetic control circuits
-
Thomas, R. Boolean formalization of genetic control circuits. J. Theor. Biol. 42, 563-585 (1973).
-
(1973)
J. Theor. Biol
, vol.42
, pp. 563-585
-
-
Thomas, R.1
-
4
-
-
0036500609
-
A genomic regulatory network for development
-
A highly detailed reconstruction of the regulatory network that controls the first 24 hours of sea urchin embryo development
-
Davidson, E. H. et al. A genomic regulatory network for development. Science 295, 1669-1678 (2002). A highly detailed reconstruction of the regulatory network that controls the first 24 hours of sea urchin embryo development.
-
(2002)
Science
, vol.295
, pp. 1669-1678
-
-
Davidson, E.H.1
-
5
-
-
38449100969
-
A gene regulatory network subcircuit drives a dynamic pattern of gene expression
-
Smith, J., Theodoris, C. & Davidson, E. H. A gene regulatory network subcircuit drives a dynamic pattern of gene expression. Science 318, 794-797 (2007).
-
(2007)
Science
, vol.318
, pp. 794-797
-
-
Smith, J.1
Theodoris, C.2
Davidson, E.H.3
-
6
-
-
52649148650
-
-
Kauffman, S. A. The Origins Of Order: Self-Organization And Selection In Evolution (Oxford University Press, Oxford, 1993). An accessible description of Kauffman's work, including the Boolean network model and its analysis.
-
Kauffman, S. A. The Origins Of Order: Self-Organization And Selection In Evolution (Oxford University Press, Oxford, 1993). An accessible description of Kauffman's work, including the Boolean network model and its analysis.
-
-
-
-
7
-
-
0345598902
-
Random Boolean network models and the yeast transcriptional network
-
Kauffman, S., Peterson, C., Samuelsson, B. & Troein, C. Random Boolean network models and the yeast transcriptional network. Proc. Natl Acad. Sci. USA 100, 14796-14799 (2003).
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 14796-14799
-
-
Kauffman, S.1
Peterson, C.2
Samuelsson, B.3
Troein, C.4
-
8
-
-
1842687878
-
The yeast cell-cycle network is robustly designed
-
Li, F., Long, T., Lu, Y., Ouyang, Q. & Tang, C. The yeast cell-cycle network is robustly designed. Proc. Natl Acad. Sci. USA 101, 4781-4786 (2004).
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 4781-4786
-
-
Li, F.1
Long, T.2
Lu, Y.3
Ouyang, Q.4
Tang, C.5
-
9
-
-
0038047901
-
On learning gene regulatory networks under the Boolean network model
-
Lähdesmäki, H., Shmulevich, I. & Yli-Harja, O. On learning gene regulatory networks under the Boolean network model. Machine Learning 52, 147-167 (2003).
-
(2003)
Machine Learning
, vol.52
, pp. 147-167
-
-
Lähdesmäki, H.1
Shmulevich, I.2
Yli-Harja, O.3
-
10
-
-
0032616683
-
Identification of genetic networks from a small number of gene expression patterns under the Boolean network model
-
Akutsu, T., Miyano, S. & Kuhara, S. Identification of genetic networks from a small number of gene expression patterns under the Boolean network model. Pac Symp. Biocomput., 17-28 (1999).
-
(1999)
Pac Symp. Biocomput
, pp. 17-28
-
-
Akutsu, T.1
Miyano, S.2
Kuhara, S.3
-
11
-
-
0031742022
-
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
-
Spellman, P. T. et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9, 3273-3297 (1998).
-
(1998)
Mol. Biol. Cell
, vol.9
, pp. 3273-3297
-
-
Spellman, P.T.1
-
12
-
-
0036184629
-
Probabilistic Boolean networks: A rule-based uncertainty model for gene regulatory networks
-
Shmulevich, I., Dougherty, E. R., Kim, S. & Zhang, W. Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics 18, 261-274 (2002).
-
(2002)
Bioinformatics
, vol.18
, pp. 261-274
-
-
Shmulevich, I.1
Dougherty, E.R.2
Kim, S.3
Zhang, W.4
-
13
-
-
0346505356
-
Steady-state analysis of genetic regulatory networks modelled by probabilistic Boolean networks
-
Shmulevich, I., Gluhovsky, I., Hashimoto, R. F., Dougherty, E. R. & Zhan, W. Steady-state analysis of genetic regulatory networks modelled by probabilistic Boolean networks. Comp. Funct. Genomics 4, 601-608 (2003).
-
(2003)
Comp. Funct. Genomics
, vol.4
, pp. 601-608
-
-
Shmulevich, I.1
Gluhovsky, I.2
Hashimoto, R.F.3
Dougherty, E.R.4
Zhan, W.5
-
15
-
-
0003860037
-
-
Chapman & Hall, Boca Raton
-
Gilks, W. R., Richardson, S. & Spiegelhalter, D. J. Markov Chain Monte Carlo In Practice (Chapman & Hall, Boca Raton, 1998).
-
(1998)
Markov Chain Monte Carlo In Practice
-
-
Gilks, W.R.1
Richardson, S.2
Spiegelhalter, D.J.3
-
16
-
-
12844254468
-
Modeling and analysis of heterogeneous regulation in biological networks
-
Gat-Viks, I., Tanay, A. & Shamir, R. Modeling and analysis of heterogeneous regulation in biological networks. J. Comput. Biol. 11, 1034-1049 (2004).
-
(2004)
J. Comput. Biol
, vol.11
, pp. 1034-1049
-
-
Gat-Viks, I.1
Tanay, A.2
Shamir, R.3
-
17
-
-
33646012325
-
-
Gat-Viks, I., Tanay, A., Raijman, D. & Shamir, R. A probabilistic methodology for integrating knowledge and experiments on biological networks. J. Comput. Biol. 13, 165-181 (2006). An exposition of the MetaReg methodology, including the probabilistic layer.
-
Gat-Viks, I., Tanay, A., Raijman, D. & Shamir, R. A probabilistic methodology for integrating knowledge and experiments on biological networks. J. Comput. Biol. 13, 165-181 (2006). An exposition of the MetaReg methodology, including the probabilistic layer.
-
-
-
-
18
-
-
0035246564
-
Factor graphs and the sum-product algorithm
-
Kschischang, F. R., Frey, B. J. & Loeliger, H. A. Factor graphs and the sum-product algorithm. IEEE Trans. Info. Theory 47, 498-519 (2001).
-
(2001)
IEEE Trans. Info. Theory
, vol.47
, pp. 498-519
-
-
Kschischang, F.R.1
Frey, B.J.2
Loeliger, H.A.3
-
20
-
-
33847708336
-
Refinement and expansion of signaling pathways: The osmotic response network in yeast
-
Gat-Viks, I. & Shamir, R. Refinement and expansion of signaling pathways: the osmotic response network in yeast. Genome Res. 17, 358-367 (2007).
-
(2007)
Genome Res
, vol.17
, pp. 358-367
-
-
Gat-Viks, I.1
Shamir, R.2
-
22
-
-
22144460567
-
STEPP - search tool for exploration of Petri net paths: A new tool for Petri net-based path analysis in biochemical networks
-
Koch, I., Schueler, M. & Heiner, M. STEPP - search tool for exploration of Petri net paths: a new tool for Petri net-based path analysis in biochemical networks. In Silico Biol. 5, 129-137 (2005).
-
(2005)
In Silico Biol
, vol.5
, pp. 129-137
-
-
Koch, I.1
Schueler, M.2
Heiner, M.3
-
23
-
-
0030026495
-
Qualitative analysis of biochemical reaction systems
-
Reddy, V. N., Liebman, M. N. & Mavrovouniotis, M. L. Qualitative analysis of biochemical reaction systems. Comput. Biol. Med. 26, 9-24 (1996).
-
(1996)
Comput. Biol. Med
, vol.26
, pp. 9-24
-
-
Reddy, V.N.1
Liebman, M.N.2
Mavrovouniotis, M.L.3
-
24
-
-
0033670135
-
Pathway analysis in metabolic databases via differential metabolic display (DMD)
-
Kuffner, R., Zimmer, R. & Lengauer, T. Pathway analysis in metabolic databases via differential metabolic display (DMD). Bioinformatics 16, 825-836 (2000).
-
(2000)
Bioinformatics
, vol.16
, pp. 825-836
-
-
Kuffner, R.1
Zimmer, R.2
Lengauer, T.3
-
25
-
-
52649136107
-
-
eds Cortadella, J. & Reisig, W, Springer, Berlin
-
Chaouiya, C., Remy, E., Ruet, P. & Thieffry, D. in Proceedings of the 25th International Conference on Applications and Theory of Petri Nets (eds Cortadella, J. & Reisig, W.) (Springer, Berlin, 2004).
-
(2004)
Proceedings of the 25th International Conference on Applications and Theory of Petri Nets
-
-
Chaouiya, C.1
Remy, E.2
Ruet, P.3
Thieffry, D.4
-
26
-
-
27544501653
-
Qualitative modelling of regulated metabolic pathways: Application to the tryptophan biosynthesis in E. coli
-
Simao, E., Remy, E., Thieffry, D. & Chaouiya, C. Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in E. coli. Bioinformatics 21, 190-196 (2005).
-
(2005)
Bioinformatics
, vol.21
, pp. 190-196
-
-
Simao, E.1
Remy, E.2
Thieffry, D.3
Chaouiya, C.4
-
27
-
-
33847304166
-
Qualitatively modelling and analysing genetic regulatory networks: A Petri net approach
-
Steggles, L. J., Banks, R., Shaw, O. & Wipat, A. Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach. Bioinformatics 23, 336-343 (2007).
-
(2007)
Bioinformatics
, vol.23
, pp. 336-343
-
-
Steggles, L.J.1
Banks, R.2
Shaw, O.3
Wipat, A.4
-
29
-
-
52649095496
-
-
Pearl, J. Probabilistic Reasoning in Intelligent Systems: Networks of Plausible Inference (Morgan Kaufmann, San Francisco, 1988). An excellent source on the foundation of probabilistic inference.
-
Pearl, J. Probabilistic Reasoning in Intelligent Systems: Networks of Plausible Inference (Morgan Kaufmann, San Francisco, 1988). An excellent source on the foundation of probabilistic inference.
-
-
-
-
30
-
-
0037941585
-
Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data
-
Segal, E. et al. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nature Genet. 34, 166-176 (2003).
-
(2003)
Nature Genet
, vol.34
, pp. 166-176
-
-
Segal, E.1
-
31
-
-
0842288337
-
Inferring cellular networks using probabilistic graphical models
-
Friedman, N. Inferring cellular networks using probabilistic graphical models. Science 303, 799-805 (2004).
-
(2004)
Science
, vol.303
, pp. 799-805
-
-
Friedman, N.1
-
32
-
-
0033707946
-
Using Bayesian networks to analyze expression data
-
A pioneering work that describes the use of Bayesian networks for recovering regulatory interactions from experimental data
-
Friedman, N., Linial, M., Nachman, I. & Pe'er, D. Using Bayesian networks to analyze expression data. J. Comput. Biol. 7, 601-620 (2000). A pioneering work that describes the use of Bayesian networks for recovering regulatory interactions from experimental data.
-
(2000)
J. Comput. Biol
, vol.7
, pp. 601-620
-
-
Friedman, N.1
Linial, M.2
Nachman, I.3
Pe'er, D.4
-
33
-
-
3142550630
-
Physical network models
-
Yeang, C. H., Ideker, T. & Jaakkola, T. Physical network models. J. Comput. Biol. 11, 243-262 (2004).
-
(2004)
J. Comput. Biol
, vol.11
, pp. 243-262
-
-
Yeang, C.H.1
Ideker, T.2
Jaakkola, T.3
-
34
-
-
33748323125
-
A joint model of regulatory and metabolic networks
-
Yeang, C. H. & Vingron, M. A joint model of regulatory and metabolic networks. BMC Bioinformatics 7, 332 (2006).
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 332
-
-
Yeang, C.H.1
Vingron, M.2
-
35
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
Lee, T. I. et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799-804 (2002).
-
(2002)
Science
, vol.298
, pp. 799-804
-
-
Lee, T.I.1
-
36
-
-
0029781898
-
Physiology and metabolic fluxes of wildtype and riboflavin-producing Bacillus subtilis
-
Sauer, U. et al. Physiology and metabolic fluxes of wildtype and riboflavin-producing Bacillus subtilis. Appl. Environ. Microbiol. 62, 3687-3696 (1996).
-
(1996)
Appl. Environ. Microbiol
, vol.62
, pp. 3687-3696
-
-
Sauer, U.1
-
37
-
-
33744509689
-
Basic microarray analysis: Strategies for successful experiments
-
Ness, S. A. Basic microarray analysis: strategies for successful experiments. Methods Mol. Biol. 316, 13-33 (2006).
-
(2006)
Methods Mol. Biol
, vol.316
, pp. 13-33
-
-
Ness, S.A.1
-
38
-
-
33645463194
-
Multiplexed protein measurement: Technologies and applications of protein and antibody arrays
-
Kingsmore, S. F. Multiplexed protein measurement: technologies and applications of protein and antibody arrays. Nature Rev. Drug Discov. 5, 310-320 (2006).
-
(2006)
Nature Rev. Drug Discov
, vol.5
, pp. 310-320
-
-
Kingsmore, S.F.1
-
39
-
-
0041864127
-
In vivo measurement of fluxes through metabolic pathways: The missing link in functional genomics and pharmaceutical research
-
Hellerstein, M. K. In vivo measurement of fluxes through metabolic pathways: the missing link in functional genomics and pharmaceutical research. Annu. Rev. Nutr. 23, 379-402 (2003).
-
(2003)
Annu. Rev. Nutr
, vol.23
, pp. 379-402
-
-
Hellerstein, M.K.1
-
40
-
-
0037197936
-
Reverse engineering gene networks using singular value decomposition and robust regression
-
Yeung, M. K., Tegner, J. & Collins, J. J. Reverse engineering gene networks using singular value decomposition and robust regression. Proc. Natl Acad. Sci. USA 99, 6163-6168 (2002).
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 6163-6168
-
-
Yeung, M.K.1
Tegner, J.2
Collins, J.J.3
-
43
-
-
33645307955
-
Inference of gene regulatory networks and compound mode of action from time course gene expression profiles
-
Bansal, M., Gatta, G. D. & di Bernardo, D. Inference of gene regulatory networks and compound mode of action from time course gene expression profiles. Bioinformatics 22, 815-822 (2006).
-
(2006)
Bioinformatics
, vol.22
, pp. 815-822
-
-
Bansal, M.1
Gatta, G.D.2
di Bernardo, D.3
-
44
-
-
2442687038
-
A mixed integer linear programming (MILP) framework for inferring time delay in gene regulatory networks
-
Dasika, M. S., Gupta, A. & Maranas, C. D. A mixed integer linear programming (MILP) framework for inferring time delay in gene regulatory networks. Pac Symp. Biocomput, 474-485 (2004).
-
(2004)
Pac Symp. Biocomput
, pp. 474-485
-
-
Dasika, M.S.1
Gupta, A.2
Maranas, C.D.3
-
45
-
-
14844307159
-
Inferring quantitative models of regulatory networks from expression data
-
Nachman, I., Regev, A. & Friedman, N. Inferring quantitative models of regulatory networks from expression data. Bioinformatics 20, 248-256 (2004).
-
(2004)
Bioinformatics
, vol.20
, pp. 248-256
-
-
Nachman, I.1
Regev, A.2
Friedman, N.3
-
46
-
-
84889389880
-
-
Klipp, E. Systems Biology In Practice: Concepts, Implementation And Application (Wiley-VCH, Weinheim, 2005). Explains basic concepts in modelling biological networks and provides an excellent introduction for the use of ODEs.
-
Klipp, E. Systems Biology In Practice: Concepts, Implementation And Application (Wiley-VCH, Weinheim, 2005). Explains basic concepts in modelling biological networks and provides an excellent introduction for the use of ODEs.
-
-
-
-
47
-
-
0000854197
-
-
eds Cooper, G. F. & Moral, S, Morgan Kaufmann, San Francisco
-
Friedman, N., Murphy, K. & Russell, S. in Proceedings of the Fourteenth Conference on Uncertainty in Artificial Intelligence (eds Cooper, G. F. & Moral, S.) 129-138 (Morgan Kaufmann, San Francisco, 1998).
-
(1998)
Proceedings of the Fourteenth Conference on Uncertainty in Artificial Intelligence
, pp. 129-138
-
-
Friedman, N.1
Murphy, K.2
Russell, S.3
-
48
-
-
0842309206
-
Inferring gene networks from time series microarray data using dynamic Bayesian networks
-
Kim, S. Y., Imoto, S. & Miyano, S. Inferring gene networks from time series microarray data using dynamic Bayesian networks. Brief Bioinform. 4, 228-235 (2003).
-
(2003)
Brief Bioinform
, vol.4
, pp. 228-235
-
-
Kim, S.Y.1
Imoto, S.2
Miyano, S.3
-
50
-
-
34547844132
-
Connecting quantitative regulatory-network models to the genome
-
Pan, Y., Durfee, T., Bockhorst, J. & Craven, M. Connecting quantitative regulatory-network models to the genome. Bioinformatics 23, 367-376 (2007).
-
(2007)
Bioinformatics
, vol.23
, pp. 367-376
-
-
Pan, Y.1
Durfee, T.2
Bockhorst, J.3
Craven, M.4
-
51
-
-
33645108505
-
Using a state-space model with hidden variables to infer transcription factor activities
-
Li, Z., Shaw, S. M., Yedwabnick, M. J. & Chan, C. Using a state-space model with hidden variables to infer transcription factor activities. Bioinformatics 22, 747-754 (2006).
-
(2006)
Bioinformatics
, vol.22
, pp. 747-754
-
-
Li, Z.1
Shaw, S.M.2
Yedwabnick, M.J.3
Chan, C.4
-
52
-
-
38749127589
-
Predicting expression patterns from regulatory sequence in Drosophila segmentation
-
Segal, E., Raveh-Sadka, T., Schroeder, M., Unnerstall, U. & Gaul, U. Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature 451, 535-540 (2008).
-
(2008)
Nature
, vol.451
, pp. 535-540
-
-
Segal, E.1
Raveh-Sadka, T.2
Schroeder, M.3
Unnerstall, U.4
Gaul, U.5
-
54
-
-
38949110777
-
A quantitative study of the division cycle of Caulobacter crescentus stalked cells
-
Li, S., Brazhnik, P., Sobral, B. & Tyson, J. J. A quantitative study of the division cycle of Caulobacter crescentus stalked cells. PLoS Comput. Biol. 4, e9 (2008).
-
(2008)
PLoS Comput. Biol
, vol.4
-
-
Li, S.1
Brazhnik, P.2
Sobral, B.3
Tyson, J.J.4
-
55
-
-
0141868933
-
A bacterial cell-cycle regulatory network operating in time and space
-
McAdams, H. H. & Shapiro, L. A bacterial cell-cycle regulatory network operating in time and space. Science 301, 1874-1877 (2003).
-
(2003)
Science
, vol.301
, pp. 1874-1877
-
-
McAdams, H.H.1
Shapiro, L.2
-
56
-
-
0034671792
-
Global analysis of the genetic network controlling a bacterial cell cycle
-
Laub, M. T., McAdams, H. H., Feldblyum, T., Fraser, C. M. & Shapiro, L. Global analysis of the genetic network controlling a bacterial cell cycle. Science 290, 2144-2148 (2000).
-
(2000)
Science
, vol.290
, pp. 2144-2148
-
-
Laub, M.T.1
McAdams, H.H.2
Feldblyum, T.3
Fraser, C.M.4
Shapiro, L.5
-
57
-
-
2342476606
-
Oscillating global regulators control the genetic circuit driving a bacterial cell cycle
-
Holtzendorff, J. et al. Oscillating global regulators control the genetic circuit driving a bacterial cell cycle. Science 304, 983-987 (2004).
-
(2004)
Science
, vol.304
, pp. 983-987
-
-
Holtzendorff, J.1
-
58
-
-
33845870386
-
Regulation of the bacterial cell cycle by an integrated genetic circuit
-
Biondi, E. G. et al. Regulation of the bacterial cell cycle by an integrated genetic circuit. Nature 444, 899-904 (2006).
-
(2006)
Nature
, vol.444
, pp. 899-904
-
-
Biondi, E.G.1
-
59
-
-
3343020085
-
Integrative analysis of cell cycle control in budding yeast
-
An ODE model for the yeast cell-cycle regulatory network that is supported by phenotypes of more than 100 mutant strains
-
Chen, K. C. et al. Integrative analysis of cell cycle control in budding yeast. Mol. Biol. Cell 15, 3841-3862 (2004). An ODE model for the yeast cell-cycle regulatory network that is supported by phenotypes of more than 100 mutant strains.
-
(2004)
Mol. Biol. Cell
, vol.15
, pp. 3841-3862
-
-
Chen, K.C.1
-
60
-
-
29544448913
-
Extension of a genetic network model by iterative experimentation and mathematical analysis
-
Locke, J. C. et al. Extension of a genetic network model by iterative experimentation and mathematical analysis. Mol. Syst. Biol. 1, 0013 (2005).
-
(2005)
Mol. Syst. Biol
, vol.1
, pp. 0013
-
-
Locke, J.C.1
-
61
-
-
23444449142
-
Integrative model of the response of yeast to osmotic shock
-
Klipp, E., Nordlander, B., Kruger, R., Gennemark, P. & Hohmann, S. Integrative model of the response of yeast to osmotic shock. Nature Biotechnol. 23, 975-982 (2005).
-
(2005)
Nature Biotechnol
, vol.23
, pp. 975-982
-
-
Klipp, E.1
Nordlander, B.2
Kruger, R.3
Gennemark, P.4
Hohmann, S.5
-
62
-
-
33947685522
-
Modeling gene regulatory networks with piecewise linear differential equations
-
Gebert, J., Radde, N. & Weber, G. Modeling gene regulatory networks with piecewise linear differential equations. Eur. J. Oper. Res. 181, 1148 (2007).
-
(2007)
Eur. J. Oper. Res
, vol.181
, pp. 1148
-
-
Gebert, J.1
Radde, N.2
Weber, G.3
-
63
-
-
33646377419
-
Qualitative simulation of the carbon starvation response in Escherichia coli
-
Ropers, D., de Jong, H., Page, M., Schneider, D. & Geiselmann, J. Qualitative simulation of the carbon starvation response in Escherichia coli. Biosystems 84, 124-152 (2006).
-
(2006)
Biosystems
, vol.84
, pp. 124-152
-
-
Ropers, D.1
de Jong, H.2
Page, M.3
Schneider, D.4
Geiselmann, J.5
-
65
-
-
0035824029
-
Regulation of gene expression in flux balance models of metabolism
-
Covert, M. W., Schilling, C. H. & Palsson, B. Regulation of gene expression in flux balance models of metabolism. J. Theor. Biol. 213, 73-88 (2001).
-
(2001)
J. Theor. Biol
, vol.213
, pp. 73-88
-
-
Covert, M.W.1
Schilling, C.H.2
Palsson, B.3
-
66
-
-
0142122303
-
Advances in flux balance analysis
-
Kauffman, K. J., Prakash, P. & Edwards, J. S. Advances in flux balance analysis. Curr. Opin. Biotechnol. 14, 491-496 (2003).
-
(2003)
Curr. Opin. Biotechnol
, vol.14
, pp. 491-496
-
-
Kauffman, K.J.1
Prakash, P.2
Edwards, J.S.3
-
67
-
-
84923570019
-
-
Palsson, B. Ø. Systems Biology: Properties Of Reconstructed Networks (Cambridge University Press, New York, 2006). An excellent book about the study of biological networks by one of the leading researchers in this field.
-
Palsson, B. Ø. Systems Biology: Properties Of Reconstructed Networks (Cambridge University Press, New York, 2006). An excellent book about the study of biological networks by one of the leading researchers in this field.
-
-
-
-
68
-
-
0036001069
-
Metabolic modelling of microbes: The flux-balance approach
-
Edwards, J. S., Covert, M. & Palsson, B. Metabolic modelling of microbes: the flux-balance approach. Environ. Microbiol 4, 133-140 (2002).
-
(2002)
Environ. Microbiol
, vol.4
, pp. 133-140
-
-
Edwards, J.S.1
Covert, M.2
Palsson, B.3
-
69
-
-
34547887655
-
Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity
-
Beg, Q. K. et al. Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity. Proc. Natl Acad. Sci. USA 104, 12663-12668 (2007).
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 12663-12668
-
-
Beg, Q.K.1
-
70
-
-
3843128481
-
Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model
-
Duarte, N. C., Herrgard, M. J. & Palsson, B. O. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res. 14, 1298-1309 (2004).
-
(2004)
Genome Res
, vol.14
, pp. 1298-1309
-
-
Duarte, N.C.1
Herrgard, M.J.2
Palsson, B.O.3
-
71
-
-
35748961978
-
Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli
-
Resendis-Antonio, O., Reed, J. L., Encarnacion, S., Collado-Vides, J. & Palsson, B. O. Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli. PLoS Comput. Biol. 3, 1887-1895 (2007).
-
(2007)
PLoS Comput. Biol
, vol.3
, pp. 1887-1895
-
-
Resendis-Antonio, O.1
Reed, J.L.2
Encarnacion, S.3
Collado-Vides, J.4
Palsson, B.O.5
-
72
-
-
34347332311
-
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
-
Feist, A. M. et al. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol. Syst. Biol. 3, 121 (2007).
-
(2007)
Mol. Syst. Biol
, vol.3
, pp. 121
-
-
Feist, A.M.1
-
73
-
-
0036350955
-
The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy
-
Papin, J. A., Price, N. D., Edwards, J. S. & Palsson, B. B. The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy. J. Theor. Biol. 215, 67-82 (2002).
-
(2002)
J. Theor. Biol
, vol.215
, pp. 67-82
-
-
Papin, J.A.1
Price, N.D.2
Edwards, J.S.3
Palsson, B.B.4
-
74
-
-
0037008673
-
Transcriptional regulation in constraints-based metabolic models of Escherichia coli
-
Covert, M. W. & Palsson, B. O. Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J. Biol. Chem. 277, 28058-28064 (2002).
-
(2002)
J. Biol. Chem
, vol.277
, pp. 28058-28064
-
-
Covert, M.W.1
Palsson, B.O.2
-
75
-
-
2342648924
-
-
Covert, M. W., Knight, E. M., Reed, J. L., Herrgard, M. J. & Palsson, B. O. Integrating high-throughput and computational data elucidates bacterial networks. Nature 429, 92-96 (2004). A large-scale model of E. coli metabolic regulation that uses quantitative metabolic flux values.
-
Covert, M. W., Knight, E. M., Reed, J. L., Herrgard, M. J. & Palsson, B. O. Integrating high-throughput and computational data elucidates bacterial networks. Nature 429, 92-96 (2004). A large-scale model of E. coli metabolic regulation that uses quantitative metabolic flux values.
-
-
-
-
76
-
-
33646920070
-
Iterative reconstruction of transcriptional regulatory networks: An algorithmic approach
-
Barrett, C. L. & Palsson, B. O. Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach. PLoS Comput. Biol. 2, e52 (2006).
-
(2006)
PLoS Comput. Biol
, vol.2
-
-
Barrett, C.L.1
Palsson, B.O.2
-
77
-
-
0033642067
-
Discovery of regulatory interactions through perturbation: Inference and experimental design
-
Ideker, T. E., Thorsson, V. & Karp, R. M. Discovery of regulatory interactions through perturbation: inference and experimental design. Pac Symp. Biocomput, 305-316 (2000).
-
(2000)
Pac Symp. Biocomput
, pp. 305-316
-
-
Ideker, T.E.1
Thorsson, V.2
Karp, R.M.3
-
78
-
-
27744521520
-
Validation and refinement of gene-regulatory pathways on a network of physical interactions
-
Yeang, C. H. et al. Validation and refinement of gene-regulatory pathways on a network of physical interactions. Genome Biol. 6, R62 (2005).
-
(2005)
Genome Biol
, vol.6
-
-
Yeang, C.H.1
-
79
-
-
33745178476
-
Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae
-
Herrgard, M. J., Lee, B. S., Portnoy, V. & Palsson, B. O. Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae. Genome Res. 16, 627-635 (2006).
-
(2006)
Genome Res
, vol.16
, pp. 627-635
-
-
Herrgard, M.J.1
Lee, B.S.2
Portnoy, V.3
Palsson, B.O.4
-
80
-
-
34247183123
-
A genome-scale computational study of the interplay between transcriptional regulation and metabolism
-
Shlomi, T., Eisenberg, Y., Sharan, R. & Ruppin, E. A genome-scale computational study of the interplay between transcriptional regulation and metabolism. Mol. Syst. Biol. 3, 101 (2007).
-
(2007)
Mol. Syst. Biol
, vol.3
, pp. 101
-
-
Shlomi, T.1
Eisenberg, Y.2
Sharan, R.3
Ruppin, E.4
-
81
-
-
33748049119
-
Matrix formalism to describe functional states of transcriptional regulatory systems
-
Gianchandani, E. P., Papin, J. A., Price, N. D., Joyce, A. R. & Palsson, B. O. Matrix formalism to describe functional states of transcriptional regulatory systems. PLoS Comput. Biol. 2, e101 (2006).
-
(2006)
PLoS Comput. Biol
, vol.2
-
-
Gianchandani, E.P.1
Papin, J.A.2
Price, N.D.3
Joyce, A.R.4
Palsson, B.O.5
-
82
-
-
0033083733
-
It's a noisy business! Genetic regulation at the nanomolar scale
-
McAdams, H. H. & Arkin, A. It's a noisy business! Genetic regulation at the nanomolar scale. Trends Genet. 15, 65-69 (1999).
-
(1999)
Trends Genet
, vol.15
, pp. 65-69
-
-
McAdams, H.H.1
Arkin, A.2
-
83
-
-
0028328719
-
Transcription of individual genes in eukaryotic cells occurs randomly and infrequently
-
Ross, I. L., Browne, C. M. & Hume, D. A. Transcription of individual genes in eukaryotic cells occurs randomly and infrequently. Immunol. Cell Biol. 72, 177-185 (1994).
-
(1994)
Immunol. Cell Biol
, vol.72
, pp. 177-185
-
-
Ross, I.L.1
Browne, C.M.2
Hume, D.A.3
-
84
-
-
0034161394
-
dCLOCK is present in limiting amounts and likely mediates daily interactions between the dCLOCK-CYC transcription factor and the PER-TIM complex
-
Bae, K., Lee, C., Hardin, P. E. & Edery, I. dCLOCK is present in limiting amounts and likely mediates daily interactions between the dCLOCK-CYC transcription factor and the PER-TIM complex. J. Neurosci. 20, 1746-1753 (2000).
-
(2000)
J. Neurosci
, vol.20
, pp. 1746-1753
-
-
Bae, K.1
Lee, C.2
Hardin, P.E.3
Edery, I.4
-
85
-
-
0029394767
-
Does replication-induced transcription regulate synthesis of the myriad low copy number proteins of Escherichia coli?
-
Guptasarma, P. Does replication-induced transcription regulate synthesis of the myriad low copy number proteins of Escherichia coli? Bioessays 17, 987-997 (1995).
-
(1995)
Bioessays
, vol.17
, pp. 987-997
-
-
Guptasarma, P.1
-
86
-
-
0018782266
-
Inactivation of prophage λ repressor in vivo
-
Bailone, A., Levine, A. & Devoret, R. Inactivation of prophage λ repressor in vivo. J. Mol. Biol. 131, 553-572 (1979).
-
(1979)
J. Mol. Biol
, vol.131
, pp. 553-572
-
-
Bailone, A.1
Levine, A.2
Devoret, R.3
-
87
-
-
0022429106
-
The OR control system of bacteriophage λ. A physical-chemical model for gene regulation
-
Shea, M. A. & Ackers, G. K. The OR control system of bacteriophage λ. A physical-chemical model for gene regulation. J. Mol. Biol. 181, 211-230 (1985).
-
(1985)
J. Mol. Biol
, vol.181
, pp. 211-230
-
-
Shea, M.A.1
Ackers, G.K.2
-
88
-
-
28944434119
-
Real-time kinetics of gene activity in individual bacteria
-
Golding, I., Paulsson, J., Zawilski, S. M. & Cox, E. C. Real-time kinetics of gene activity in individual bacteria. Cell 123, 1025-1036 (2005).
-
(2005)
Cell
, vol.123
, pp. 1025-1036
-
-
Golding, I.1
Paulsson, J.2
Zawilski, S.M.3
Cox, E.C.4
-
89
-
-
0036578645
-
Regulation of noise in the expression of a single gene
-
Ozbudak, E. M., Thattai, M., Kurtser, I., Grossman, A. D. & van Oudenaarden, A. Regulation of noise in the expression of a single gene. Nature Genet. 31, 69-73 (2002).
-
(2002)
Nature Genet
, vol.31
, pp. 69-73
-
-
Ozbudak, E.M.1
Thattai, M.2
Kurtser, I.3
Grossman, A.D.4
van Oudenaarden, A.5
-
90
-
-
33748994704
-
Stochastic mRNA synthesis in mammalian cells
-
Raj, A., Peskin, C. S., Tranchina, D., Vargas, D. Y. & Tyagi, S. Stochastic mRNA synthesis in mammalian cells. PLoS Biol. 4, e309 (2006).
-
(2006)
PLoS Biol
, vol.4
-
-
Raj, A.1
Peskin, C.S.2
Tranchina, D.3
Vargas, D.Y.4
Tyagi, S.5
-
91
-
-
33645027986
-
Stochastic protein expression in individual cells at the single molecule level
-
Cai, L., Friedman, N. & Xie, X. S. Stochastic protein expression in individual cells at the single molecule level. Nature 440, 358-362 (2006).
-
(2006)
Nature
, vol.440
, pp. 358-362
-
-
Cai, L.1
Friedman, N.2
Xie, X.S.3
-
92
-
-
33645033645
-
Probing gene expression in live cells, one protein molecule at a time
-
Yu, J., Xiao, J., Ren, X., Lao, K. & Xie, X. S. Probing gene expression in live cells, one protein molecule at a time. Science 311, 1600-1603 (2006).
-
(2006)
Science
, vol.311
, pp. 1600-1603
-
-
Yu, J.1
Xiao, J.2
Ren, X.3
Lao, K.4
Xie, X.S.5
-
93
-
-
34249950625
-
Stochastic simulation of chemical kinetics
-
Gillespie, D. T. Stochastic simulation of chemical kinetics. Annu. Rev. Phys. Chem. 58, 35-55 (2007).
-
(2007)
Annu. Rev. Phys. Chem
, vol.58
, pp. 35-55
-
-
Gillespie, D.T.1
-
94
-
-
0031029852
-
Stochastic mechanisms in gene expression
-
McAdams and Arkin describe their modelling methodology, which uses Gillespie's SSA, and present simulation results of a simple system that exhibits protein bursts
-
McAdams, H. H. & Arkin, A. Stochastic mechanisms in gene expression. Proc. Natl Acad. Sci. USA 94, 814-819 (1997). McAdams and Arkin describe their modelling methodology, which uses Gillespie's SSA, and present simulation results of a simple system that exhibits protein bursts.
-
(1997)
Proc. Natl Acad. Sci. USA
, vol.94
, pp. 814-819
-
-
McAdams, H.H.1
Arkin, A.2
-
95
-
-
0017030517
-
A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
-
Gillespie presents his SSA, the understanding of which is of major importance for computational modelling
-
Gillespie, D. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J. Comp. Phys. 22, 403-434 (1976). Gillespie presents his SSA, the understanding of which is of major importance for computational modelling.
-
(1976)
J. Comp. Phys
, vol.22
, pp. 403-434
-
-
Gillespie, D.1
-
96
-
-
33645429016
-
Exact stochastic simulation of coupled chemical reactions
-
Gillespie, D. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81, 2340-2361 (1977).
-
(1977)
J. Phys. Chem
, vol.81
, pp. 2340-2361
-
-
Gillespie, D.1
-
97
-
-
3042579602
-
How do site-specific DNA-binding proteins find their targets?
-
Halford, S. E. & Marko, J. F. How do site-specific DNA-binding proteins find their targets? Nucleic Acids Res. 32, 3040-3052 (2004).
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 3040-3052
-
-
Halford, S.E.1
Marko, J.F.2
-
98
-
-
36749081534
-
Crossing the nuclear envelope: Hierarchical regulation of nucleocytoplasmic transport
-
Terry, L. J., Shows, E. B. & Wente, S. R. Crossing the nuclear envelope: hierarchical regulation of nucleocytoplasmic transport. Science 318, 1412-1416 (2007).
-
(2007)
Science
, vol.318
, pp. 1412-1416
-
-
Terry, L.J.1
Shows, E.B.2
Wente, S.R.3
-
99
-
-
0029952518
-
Protein transport across the eukaryotic endoplasmic reticulum and bacterial inner membranes
-
Rapoport, T. A., Jungnickel, B. & Kutay, U. Protein transport across the eukaryotic endoplasmic reticulum and bacterial inner membranes. Annu. Rev. Biochem. 65, 271-303 (1996).
-
(1996)
Annu. Rev. Biochem
, vol.65
, pp. 271-303
-
-
Rapoport, T.A.1
Jungnickel, B.2
Kutay, U.3
-
100
-
-
33745725676
-
Circadian rhythms and molecular noise
-
Gonze, D. & Goldbeter, A. Circadian rhythms and molecular noise. Chaos 16, 026110 (2006).
-
(2006)
Chaos
, vol.16
, pp. 026110
-
-
Gonze, D.1
Goldbeter, A.2
-
101
-
-
25644440059
-
Modelling of translation of human protein disulfide isomerase in Escherichia coli - a case study of gene optimisation
-
Niemitalo, O. et al. Modelling of translation of human protein disulfide isomerase in Escherichia coli - a case study of gene optimisation. J. Biotechnol. 120, 11-24 (2005).
-
(2005)
J. Biotechnol
, vol.120
, pp. 11-24
-
-
Niemitalo, O.1
-
102
-
-
36749100036
-
Molecular level stochastic model for competence cycles in Bacillus subtilis
-
Schultz, D., Ben Jacob, E., Onuchic, J. N. & Wolynes, P. G. Molecular level stochastic model for competence cycles in Bacillus subtilis. Proc. Natl Acad. Sci. USA 104, 17582-17587 (2007).
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 17582-17587
-
-
Schultz, D.1
Ben Jacob, E.2
Onuchic, J.N.3
Wolynes, P.G.4
-
103
-
-
22744441386
-
Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity
-
Weinberger, L. S., Burnett, J. C., Toettcher, J. E., Arkin, A. P. & Schaffer, D. V. Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity. Cell 122, 169-182 (2005).
-
(2005)
Cell
, vol.122
, pp. 169-182
-
-
Weinberger, L.S.1
Burnett, J.C.2
Toettcher, J.E.3
Arkin, A.P.4
Schaffer, D.V.5
-
104
-
-
0031879114
-
Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected Escherichia coli cells
-
A seminal work that quantitatively explains how phage λ makes a stochastic decision between lysis and lysogeny using regulatory network simulation
-
Arkin, A., Ross, J. & McAdams, H. H. Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected Escherichia coli cells. Genetics 149, 1633-1648 (1998). A seminal work that quantitatively explains how phage λ makes a stochastic decision between lysis and lysogeny using regulatory network simulation.
-
(1998)
Genetics
, vol.149
, pp. 1633-1648
-
-
Arkin, A.1
Ross, J.2
McAdams, H.H.3
-
105
-
-
0001144902
-
Efficient exact stochastic simulation of chemical systems with many species and many channels
-
Gibson, M. & Bruck, J. Efficient exact stochastic simulation of chemical systems with many species and many channels. J. Phys. Chem. 104, 1876-1889 (1999).
-
(1999)
J. Phys. Chem
, vol.104
, pp. 1876-1889
-
-
Gibson, M.1
Bruck, J.2
-
106
-
-
0035933994
-
Approximate accelerated stochastic simulation of chemically reacting systems
-
Gillespie, D. Approximate accelerated stochastic simulation of chemically reacting systems. J. Chem. Phys. 115, 1716-1733 (2001).
-
(2001)
J. Chem. Phys
, vol.115
, pp. 1716-1733
-
-
Gillespie, D.1
-
107
-
-
38949164415
-
Algorithms and software for stochastic simulation of biochemical reacting systems
-
Li, H., Cao, Y., Petzold, L. R. & Gillespie, D. T. Algorithms and software for stochastic simulation of biochemical reacting systems. Biotechnol. Prog. 24, 56-61 (2008).
-
(2008)
Biotechnol. Prog
, vol.24
, pp. 56-61
-
-
Li, H.1
Cao, Y.2
Petzold, L.R.3
Gillespie, D.T.4
-
108
-
-
1342309249
-
Hybrid simulation of cellular behavior
-
Kiehl, T. R., Mattheyses, R. M. & Simmons, M. K. Hybrid simulation of cellular behavior. Bioinformatics 20, 316-322 (2004).
-
(2004)
Bioinformatics
, vol.20
, pp. 316-322
-
-
Kiehl, T.R.1
Mattheyses, R.M.2
Simmons, M.K.3
-
109
-
-
33750970021
-
Dynamic partitioning for hybrid simulation of the bistable HIV-1 transactivation network
-
Griffith, M., Courtney, T., Peccoud, J. & Sanders, W. H. Dynamic partitioning for hybrid simulation of the bistable HIV-1 transactivation network. Bioinformatics 22, 2782-2789 (2006).
-
(2006)
Bioinformatics
, vol.22
, pp. 2782-2789
-
-
Griffith, M.1
Courtney, T.2
Peccoud, J.3
Sanders, W.H.4
-
110
-
-
1542400036
-
A multialgorithm, multi-timescale method for cell simulation
-
Takahashi, K., Kaizu, K., Hu, B. & Tomita, M. A multialgorithm, multi-timescale method for cell simulation. Bioinformatics 20, 538-546 (2004).
-
(2004)
Bioinformatics
, vol.20
, pp. 538-546
-
-
Takahashi, K.1
Kaizu, K.2
Hu, B.3
Tomita, M.4
-
111
-
-
33845369407
-
-
Ribeiro, A., Zhu, R. & Kauffman, S. A. A general modeling strategy for gene regulatory networks with stochastic dynamics. J. Comput. Biol. 13, 1630-1639 (2006).
-
Ribeiro, A., Zhu, R. & Kauffman, S. A. A general modeling strategy for gene regulatory networks with stochastic dynamics. J. Comput. Biol. 13, 1630-1639 (2006).
-
-
-
-
112
-
-
34248147640
-
Studying genetic regulatory networks at the molecular level: Delayed reaction stochastic models
-
Zhu, R., Ribeiro, A. S., Salahub, D. & Kauffman, S. A. Studying genetic regulatory networks at the molecular level: delayed reaction stochastic models. J. Theor. Biol. 246, 725-745 (2007).
-
(2007)
J. Theor. Biol
, vol.246
, pp. 725-745
-
-
Zhu, R.1
Ribeiro, A.S.2
Salahub, D.3
Kauffman, S.A.4
-
113
-
-
0037444724
-
Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm
-
Rao, C. & Arkin, A. Stochastic chemical kinetics and the quasi-steady-state assumption: application to the Gillespie algorithm. J. Chem. Phys. 118, 4999-5010 (2003).
-
(2003)
J. Chem. Phys
, vol.118
, pp. 4999-5010
-
-
Rao, C.1
Arkin, A.2
-
114
-
-
43049144658
-
A topographical map of spatiotemporal patterns of gene expression
-
Furlong, E. E. A topographical map of spatiotemporal patterns of gene expression. Dev. Cell 14, 639-640 (2008).
-
(2008)
Dev. Cell
, vol.14
, pp. 639-640
-
-
Furlong, E.E.1
-
115
-
-
0034225547
-
The chemical Langevin equation
-
Gillespie, D. The chemical Langevin equation. J. Chem. Phys. 113, 297-306 (2000).
-
(2000)
J. Chem. Phys
, vol.113
, pp. 297-306
-
-
Gillespie, D.1
-
116
-
-
0037162469
-
Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays
-
Bernstein, J. A., Khodursky, A. B., Lin, P. H., Lin-Chao, S. & Cohen, S. N. Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc. Natl Acad. Sci. USA 99, 9697-9702 (2002).
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 9697-9702
-
-
Bernstein, J.A.1
Khodursky, A.B.2
Lin, P.H.3
Lin-Chao, S.4
Cohen, S.N.5
-
117
-
-
18344369543
-
MicroRNA biogenesis: Coordinated cropping and dicing
-
Kim, V. N. MicroRNA biogenesis: coordinated cropping and dicing. Nature Rev. Mol. Cell Biol. 6, 376-385 (2005).
-
(2005)
Nature Rev. Mol. Cell Biol
, vol.6
, pp. 376-385
-
-
Kim, V.N.1
-
118
-
-
2142765527
-
Nuclear architecture and genome functioning in plants and animals: What can we learn from both?
-
van Driel, R. & Fransz, P. Nuclear architecture and genome functioning in plants and animals: what can we learn from both? Exp. Cell Res. 296, 86-90 (2004).
-
(2004)
Exp. Cell Res
, vol.296
, pp. 86-90
-
-
van Driel, R.1
Fransz, P.2
-
119
-
-
0035834705
-
p53 targets chromatin structure alteration to repress α-fetoprotein gene expression
-
Ogden, S. K. et al. p53 targets chromatin structure alteration to repress α-fetoprotein gene expression. J. Biol. Chem. 276, 42057-42062 (2001).
-
(2001)
J. Biol. Chem
, vol.276
, pp. 42057-42062
-
-
Ogden, S.K.1
-
120
-
-
34547572517
-
Single-cell zeroth-order protein degradation enhances the robustness of synthetic oscillator
-
Wong, W. W., Tsai, T. Y. & Liao, J. C. Single-cell zeroth-order protein degradation enhances the robustness of synthetic oscillator. Mol. Syst. Biol. 3, 130 (2007).
-
(2007)
Mol. Syst. Biol
, vol.3
, pp. 130
-
-
Wong, W.W.1
Tsai, T.Y.2
Liao, J.C.3
-
121
-
-
33645787282
-
Spatiotemporal expression control correlates with intragenic scaffold matrix attachment regions (S/MARs) in Arabidopsis thaliana
-
Tetko, I. V. et al. Spatiotemporal expression control correlates with intragenic scaffold matrix attachment regions (S/MARs) in Arabidopsis thaliana. PLoS Comput. Biol. 2, e21 (2006).
-
(2006)
PLoS Comput. Biol
, vol.2
-
-
Tetko, I.V.1
-
122
-
-
37249015899
-
Transcribing RNA polymerase II is phosphorylated at CTD residue serine-7
-
Chapman, R. D. et al. Transcribing RNA polymerase II is phosphorylated at CTD residue serine-7. Science 318, 1780-1782 (2007).
-
(2007)
Science
, vol.318
, pp. 1780-1782
-
-
Chapman, R.D.1
-
123
-
-
45849122499
-
Widespread translational inhibition by plant miRNAs and siRNAs
-
Brodersen, P. et al. Widespread translational inhibition by plant miRNAs and siRNAs. Science 320, 1185-1190 (2008).
-
(2008)
Science
, vol.320
, pp. 1185-1190
-
-
Brodersen, P.1
-
124
-
-
34247527312
-
Identification of primary transcriptional regulation of cell cycle-regulated genes upon DNA damage
-
Zhou, T. et al. Identification of primary transcriptional regulation of cell cycle-regulated genes upon DNA damage. Cell Cycle 6, 972-981 (2007).
-
(2007)
Cell Cycle
, vol.6
, pp. 972-981
-
-
Zhou, T.1
-
125
-
-
0142027814
-
Structure and function of the feed-forward loop network motif
-
Mangan, S. & Alon, U. Structure and function of the feed-forward loop network motif. Proc. Natl Acad. Sci. USA 100, 11980-11985 (2003).
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 11980-11985
-
-
Mangan, S.1
Alon, U.2
-
126
-
-
33745780500
-
Network motifs: Structure does not determine function
-
Ingram, P. J., Stumpf, M. P. & Stark, J. Network motifs: structure does not determine function. BMC Genomics 7, 108 (2006).
-
(2006)
BMC Genomics
, vol.7
, pp. 108
-
-
Ingram, P.J.1
Stumpf, M.P.2
Stark, J.3
-
127
-
-
49549085003
-
Graphic requirements for multistability and attractive cycles in a Boolean dynamical framework
-
Remy, É., Ruet, P. & Thieffry, D. Graphic requirements for multistability and attractive cycles in a Boolean dynamical framework. Adv. Appl. Math. (2008).
-
(2008)
Adv. Appl. Math
-
-
Remy, E.1
Ruet, P.2
Thieffry, D.3
-
128
-
-
35448971021
-
Necessary conditions for multistationarity in discrete dynamical systems
-
Richard, A. & Comet, J. Necessary conditions for multistationarity in discrete dynamical systems. Dis. Appl. Math. 155, 2403-2413 (2007).
-
(2007)
Dis. Appl. Math
, vol.155
, pp. 2403-2413
-
-
Richard, A.1
Comet, J.2
-
129
-
-
34247487796
-
Genome-wide transcriptional plasticity underlies cellular adaptation to novel challenge
-
Stern, S., Dror, T., Stolovicki, E., Brenner, N. & Braun, E. Genome-wide transcriptional plasticity underlies cellular adaptation to novel challenge. Mol. Syst. Biol. 3, 106 (2007).
-
(2007)
Mol. Syst. Biol
, vol.3
, pp. 106
-
-
Stern, S.1
Dror, T.2
Stolovicki, E.3
Brenner, N.4
Braun, E.5
-
130
-
-
33745287724
-
Noise in protein expression scales with natural protein abundance
-
Bar-Even, A. et al. Noise in protein expression scales with natural protein abundance. Nature Genet. 38, 636-643 (2006).
-
(2006)
Nature Genet
, vol.38
, pp. 636-643
-
-
Bar-Even, A.1
-
131
-
-
0025038122
-
On the dominance ratio. Reprint in Bull
-
Fisher, R. A. On the dominance ratio. Reprint in Bull. Math. Biol. 52, 297-318 (1990).
-
(1990)
Math. Biol
, vol.52
, pp. 297-318
-
-
Fisher, R.A.1
-
134
-
-
0001771498
-
Evolution in mendelian populations
-
Wright, S. Evolution in mendelian populations. Genetics 16, 97-159 (1931).
-
(1931)
Genetics
, vol.16
, pp. 97-159
-
-
Wright, S.1
-
135
-
-
44949247269
-
Dynamic analysis of integrated signaling, metabolic, and regulatory networks
-
Min. Lee, J., Gianchandani, E. P., Eddy, J. A. & Papin, J. A. Dynamic analysis of integrated signaling, metabolic, and regulatory networks. PLoS Comput. Biol. 4, e1000086 (2008).
-
(2008)
PLoS Comput. Biol
, vol.4
-
-
Min1
Lee, J.2
Gianchandani, E.P.3
Eddy, J.A.4
Papin, J.A.5
-
136
-
-
0033031386
-
E-CELL: Software environment for whole-cell simulation
-
Tomita, M. et al. E-CELL: software environment for whole-cell simulation. Bioinformatics 15, 72-84 (1999).
-
(1999)
Bioinformatics
, vol.15
, pp. 72-84
-
-
Tomita, M.1
-
137
-
-
0029028963
-
Circuit simulation of genetic networks
-
McAdams, H. H. & Shapiro, L. Circuit simulation of genetic networks. Science 269, 650-656 (1995).
-
(1995)
Science
, vol.269
, pp. 650-656
-
-
McAdams, H.H.1
Shapiro, L.2
-
138
-
-
0036204115
-
Stochastic kinetic simulations of biochemical systems with Gillespie algorithm
-
Kierzek, A. M. STOCKS: Stochastic kinetic simulations of biochemical systems with Gillespie algorithm. Bioinformatics 18, 470-481 (2002).
-
(2002)
Bioinformatics
, vol.18
, pp. 470-481
-
-
Kierzek, A.1
STOCKS, M.2
|