-
1
-
-
0001422329
-
Quantitative model for gene regulation by lambda phage repressor
-
Ackers, G. K., Johnson, A. D., & Shea, M. A. (1982). Quantitative model for gene regulation by lambda phage repressor. Proc. Natl. Acad. Sci. USA, 79, 1129-1133.
-
(1982)
Proc. Natl. Acad. Sci. USA
, vol.79
, pp. 1129-1133
-
-
Ackers, G.K.1
Johnson, A.D.2
Shea, M.A.3
-
2
-
-
84902031544
-
The matrix of maximum out forests of a digraph and its applications
-
Agaev, R. P., & Chebotarev, P. Y. (2000). The matrix of maximum out forests of a digraph and its applications. Autom. Remote Control, 61, 1424-1450.
-
(2000)
Autom. Remote Control
, vol.61
, pp. 1424-1450
-
-
Agaev, R.P.1
Chebotarev, P.Y.2
-
3
-
-
84892878687
-
-
in preparation
-
Ahsendorf, T., Wong, F., Eils, R., & Gunawardena, J. (2013, in preparation). A framework for modelling eukaryotic gene regulation that accommodates non-equilibrium mechanisms.
-
(2013)
A framework for modelling eukaryotic gene regulation that accommodates non-equilibrium mechanisms
-
-
Ahsendorf, T.1
Wong, F.2
Eils, R.3
Gunawardena, J.4
-
4
-
-
15744387380
-
Transcriptional regulation by the numbers: applications
-
Bintu, L., Buchler, N. E., Garcia, G. G., Gerland, U., Hwa, T., Kondev, J., Kuhlman, T., & Phillips, R. (2005a). Transcriptional regulation by the numbers: applications. Curr. Opin. Genet. Dev., 15, 125-135.
-
(2005)
Curr. Opin. Genet. Dev.
, vol.15
, pp. 125-135
-
-
Bintu, L.1
Buchler, N.E.2
Garcia, G.G.3
Gerland, U.4
Hwa, T.5
Kondev, J.6
Kuhlman, T.7
Phillips, R.8
-
5
-
-
15744387380
-
Transcriptional regulation by the numbers: models
-
Bintu, L., Buchler, N. E., Garcia, G. G., Gerland, U., Hwa, T., Kondev, J., & Phillips, R. (2005b). Transcriptional regulation by the numbers: models. Curr. Opin. Genet. Dev., 15, 116-124.
-
(2005)
Curr. Opin. Genet. Dev.
, vol.15
, pp. 116-124
-
-
Bintu, L.1
Buchler, N.E.2
Garcia, G.G.3
Gerland, U.4
Hwa, T.5
Kondev, J.6
Phillips, R.7
-
6
-
-
0012034825
-
Matrices and trees
-
O. Morgenstern (Ed.), New York: Wiley
-
Bott, R., & Mayberry, J. P. (1954). Matrices and trees. In O. Morgenstern (Ed.), Economic activity analysis (pp. 391-400). New York: Wiley.
-
(1954)
Economic Activity Analysis
, pp. 391-400
-
-
Bott, R.1
Mayberry, J.P.2
-
7
-
-
70249121045
-
The logic of chromatin architecture and remodelling at promoters
-
Cairns, B. R. (2009). The logic of chromatin architecture and remodelling at promoters. Nature, 461, 193-198.
-
(2009)
Nature
, vol.461
, pp. 193-198
-
-
Cairns, B.R.1
-
8
-
-
77953676122
-
Comment on 'Consensus and cooperation in networked multi-agent systems
-
Chebotarev, P. (2010). Comment on 'Consensus and cooperation in networked multi-agent systems'. Proc. IEEE, 98, 1353-1354.
-
(2010)
Proc. IEEE
, vol.98
, pp. 1353-1354
-
-
Chebotarev, P.1
-
9
-
-
84969165400
-
Forest matrices around the Laplacian matrix
-
Chebotarev, P., & Agaev, R. (2002). Forest matrices around the Laplacian matrix. Linear Algebra Appl., 356, 253-274.
-
(2002)
Linear Algebra Appl.
, vol.356
, pp. 253-274
-
-
Chebotarev, P.1
Agaev, R.2
-
10
-
-
67650260404
-
Coordination in multiagent systems and Laplacian spectra of digraphs
-
Chebotarev, P. Y., & Agaev, R. P. (2009). Coordination in multiagent systems and Laplacian spectra of digraphs. Autom. Remote Control, 70, 469-483.
-
(2009)
Autom. Remote Control
, vol.70
, pp. 469-483
-
-
Chebotarev, P.Y.1
Agaev, R.P.2
-
12
-
-
84892838571
-
-
Regional conference series in mathematics, Providence: Am. Math. Soc
-
Chung, F. R. K. (1997). Spectral graph theory. Regional conference series in mathematics: Vol. 92. Providence: Am. Math. Soc.
-
(1997)
Spectral Graph Theory
, vol.92
-
-
Chung, F.R.K.1
-
13
-
-
30444460582
-
The quantitative analysis of drug-receptor interactions: a short history
-
Colquhoun, D. (2006). The quantitative analysis of drug-receptor interactions: a short history. Trends Pharmacol. Sci., 27, 149-157.
-
(2006)
Trends Pharmacol. Sci.
, vol.27
, pp. 149-157
-
-
Colquhoun, D.1
-
15
-
-
84872988068
-
-
Submitted
-
Dasgupta, T., Croll, D. H., Owen, J. A., Vander Heiden, M. G., Locasale, J. W., Alon, U., Cantley, L. C., & Gunawardena, J. (2013). A fundamental trade off in covalent switching and its circumvention in glucose homeostasis. Submitted.
-
(2013)
A fundamental trade off in covalent switching and its circumvention in glucose homeostasis
-
-
Dasgupta, T.1
Croll, D.H.2
Owen, J.A.3
Vander Heiden, M.G.4
Locasale, J.W.5
Alon, U.6
Cantley, L.C.7
Gunawardena, J.8
-
16
-
-
0017731760
-
Chemical mechanism structure and the coincidence of the stoichiometric and kinetic subspace
-
Feinberg, M., & Horn, F. (1977). Chemical mechanism structure and the coincidence of the stoichiometric and kinetic subspace. Arch. Ration. Mech. Anal., 66, 83-97.
-
(1977)
Arch. Ration. Mech. Anal.
, vol.66
, pp. 83-97
-
-
Feinberg, M.1
Horn, F.2
-
17
-
-
58149354385
-
Analysis of combinatorial cis-regulation in synthetic and genomic promoters
-
Gertz, J., Siggia, E. D., & Cohen, B. A. (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
-
18
-
-
84860996633
-
A linear framework for time-scale separation in nonlinear biochemical systems
-
e36321
-
Gunawardena, J. (2012). A linear framework for time-scale separation in nonlinear biochemical systems. PLoS ONE, 7, e36321.
-
(2012)
PLoS ONE
, vol.7
-
-
Gunawardena, J.1
-
19
-
-
78049450019
-
Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression
-
e1000935
-
He, X., Samee, M. A. H., Blatti, C., & Sinha, S. (2010). Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression. PLoS Comput. Biol., 6, e1000935.
-
(2010)
PLoS Comput. Biol.
, vol.6
-
-
He, X.1
Samee, M.A.H.2
Blatti, C.3
Sinha, S.4
-
20
-
-
0013895045
-
Studies in irreversible thermodynamics IV. Diagrammatic representation of steady state fluxes for unimolecular systems
-
Hill, T. L. (1966). Studies in irreversible thermodynamics IV. Diagrammatic representation of steady state fluxes for unimolecular systems. J. Theor. Biol., 10, 442-459.
-
(1966)
J. Theor. Biol.
, vol.10
, pp. 442-459
-
-
Hill, T.L.1
-
23
-
-
0000359208
-
Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity
-
Hopfield, J. J. (1974). Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. Proc. Natl. Acad. Sci. USA, 71, 4135-4139.
-
(1974)
Proc. Natl. Acad. Sci. USA
, vol.71
, pp. 4135-4139
-
-
Hopfield, J.J.1
-
25
-
-
0005142379
-
Divergence of perturbation theory for bosons
-
Jaffe, A. (1965). Divergence of perturbation theory for bosons. Commun. Math. Phys., 1, 127-149.
-
(1965)
Commun. Math. Phys.
, vol.1
, pp. 127-149
-
-
Jaffe, A.1
-
26
-
-
33749137281
-
Quantitative and predictive model of transcriptional control of the drosophila melanogaster even skipped gene
-
Janssens, H., Hou, S., Jaeger, J., Kim, A. R., Myasnikova, E., Sharp, D., & Reinitz, J. (2006). Quantitative and predictive model of transcriptional control of the drosophila melanogaster even skipped gene. Nat. Genet., 38, 1159-1165.
-
(2006)
Nat. Genet.
, vol.38
, pp. 1159-1165
-
-
Janssens, H.1
Hou, S.2
Jaeger, J.3
Kim, A.R.4
Myasnikova, E.5
Sharp, D.6
Reinitz, J.7
-
29
-
-
27844519281
-
New concepts in drug discovery: collateral efficacy and permissive antagonism
-
Kenakin, T. (2005). New concepts in drug discovery: collateral efficacy and permissive antagonism. Nat. Rev. Drug Discov., 4, 919-927.
-
(2005)
Nat. Rev. Drug Discov.
, vol.4
, pp. 919-927
-
-
Kenakin, T.1
-
30
-
-
55549113874
-
A quantitative model of transcription factor-activated gene expression
-
Kim, H. D., & O'Shea, E. K. (2008). A quantitative model of transcription factor-activated gene expression. Nat. Struct. Mol. Biol., 15, 1192-1198.
-
(2008)
Nat. Struct. Mol. Biol.
, vol.15
, pp. 1192-1198
-
-
Kim, H.D.1
O'Shea, E.K.2
-
31
-
-
33947472850
-
A schematic method of deriving the rate laws for enzyme-catalyzed reactions
-
King, E. L., & Altman, C. (1956). A schematic method of deriving the rate laws for enzyme-catalyzed reactions. J. Phys. Chem., 60, 1375-1378.
-
(1956)
J. Phys. Chem.
, vol.60
, pp. 1375-1378
-
-
King, E.L.1
Altman, C.2
-
32
-
-
4944257625
-
Über die Auflösung der Gleichungen, auf welche man bei der Untersuchung der linearen Verteilung galvanischer Ströme geführt wird
-
Kirchhoff, G. (1847). Über die Auflösung der Gleichungen, auf welche man bei der Untersuchung der linearen Verteilung galvanischer Ströme geführt wird. Ann. Phys. Chem., 72, 497-508.
-
(1847)
Ann. Phys. Chem.
, vol.72
, pp. 497-508
-
-
Kirchhoff, G.1
-
33
-
-
0013863816
-
Comparison of experimental binding data and theoretical models in proteins containing subunits
-
Koshland, D. E., Némethy, G., & Filmer, D. (1966). Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry, 5, 365-385.
-
(1966)
Biochemistry
, vol.5
, pp. 365-385
-
-
Koshland, D.E.1
Némethy, G.2
Filmer, D.3
-
34
-
-
34347232364
-
Combinatorial transcriptional control of the lactose operon of Escherichia coli
-
Kuhlman, T., Zhang, Z., Saier, M. H. Jr., & Hwa, T. (2007). Combinatorial transcriptional control of the lactose operon of Escherichia coli. Proc. Natl. Acad. Sci. USA, 104, 6043-6048.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 6043-6048
-
-
Kuhlman, T.1
Zhang, Z.2
Saier Jr., M.H.3
Hwa, T.4
-
35
-
-
43449096915
-
Chromatin decouples promoter threshold from dynamic range
-
Lam, F. H., Steger, D. J., & O'Shea, E. K. (2008). Chromatin decouples promoter threshold from dynamic range. Nature, 453, 246-250.
-
(2008)
Nature
, vol.453
, pp. 246-250
-
-
Lam, F.H.1
Steger, D.J.2
O'Shea, E.K.3
-
36
-
-
0019137579
-
A ternary complex model explains the agonist-specific binding properties of the adenylate cyclase-coupled β-adrenergic receptor
-
Lean, A. D., Stadel, J. M., & Lefkowitz, R. J. (1980). A ternary complex model explains the agonist-specific binding properties of the adenylate cyclase-coupled β-adrenergic receptor. J. Biol. Chem., 255, 7108-7117.
-
(1980)
J. Biol. Chem.
, vol.255
, pp. 7108-7117
-
-
Lean, A.D.1
Stadel, J.M.2
Lefkowitz, R.J.3
-
37
-
-
0001743153
-
A new principle of equilibrium
-
Lewis, G. N. (1925). A new principle of equilibrium. Proc. Natl. Acad. Sci. USA, 11, 179-183.
-
(1925)
Proc. Natl. Acad. Sci. USA
, vol.11
, pp. 179-183
-
-
Lewis, G.N.1
-
39
-
-
33750999449
-
Laplacian matrices of graphs: a survey
-
Merris, R. (1994). Laplacian matrices of graphs: a survey. Linear Algebra Appl., 198, 143-176.
-
(1994)
Linear Algebra Appl.
, vol.198
, pp. 143-176
-
-
Merris, R.1
-
40
-
-
0000870544
-
Die kinetik der Invertinwirkung
-
Michaelis, L., & Menten, M. (1913). Die kinetik der Invertinwirkung. Biochem. Z., 49, 333-369.
-
(1913)
Biochem. Z.
, vol.49
, pp. 333-369
-
-
Michaelis, L.1
Menten, M.2
-
41
-
-
78651107675
-
Nucleosome-mediated cooperativity between transcription factors
-
Mirny, L. (2010). Nucleosome-mediated cooperativity between transcription factors. Proc. Natl. Acad. Sci. USA, 107(22), 534-539.
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, Issue.22
, pp. 534-539
-
-
Mirny, L.1
-
42
-
-
78651189765
-
On the nature of allosteric transitions: a plausible model
-
Monod, J., Wyman, J., & Changeux, J. P. (1965). On the nature of allosteric transitions: a plausible model. J. Mol. Biol., 12, 88-118.
-
(1965)
J. Mol. Biol.
, vol.12
, pp. 88-118
-
-
Monod, J.1
Wyman, J.2
Changeux, J.P.3
-
43
-
-
84892891523
-
-
Canadian mathematical monographs, Ottawa: Canadian Mathematical Society
-
Moon, J. W. (1970). Counting Labelled Trees. Canadian mathematical monographs: Vol. 1. Ottawa: Canadian Mathematical Society.
-
(1970)
Counting Labelled Trees
, vol.1
-
-
Moon, J.W.1
-
44
-
-
77953741594
-
Network synchronization landscape reveals compensatory structures, quantization, and the positive effect of negative interactions
-
Nishikawa, T., & Motter, A. E. (2010). Network synchronization landscape reveals compensatory structures, quantization, and the positive effect of negative interactions. Proc. Natl. Acad. Sci. USA, 107(10), 342-347.
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, Issue.10
, pp. 342-347
-
-
Nishikawa, T.1
Motter, A.E.2
-
45
-
-
64149119332
-
Consensus and cooperation in networked multi-agent systems
-
Olfati-Saber, R., Fax, J. A., & Murray, R. M. (2007). Consensus and cooperation in networked multi-agent systems. Proc. IEEE, 95, 215-233.
-
(2007)
Proc. IEEE
, vol.95
, pp. 215-233
-
-
Olfati-Saber, R.1
Fax, J.A.2
Murray, R.M.3
-
46
-
-
4644244041
-
Consensus problems in networks of agents with switching topology and time-delays
-
Olfati-Saber, R., & Murray, R. M. (2004). Consensus problems in networks of agents with switching topology and time-delays. IEEE Trans. Autom. Control, 49, 1520-1533.
-
(2004)
IEEE Trans. Autom. Control
, vol.49
, pp. 1520-1533
-
-
Olfati-Saber, R.1
Murray, R.M.2
-
47
-
-
4243241129
-
Master stability functions for synchronized coupled systems
-
Pecora, L. M., & Carroll, T. L. (1998). Master stability functions for synchronized coupled systems. Phys. Rev. Lett., 80, 2109-2112.
-
(1998)
Phys. Rev. Lett.
, vol.80
, pp. 2109-2112
-
-
Pecora, L.M.1
Carroll, T.L.2
-
48
-
-
68049083831
-
Incorporating nucleosomes into thermodynamic models of transcription regulation
-
Raveh-Sadka, T., Levo, M., & Segal, E. (2009). Incorporating nucleosomes into thermodynamic models of transcription regulation. Genome Res., 19, 1480-1496.
-
(2009)
Genome Res.
, vol.19
, pp. 1480-1496
-
-
Raveh-Sadka, T.1
Levo, M.2
Segal, E.3
-
49
-
-
0000013996
-
Network theory of microscopic and macroscopic behaviour of master equation systems
-
Schnakenberg, J. (1976). Network theory of microscopic and macroscopic behaviour of master equation systems. Rev. Mod. Phys., 48, 571-586.
-
(1976)
Rev. Mod. Phys.
, vol.48
, pp. 571-586
-
-
Schnakenberg, J.1
-
50
-
-
38749127589
-
Predicting expression patters from regulatory sequence in Drosophila segmentation
-
Segal, E., Raveh-Sadka, T., Schroeder, M., Unnerstall, U., & Gaul, U. (2008). Predicting expression patters from regulatory sequence in Drosophila segmentation. Nature, 451, 535-540.
-
(2008)
Nature
, vol.451
, pp. 535-540
-
-
Segal, E.1
Raveh-Sadka, T.2
Schroeder, M.3
Unnerstall, U.4
Gaul, U.5
-
51
-
-
67649826220
-
From DNA sequence to transcriptional behaviour: a quantitative approach
-
Segal, E., & Widom, J. (2009). From DNA sequence to transcriptional behaviour: a quantitative approach. Nat. Rev. Genet., 10, 443-456.
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 443-456
-
-
Segal, E.1
Widom, J.2
-
52
-
-
0038610819
-
Detailed map of a cis-regulatory input function
-
Setty, Y., Mayo, A. E., Surette, M. G., & Alon, U. (2003). Detailed map of a cis-regulatory input function. Proc. Natl. Acad. Sci. USA, 100, 7702-7707.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 7702-7707
-
-
Setty, Y.1
Mayo, A.E.2
Surette, M.G.3
Alon, U.4
-
53
-
-
84861120417
-
Thermodynamic state ensemble models of cis-regulation
-
e1002407
-
Sherman, M. S., & Cohen, B. A. (2012). Thermodynamic state ensemble models of cis-regulation. PLoS Comput. Biol., 8, e1002407.
-
(2012)
PLoS Comput. Biol.
, vol.8
-
-
Sherman, M.S.1
Cohen, B.A.2
-
54
-
-
84865859048
-
What does our genome encode?
-
Stamatoyannopoulos, J. (2012). What does our genome encode? Genome Res., 22, 1602-1611.
-
(2012)
Genome Res.
, vol.22
, pp. 1602-1611
-
-
Stamatoyannopoulos, J.1
-
55
-
-
70350575331
-
The rational parameterisation theorem for multisite post-translational modification systems
-
Thomson, M., & Gunawardena, J. (2009a). The rational parameterisation theorem for multisite post-translational modification systems. J. Theor. Biol., 261, 626-636.
-
(2009)
J. Theor. Biol.
, vol.261
, pp. 626-636
-
-
Thomson, M.1
Gunawardena, J.2
-
56
-
-
67650360968
-
Unlimited multistability in multisite phosphorylation systems
-
Thomson, M., & Gunawardena, J. (2009b). Unlimited multistability in multisite phosphorylation systems. Nature, 460, 274-277.
-
(2009)
Nature
, vol.460
, pp. 274-277
-
-
Thomson, M.1
Gunawardena, J.2
-
57
-
-
43749088127
-
Two strategies for gene regulation by promoter nucleosomes
-
Tirosh, I., & Barkai, N. (2008). Two strategies for gene regulation by promoter nucleosomes. Genome Res., 18, 1084-1091.
-
(2008)
Genome Res.
, vol.18
, pp. 1084-1091
-
-
Tirosh, I.1
Barkai, N.2
-
59
-
-
84946454140
-
The dissection of equilateral triangles into equilateral triangles
-
Tutte, W. T. (1948). The dissection of equilateral triangles into equilateral triangles. Proc. Camb. Philol. Soc., 44, 463-482.
-
(1948)
Proc. Camb. Philol. Soc.
, vol.44
, pp. 463-482
-
-
Tutte, W.T.1
-
60
-
-
0003702909
-
-
Encyclopedia of mathematics and its applications, Cambridge: Cambridge University Press
-
Tutte, W. T. (2001). Graph theory. Encyclopedia of mathematics and its applications: Vol. 21. Cambridge: Cambridge University Press.
-
(2001)
Graph Theory
, vol.21
-
-
Tutte, W.T.1
-
61
-
-
84892835792
-
An economic application of 'Matrices and trees
-
O. Morgenstern (Ed.), New York: Wiley
-
Whitin, T. M. (1954). An economic application of 'Matrices and trees'. In O. Morgenstern (Ed.), Economic activity analysis (pp. 401-418). New York: Wiley.
-
(1954)
Economic Activity Analysis
, pp. 401-418
-
-
Whitin, T.M.1
-
62
-
-
84865575045
-
Realistic enzymology for post-translational modification: zero-order ultrasensitivity revisited
-
Xu, Y., & Gunawardena, J. (2012). Realistic enzymology for post-translational modification: zero-order ultrasensitivity revisited. J. Theor. Biol., 311, 139-152.
-
(2012)
J. Theor. Biol.
, vol.311
, pp. 139-152
-
-
Xu, Y.1
Gunawardena, J.2
-
63
-
-
60149099539
-
Fidelity at the molecular level: lessons from protein synthesis
-
Zaher, H. S., & Green, R. (2009). Fidelity at the molecular level: lessons from protein synthesis. Cell, 136, 746-762.
-
(2009)
Cell
, vol.136
, pp. 746-762
-
-
Zaher, H.S.1
Green, R.2
-
64
-
-
33745658106
-
Computational models for neurogenic gene expression in the Drosophila embryo
-
Zinzen, R. P., Senger, K., Levine, M., & Papatsenko, D. (2006). Computational models for neurogenic gene expression in the Drosophila embryo. Curr. Biol., 16, 1358-1365.
-
(2006)
Curr. Biol.
, vol.16
, pp. 1358-1365
-
-
Zinzen, R.P.1
Senger, K.2
Levine, M.3
Papatsenko, D.4
|