-
1
-
-
26244441397
-
Modular-based modelling of protein synthesis regulation
-
Maria, G., Modular-based modelling of protein synthesis regulation, Chemical and Biochemical Engineering Quarterly 19 (2005) 213-233.
-
(2005)
Chemical and Biochemical Engineering Quarterly
, vol.19
, pp. 213-233
-
-
Maria, G.1
-
2
-
-
33846599311
-
Application of lumping analysis in modelling the living systems. A trade-off between simplicity and model quality
-
Maria, G., Application of lumping analysis in modelling the living systems. A trade-off between simplicity and model quality, Chemical and Biochemical Engineering Quarterly 20 (2006) 353-373.
-
(2006)
Chemical and Biochemical Engineering Quarterly
, vol.20
, pp. 353-373
-
-
Maria, G.1
-
3
-
-
46949106064
-
-
SRI Intl, The Institute for Genomic Research, Univ. of California at San Diego
-
EcoCyc, Encyclopedia of Escherichia coli K-12 genes and metabolism, SRI Intl., The Institute for Genomic Research, Univ. of California at San Diego, 2005. http://ecocyc.org/
-
(2005)
Encyclopedia of Escherichia coli K-12 genes and metabolism
-
-
-
4
-
-
46949101966
-
-
KEGG, Kyoto encyclopedia of genes and genomes, Kyoto University and Univ. of Tokyo, 2007. /www.genome.jp/keg/
-
KEGG, Kyoto encyclopedia of genes and genomes, Kyoto University and Univ. of Tokyo, 2007. /www.genome.jp/keg/
-
-
-
-
8
-
-
33644847072
-
Programming cellular function
-
Voigt, C. A., Keasling, J. D., Programming cellular function, Nat. Chem. Biol. 1 (2005) 304-307.
-
(2005)
Nat. Chem. Biol
, vol.1
, pp. 304-307
-
-
Voigt, C.A.1
Keasling, J.D.2
-
9
-
-
33751013018
-
Synthetic Biology - putting engineering into biology
-
Heinemann, M., Panke, S., Synthetic Biology - putting engineering into biology, Bioinformatics 22 (2006) 2790-2799.
-
(2006)
Bioinformatics
, vol.22
, pp. 2790-2799
-
-
Heinemann, M.1
Panke, S.2
-
10
-
-
28544440364
-
Reconstruction of genetic circuits
-
Sprinzak, D., Elowitz, M.B., Reconstruction of genetic circuits, Nature 438 (2005) 443-448.
-
(2005)
Nature
, vol.438
, pp. 443-448
-
-
Sprinzak, D.1
Elowitz, M.B.2
-
11
-
-
0141757323
-
Reprogramming control of an allosteric signalling switch through modular recombination
-
Dueber, J. E., Yeh, B. J., Chak, K., Lim, W. A., Reprogramming control of an allosteric signalling switch through modular recombination, Science 301 (2003) 1904-1908.
-
(2003)
Science
, vol.301
, pp. 1904-1908
-
-
Dueber, J.E.1
Yeh, B.J.2
Chak, K.3
Lim, W.A.4
-
12
-
-
28544433105
-
-
Chan, L. Y., Kosuri, S., Endy, D., Refactoring bacteriophage T7, Mol. Syst. Biol. 1:2005.0018 (2005).
-
Chan, L. Y., Kosuri, S., Endy, D., Refactoring bacteriophage T7, Mol. Syst. Biol. 1:2005.0018 (2005).
-
-
-
-
13
-
-
0003754794
-
-
Springer Verlag, Berlin
-
Schügerl, K., Bellgardt, K. H., Bioreaction engineering, Springer Verlag, Berlin, 2000.
-
(2000)
Bioreaction engineering
-
-
Schügerl, K.1
Bellgardt, K.H.2
-
14
-
-
0038391517
-
Engineering a mevalonate pathway in E. coli for production of terpenoids
-
Martin, V. J. J., Pitera, D. J., Withers, S. T., Newman, J. D., Keasling, J. D., Engineering a mevalonate pathway in E. coli for production of terpenoids, Nature Biotechnol. 21 (2003) 796-802.
-
(2003)
Nature Biotechnol
, vol.21
, pp. 796-802
-
-
Martin, V.J.J.1
Pitera, D.J.2
Withers, S.T.3
Newman, J.D.4
Keasling, J.D.5
-
15
-
-
40849100380
-
Identifying synergistically switching pathways for multi-product strain improvement using multiobjective flux balance analysis
-
Bucharest
-
Selvarasu, S., Lee, D. Y., Karimi, I. A., Identifying synergistically switching pathways for multi-product strain improvement using multiobjective flux balance analysis, Proc. ESCAPE-17 Symp., Bucharest, 2007.
-
(2007)
Proc. ESCAPE-17 Symp
-
-
Selvarasu, S.1
Lee, D.Y.2
Karimi, I.A.3
-
16
-
-
15744378289
-
Numerical simulation of stochastic gene circuits
-
Salis, H., Kaznessis, Y., Numerical simulation of stochastic gene circuits, Comp. Chem. Eng. 29 (2005) 577-588.
-
(2005)
Comp. Chem. Eng
, vol.29
, pp. 577-588
-
-
Salis, H.1
Kaznessis, Y.2
-
17
-
-
27844576653
-
Multi-scale models for gene network engineering
-
Kaznessis, Y. N., Multi-scale models for gene network engineering, Chemical Engineering Science 61 (2006) 940-953.
-
(2006)
Chemical Engineering Science
, vol.61
, pp. 940-953
-
-
Kaznessis, Y.N.1
-
18
-
-
0038241770
-
Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli
-
Atkinson, M. R., Savageau, M. A., Myers, J. T., Ninfa, A. J., Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli, Cell 113 (2003) 597-607.
-
(2003)
Cell
, vol.113
, pp. 597-607
-
-
Atkinson, M.R.1
Savageau, M.A.2
Myers, J.T.3
Ninfa, A.J.4
-
19
-
-
23444449142
-
Integrative model of the response of yeast to osmotic shock
-
Klipp, E., Nordlander, B., Krüger, R., Gennemark, P., Hohmann, S., Integrative model of the response of yeast to osmotic shock, Nature Biotechnology 23 (2005) 975-982.
-
(2005)
Nature Biotechnology
, vol.23
, pp. 975-982
-
-
Klipp, E.1
Nordlander, B.2
Krüger, R.3
Gennemark, P.4
Hohmann, S.5
-
20
-
-
28644440579
-
Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signalling elements from Arabidopsis thaliana
-
Chen, M. T., Weiss, R., Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signalling elements from Arabidopsis thaliana, Nat. Biotechnol. 23 (2005) 1551-1555.
-
(2005)
Nat. Biotechnol
, vol.23
, pp. 1551-1555
-
-
Chen, M.T.1
Weiss, R.2
-
21
-
-
33744811457
-
Stochastic models for regulatory networks of the genetic toggle switch
-
Tian, T., Burrage, K., Stochastic models for regulatory networks of the genetic toggle switch, Proc. Natl. Acad. Sci. USA. 103 (2006) 8372-8377.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 8372-8377
-
-
Tian, T.1
Burrage, K.2
-
22
-
-
34447518290
-
Synthetic tetracy-cline- inducible regulatory networks: Computer-aided design of dynamic phenotypes, BMC
-
Jan 9 , doi:10.1186/1752-0509-l-7
-
Sotiropoulos, V., Kaznessis, Y. N., Synthetic tetracy-cline- inducible regulatory networks: computer-aided design of dynamic phenotypes, BMC Syst Biol., Jan 9 (2007) 1-7 (doi:10.1186/1752-0509-l-7).
-
(2007)
Syst Biol
, pp. 1-7
-
-
Sotiropoulos, V.1
Kaznessis, Y.N.2
-
23
-
-
33751204469
-
Optimization of a stochastically simulated gene network model via simulated annealing
-
Tomshine, J., Kaznessis, Y. N., Optimization of a stochastically simulated gene network model via simulated annealing, Biophys J. 91 (2006) 3196-3205.
-
(2006)
Biophys J
, vol.91
, pp. 3196-3205
-
-
Tomshine, J.1
Kaznessis, Y.N.2
-
24
-
-
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 (2007) 725-45.
-
(2007)
J Theor Biol
, vol.246
, pp. 725-745
-
-
Zhu, R.1
Ribeiro, A.S.2
Salahub, D.3
Kauffman, S.A.4
-
25
-
-
2942614884
-
Programmable cells: Interfacing natural and engineered gene networks
-
Kobayashi, H., Kaern, M., Araki, M., Chung, K., Gardner, T. S., Cantor, C. R., Collins, J. J., Programmable cells: Interfacing natural and engineered gene networks, PNAS 101 (2004) 8414-8419
-
(2004)
PNAS
, vol.101
, pp. 8414-8419
-
-
Kobayashi, H.1
Kaern, M.2
Araki, M.3
Chung, K.4
Gardner, T.S.5
Cantor, C.R.6
Collins, J.J.7
-
26
-
-
5644297178
-
-
Morgan, J. J., Surovtsev, I. V., Lindahl, P. A., A framework for whole-cell mathematical modelling, Jl. theor. Biology 231 (2004) 581-596.
-
Morgan, J. J., Surovtsev, I. V., Lindahl, P. A., A framework for whole-cell mathematical modelling, Jl. theor. Biology 231 (2004) 581-596.
-
-
-
-
27
-
-
0038440450
-
Dynamic responses of protein homeostatic regulatory mechanisms to perturbations from steady state
-
Yang, Q., Lindahl, P., Morgan, J., Dynamic responses of protein homeostatic regulatory mechanisms to perturbations from steady state, J. theor. Biol. 222 (2003) 407-423.
-
(2003)
J. theor. Biol
, vol.222
, pp. 407-423
-
-
Yang, Q.1
Lindahl, P.2
Morgan, J.3
-
28
-
-
0038648790
-
Evaluation of protein regulatory kinetics schemes in perturbed cell growth environments by using sensitivity methods
-
Maria, G., Evaluation of protein regulatory kinetics schemes in perturbed cell growth environments by using sensitivity methods, Chemical and Biochemical Engineering Quarterly 17 (2003) 99-117.
-
(2003)
Chemical and Biochemical Engineering Quarterly
, vol.17
, pp. 99-117
-
-
Maria, G.1
-
29
-
-
15744367955
-
Overview of computational methods for the inference of gene regulatory networks
-
Styczynski, M. P., Stephanopoulos, G., Overview of computational methods for the inference of gene regulatory networks, Comp. Chem. Eng. 29 (2005) 519-534.
-
(2005)
Comp. Chem. Eng
, vol.29
, pp. 519-534
-
-
Styczynski, M.P.1
Stephanopoulos, G.2
-
30
-
-
15744369730
-
Unconventional systems analysis problems in molecular biology: A case study in gene regulatory network modelling
-
Zak, D. E., Vadigepalli, R., Gonye, G. E., Doyle III, F. J., Schwaber, J. S., Ogunnaike, B. A., Unconventional systems analysis problems in molecular biology: A case study in gene regulatory network modelling, Comp. Chem. Eng. 29 (2005) 547-563.
-
(2005)
Comp. Chem. Eng
, vol.29
, pp. 547-563
-
-
Zak, D.E.1
Vadigepalli, R.2
Gonye, G.E.3
Doyle III, F.J.4
Schwaber, J.S.5
Ogunnaike, B.A.6
-
31
-
-
1242274449
-
Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems
-
Angeli, D., Ferrell, J. E. Jr., Sontag, E. D., Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems, Proceedings of the National Academy of Sciences of the USA 101 (2004) 1822-1827.
-
(2004)
Proceedings of the National Academy of Sciences of the USA
, vol.101
, pp. 1822-1827
-
-
Angeli, D.1
Ferrell Jr., J.E.2
Sontag, E.D.3
-
32
-
-
0019002639
-
Feedback kinetics in physicochemical oscillators
-
Franck, U. F., Feedback kinetics in physicochemical oscillators, Ber. Bunsenges. Phys. Chem. 84 (1980) 334-341.
-
(1980)
Ber. Bunsenges. Phys. Chem
, vol.84
, pp. 334-341
-
-
Franck, U.F.1
-
33
-
-
31144466208
-
Smooth bistable S-systems
-
Voit, E. O., Smooth bistable S-systems, IEE Proc. Syst. Biol. 152 (2005) 207-213.
-
(2005)
IEE Proc. Syst. Biol
, vol.152
, pp. 207-213
-
-
Voit, E.O.1
-
34
-
-
0036846553
-
Alternatives designs for a genetic switch: Analysis of switching times using the piecewise power-law representation
-
Savageau, M. A., Alternatives designs for a genetic switch: Analysis of switching times using the piecewise power-law representation, Math. Biosciences 180 (2002) 237-253.
-
(2002)
Math. Biosciences
, vol.180
, pp. 237-253
-
-
Savageau, M.A.1
-
35
-
-
0342349799
-
Recasting nonlinear differential equations as S-systems: A canonical nonlinear form
-
Savageau, M. A., Voit, E. O., Recasting nonlinear differential equations as S-systems: A canonical nonlinear form. Math. Biosciences 87 (1987) 83-115.
-
(1987)
Math. Biosciences
, vol.87
, pp. 83-115
-
-
Savageau, M.A.1
Voit, E.O.2
-
36
-
-
0031588690
-
Completely uncoupled and perfectly coupled gene expression in repressive systems
-
Hlavacek, W. S., Savageau, M. A., Completely uncoupled and perfectly coupled gene expression in repressive systems, J. Mol. Biol. 266 (1997) 538-558.
-
(1997)
J. Mol. Biol
, vol.266
, pp. 538-558
-
-
Hlavacek, W.S.1
Savageau, M.A.2
-
37
-
-
0037399803
-
Multi-criterion optimization for genetic network modelling
-
Van Someren, E. P., Wessels, L. F. A., Backer, E., Reinders, M. J. T., Multi-criterion optimization for genetic network modelling, Signal Processing 83 (2003) 763-775.
-
(2003)
Signal Processing
, vol.83
, pp. 763-775
-
-
Van Someren, E.P.1
Wessels, L.F.A.2
Backer, E.3
Reinders, M.J.T.4
-
38
-
-
15244353650
-
Improved methods for the mathematically controlled comparison of biochemical systems
-
Schwacke, J. H., Voit, E. O., Improved methods for the mathematically controlled comparison of biochemical systems, Theoretical Biology and Medical Modelling 1 (2004) 1-18.
-
(2004)
Theoretical Biology and Medical Modelling
, vol.1
, pp. 1-18
-
-
Schwacke, J.H.1
Voit, E.O.2
-
39
-
-
46949097165
-
-
Eden, P., Course on bioinformatics and computational biology, Faculty of Medicine, Dept. of Theoretical Physics, Lund University (Sweden), 2003. webmaster@thep.lu.se.
-
Eden, P., Course on bioinformatics and computational biology, Faculty of Medicine, Dept. of Theoretical Physics, Lund University (Sweden), 2003. webmaster@thep.lu.se.
-
-
-
-
43
-
-
0036428761
-
Negative autoregulation speeds the response times of transcription networks
-
Rosenfeld, N., Elowitz, M, B., Alon, U., Negative autoregulation speeds the response times of transcription networks, J. Mol. Biol. 323 (2002) 785-793.
-
(2002)
J. Mol. Biol
, vol.323
, pp. 785-793
-
-
Rosenfeld, N.1
Elowitz, M.B.2
Alon, U.3
-
44
-
-
0034688173
-
A synthetic oscillatory network of transcriptional regulators
-
Elowitz, M. B., Leibler, S., A synthetic oscillatory network of transcriptional regulators, Nature 403 (2000) 335-338.
-
(2000)
Nature
, vol.403
, pp. 335-338
-
-
Elowitz, M.B.1
Leibler, S.2
-
45
-
-
0036346420
-
Analysis of protein regulatory mechanisms in perturbed environments at steady state
-
Sewell, C., Morgan, J., Lindahl, P., Analysis of protein regulatory mechanisms in perturbed environments at steady state, J. theor. Biol. 215 (2002) 151-167.
-
(2002)
J. theor. Biol
, vol.215
, pp. 151-167
-
-
Sewell, C.1
Morgan, J.2
Lindahl, P.3
-
46
-
-
0036789922
-
Untangling the wires: A strategy to trace functional interactions in signalling and gene networks
-
Kholodenko, B. N., Kiyatkin, A., Bruggeman, F. J., Sontag, E., Westerhoff, H. V., Hoek, J. B., Untangling the wires: A strategy to trace functional interactions in signalling and gene networks, Proceedings of the National Academy of Sciences of the USA 99 (2002) 12841-12846.
-
(2002)
Proceedings of the National Academy of Sciences of the USA
, vol.99
, pp. 12841-12846
-
-
Kholodenko, B.N.1
Kiyatkin, A.2
Bruggeman, F.J.3
Sontag, E.4
Westerhoff, H.V.5
Hoek, J.B.6
-
48
-
-
4444234772
-
Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph
-
Ma, H. W., Zhao, X. M., Yuan, Y. J., Zeng, A. P., Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph, Bioinformatics 20 (2004) 1870-1876.
-
(2004)
Bioinformatics
, vol.20
, pp. 1870-1876
-
-
Ma, H.W.1
Zhao, X.M.2
Yuan, Y.J.3
Zeng, A.P.4
-
49
-
-
0041825399
-
Design principles for regulator gene expression in a repressible gene circuit
-
Wall, M. E., Hlavacek, W. S., Savageau, M. A., Design principles for regulator gene expression in a repressible gene circuit, J. Mol. Biol. 332 (2003) 861-876.
-
(2003)
J. Mol. Biol
, vol.332
, pp. 861-876
-
-
Wall, M.E.1
Hlavacek, W.S.2
Savageau, M.A.3
-
50
-
-
54249116230
-
Genetic regulatory mechanisms in the synthesis of proteins
-
Jacob, F., Monod, J., Genetic regulatory mechanisms in the synthesis of proteins, J. Mol. Biol. 3 (1961) 318-356.
-
(1961)
J. Mol. Biol
, vol.3
, pp. 318-356
-
-
Jacob, F.1
Monod, J.2
-
51
-
-
0032502685
-
Kinetic and thermodynamic studies of purine repressor binding to corepressor and operator DNA
-
Xu, H., Moraitis, M., Reedstrom, R. J., Matthews, K. S., Kinetic and thermodynamic studies of purine repressor binding to corepressor and operator DNA, Jl. Biological Chemistry 273 (1998) 8958-8964.
-
(1998)
Jl. Biological Chemistry
, vol.273
, pp. 8958-8964
-
-
Xu, H.1
Moraitis, M.2
Reedstrom, R.J.3
Matthews, K.S.4
-
52
-
-
0025012825
-
-
Meng, L. M., Kilstrup, M., Nygaard, P., Autoregulation of PurR repressor synthesis and involvement of purr in the regulation of purB, purC, purl, purMN and guaBA expression in Escherichia coli, Eur. J. Biochem. 187 (1990) 373-379.
-
Meng, L. M., Kilstrup, M., Nygaard, P., Autoregulation of PurR repressor synthesis and involvement of purr in the regulation of purB, purC, purl, purMN and guaBA expression in Escherichia coli, Eur. J. Biochem. 187 (1990) 373-379.
-
-
-
-
53
-
-
0036578795
-
Network motifs in the transcriptional regulation network of Escherichia coli
-
Shen-Orr, S. S., Milo, R., Mangan, S., Alon, U., Network motifs in the transcriptional regulation network of Escherichia coli, Nature Genetics 31 (2002) 64-68.
-
(2002)
Nature Genetics
, vol.31
, pp. 64-68
-
-
Shen-Orr, S.S.1
Milo, R.2
Mangan, S.3
Alon, U.4
-
56
-
-
0003820984
-
-
Chapman & Hall, New York
-
Heinrich, R., Schuster, S., The regulation of cellular systems, Chapman & Hall, New York, 1996.
-
(1996)
The regulation of cellular systems
-
-
Heinrich, R.1
Schuster, S.2
-
57
-
-
0019927659
-
Theoretical investigations of dynamic behavior of isothermal continuous stirred tank biological reactors
-
Agrawal, P., Lee, C., Lim, H. C., Ramkrishna, D., Theoretical investigations of dynamic behavior of isothermal continuous stirred tank biological reactors, Chemical Engineering Science 37 (1982) 453-462.
-
(1982)
Chemical Engineering Science
, vol.37
, pp. 453-462
-
-
Agrawal, P.1
Lee, C.2
Lim, H.C.3
Ramkrishna, D.4
-
58
-
-
0015103748
-
Concepts relating the behaviour of biochemical systems to their underlying molecular properties
-
Savageau, M. A., Concepts relating the behaviour of biochemical systems to their underlying molecular properties, Archives of Biochemistry and Biophysics 145 (1971), 612-621.
-
(1971)
Archives of Biochemistry and Biophysics
, vol.145
, pp. 612-621
-
-
Savageau, M.A.1
-
59
-
-
0024442732
-
Constraints among molecular and systemic properties: Implications for physiological genetics
-
Savageau, M. A., Sorribas, A., Constraints among molecular and systemic properties: Implications for physiological genetics, Journal of Theoretical Biology 141 (1989) 93-115.
-
(1989)
Journal of Theoretical Biology
, vol.141
, pp. 93-115
-
-
Savageau, M.A.1
Sorribas, A.2
-
60
-
-
0029033413
-
Subunit structure of regulator proteins influences the design of gene circuitry: Analysis of perfectly coupled and completely uncoupled circuits
-
Hlavacek, W. S., Savageau, M. A., Subunit structure of regulator proteins influences the design of gene circuitry: Analysis of perfectly coupled and completely uncoupled circuits, Journal of Molecular Biology 248 (1995), 739-755.
-
(1995)
Journal of Molecular Biology
, vol.248
, pp. 739-755
-
-
Hlavacek, W.S.1
Savageau, M.A.2
-
61
-
-
0030002954
-
Rules for coupled expression of regulator and effector genes in inducible circuits
-
Hlavacek, W. S., Savageau, M. A., Rules for coupled expression of regulator and effector genes in inducible circuits, Journal of Molecular Biology 255 (1996), 121-139.
-
(1996)
Journal of Molecular Biology
, vol.255
, pp. 121-139
-
-
Hlavacek, W.S.1
Savageau, M.A.2
-
62
-
-
0014337273
-
-
Grainger, J. N. R., Gaffney, P. E., West, T. T., A model of a growing steady-state system with a changing surface-ratio, J. theor. Biol. 21 (1968) 123-130.
-
Grainger, J. N. R., Gaffney, P. E., West, T. T., A model of a growing steady-state system with a changing surface-volume ratio, J. theor. Biol. 21 (1968) 123-130.
-
-
-
-
63
-
-
15044359039
-
-
Longman, London
-
Wallwork, S. C., Grant, D. J. W., Physical Chemistry, Longman, London, 1977.
-
(1977)
Physical Chemistry
-
-
Wallwork, S.C.1
Grant, D.J.W.2
-
64
-
-
0025955433
-
The priB gene encoding the primosomal replication n-protein of E. coli
-
Allen, G .C. Jr., Kornberg, A., The priB gene encoding the primosomal replication n-protein of E. coli, Jl. Biological Chemistry 266 (1991) 11610-11613.
-
(1991)
Jl. Biological Chemistry
, vol.266
, pp. 11610-11613
-
-
Allen Jr., G.C.1
Kornberg, A.2
|