-
1
-
-
0037197850
-
Mechanisms of noise-resistance in genetic oscillators
-
Vilar, J. M. G., Kueh, H. Y., Barkai, N., and Leibler, S. "Mechanisms of noise-resistance in genetic oscillators", Proceedings of the National Academy of Sciences of the USA vol. 99, no. 9, pp.5988-5992, 2002.
-
(2002)
Proceedings of the National Academy of Sciences of the USA
, vol.99
, Issue.9
, pp. 5988-5992
-
-
Vilar, J.M.G.1
Kueh, H.Y.2
Barkai, N.3
Leibler, S.4
-
2
-
-
70350344969
-
Quiet gene circuit more fragile than its noisy peer
-
Bollenbach, T. & Kishony, R. (2009). Quiet gene circuit more fragile than its noisy peer. Cell 139: 460-461.
-
(2009)
Cell
, vol.139
, pp. 460-461
-
-
Bollenbach, T.1
Kishony, R.2
-
3
-
-
34347260600
-
Living with noisy genes: How cells function reliably with inherent variability in gene expression
-
Maheshri, N., and O"Shea, E. K. "Living with noisy genes: How cells function reliably with inherent variability in gene expression", Annual Review of Biophysics and Biomolecular Structure vol. 36, pp.413-434, 2007
-
(2007)
Annual Review of Biophysics and Biomolecular Structure
, vol.36
, pp. 413-434
-
-
Maheshri, N.1
Oshea, E.K.2
-
4
-
-
70350336588
-
Architecture-dependent noise discriminates functionally analogous differentiation circuits
-
Cagatay, T., Turcotte, M., Elowitz, M. B., Garcia-Ojalvo, J., and Suel, G. M. "Architecture-dependent noise discriminates functionally analogous differentiation circuits", Cell vol. 139, pp.512-522, 2009.
-
(2009)
Cell
, vol.139
, pp. 512-522
-
-
Cagatay, T.1
Turcotte, M.2
Elowitz, M.B.3
Garcia-Ojalvo, J.4
Suel, G.M.5
-
5
-
-
28544451327
-
Foundations for engineering biology
-
Endy, D. "Foundations for engineering biology", Nature vol. 438, pp.449-453, 2005.
-
(2005)
Nature
, vol.438
, pp. 449-453
-
-
Endy, D.1
-
6
-
-
31044439550
-
Essential genes of a minimal bacterium
-
Glass, J. I., Assad-Garcia, N., Alperovitch, N., Yooseph, S., Lewis, M. R., Maruf, M., Hutchinson, C. A., Smith, H. O. & Venter, J. C. "Essential genes of a minimal bacterium", Proceedings of the National Academy of Sciences of the USA vol. 103, no. 2, pp.425-434, 2006.
-
(2006)
Proceedings of the National Academy of Sciences of the USA
, vol.103
, Issue.2
, pp. 425-434
-
-
Glass, J.I.1
Assad-Garcia, N.2
Alperovitch, N.3
Yooseph, S.4
Lewis, M.R.5
Maruf, M.6
Hutchinson, C.A.7
Smith, H.O.8
Venter, J.C.9
-
7
-
-
70349324305
-
Creating bacterial strains from genomes that have been grown and engineered in yeast
-
Lartigue, C., Vashee, S., Algire, M. A., Chuang, R.-Y., Benders, G. A. & Ma, L. "Creating bacterial strains from genomes that have been grown and engineered in yeast", Science vol. 325, no. 5948, pp.1693-1696, 2009.
-
(2009)
Science
, vol.325
, Issue.5948
, pp. 1693-1696
-
-
Lartigue, C.1
Vashee, S.2
Algire, M.A.3
Chuang, R.-Y.4
Benders, G.A.5
Ma, L.6
-
8
-
-
66249088017
-
The second wave of synthetic biology: From modules to systems
-
Pumick, P. E. M., and Weiss, R. "The second wave of synthetic biology: From modules to systems.", Nature Reviews Molecular Cell Biology vol. 10, pp.410-422, 2009
-
(2009)
Nature Reviews Molecular Cell Biology
, vol.10
, pp. 410-422
-
-
Pumick, P.E.M.1
Weiss, R.2
-
9
-
-
33751013018
-
Synthetic biology - Putting engineering into biology
-
Heinemann, M., and Panke, S. "Synthetic biology - putting engineering into biology", Bioinformatics vol. 22, no. 22, pp.2790-2799, 2006.
-
(2006)
Bioinformatics
, vol.22
, Issue.22
, pp. 2790-2799
-
-
Heinemann, M.1
Panke, S.2
-
10
-
-
1442354192
-
Multistability in the lactose utilization network of Escherichia coli
-
Ozbudak, E. M., Thattai, M., Lim, H. N., and van Oudenaarden, A. "Multistability in the lactose utilization network of Escherichia coli", Nature vol. 427, pp.737-740, 2004.
-
(2004)
Nature
, vol.427
, pp. 737-740
-
-
Ozbudak, E.M.1
Thattai, M.2
Lim, H.N.3
Van Oudenaarden, A.4
-
11
-
-
0038610819
-
Detailed map of a cis-regulatory input function
-
Setty, Y. E., Mayo, A., Surette, M. G., and Alon, U. "Detailed map of a cis-regulatory input function", Proceedings of the National Academy of Sciences of the USA vol. 100, pp.7702-7707, 2003.
-
(2003)
Proceedings of the National Academy of Sciences of the USA
, vol.100
, pp. 7702-7707
-
-
Setty, Y.E.1
Mayo, A.2
Surette, M.G.3
Alon, U.4
-
12
-
-
0034644270
-
The segment polarity network is a robust developmental module
-
von Dassow, G., Meir, E., Munro, E. M., and Odell, G. M. "The segment polarity network is a robust developmental module", Nature vol. 406, pp.188-192, 2000.
-
(2000)
Nature
, vol.406
, pp. 188-192
-
-
Von Dassow, G.1
Meir, E.2
Munro, E.M.3
Odell, G.M.4
-
13
-
-
0037076210
-
Robustness, flexibility and the role of lateral inhibition in the neurogenic network
-
Meir, E., von Dassau, G., Munro, E., and O'Dell, G. M. "Robustness, flexibility and the role of lateral inhibition in the neurogenic network", Current Biology vol. 12, pp.778-785, 2002.
-
(2002)
Current Biology
, vol.12
, pp. 778-785
-
-
Meir, E.1
Von Dassau, G.2
Munro, E.3
O'dell, G.M.4
-
14
-
-
0038241770
-
Development of genetic circuitry exhibiting toggle switch or oscillatory behaviour in Escherichia coli
-
Atkinson, M. R., Savageau, M. A., Myers, J. T., and Ninfa, A. J. "Development of genetic circuitry exhibiting toggle switch or oscillatory behaviour in Escherichia coli", Cell vol. 113, pp.597-607, 2003.
-
(2003)
Cell
, vol.113
, pp. 597-607
-
-
Atkinson, M.R.1
Savageau, M.A.2
Myers, J.T.3
Ninfa, A.J.4
-
15
-
-
17444387728
-
The Bacillus subtilis sin operon: An evolveable network motif
-
Voigt, C. A., Wolf, D. M., and Arkin, A. P. "The Bacillus subtilis sin operon: An evolveable network motif", Genetics vol. 169, pp.1187-1202, 2005.
-
(2005)
Genetics
, vol.169
, pp. 1187-1202
-
-
Voigt, C.A.1
Wolf, D.M.2
Arkin, A.P.3
-
16
-
-
0033517148
-
Robustness of a gene regulatory circuit
-
Little, J. W., Shepley, D. P., and Wert, D. W. "Robustness of a gene regulatory circuit", EMBO Journal vol. 18, pp.4299-4307, 1999.
-
(1999)
EMBO Journal
, vol.18
, pp. 4299-4307
-
-
Little, J.W.1
Shepley, D.P.2
Wert, D.W.3
-
17
-
-
1642269636
-
Stochastic processes influence stationary-phase decisions in Bacillus subtilis
-
Maughan, H., and Nicholson, W. L. "Stochastic processes influence stationary-phase decisions in Bacillus subtilis", Journal of Bacteriology vol. 186, pp.2212-2214, 2004.
-
(2004)
Journal of Bacteriology
, vol.186
, pp. 2212-2214
-
-
Maughan, H.1
Nicholson, W.L.2
-
18
-
-
0037403153
-
Evolution of evolvability via adaptation of mutation rates
-
Bedau, M. A., and Packard, N. H. "Evolution of evolvability via adaptation of mutation rates", Biosystems vol. 69, pp.143-162, 2003.
-
(2003)
Biosystems
, vol.69
, pp. 143-162
-
-
Bedau, M.A.1
Packard, N.H.2
-
19
-
-
58549110252
-
Stochastic modelling for quantitative description of heterogeneous biological systems
-
Wilkinson, D. J. "Stochastic modelling for quantitative description of heterogeneous biological systems", Nature Reviews Genetics vol. 10, pp.122-133, 2009.
-
(2009)
Nature Reviews Genetics
, vol.10
, pp. 122-133
-
-
Wilkinson, D.J.1
-
20
-
-
1442297962
-
Basins of attraction
-
Nusse, H. E., and Yorke, J. E. "Basins of attraction", Science vol. 5254, pp.1376-1380, 1996.
-
(1996)
Science
, vol.5254
, pp. 1376-1380
-
-
Nusse, H.E.1
Yorke, J.E.2
-
21
-
-
0001134202
-
Requirements for transformation in Bacillus subtilis
-
Anagnostopoulos, C., and Spizizen, J. "Requirements for transformation in Bacillus subtilis", Journal of Bacteriology vol. 81, no. 5, pp.741-746, 1961.
-
(1961)
Journal of Bacteriology
, vol.81
, Issue.5
, pp. 741-746
-
-
Anagnostopoulos, C.1
Spizizen, J.2
-
22
-
-
0030731108
-
The complete genome sequence of the Grampositive bacterium Bacillus subtilis
-
Kunst, F., et al. "The complete genome sequence of the Grampositive bacterium Bacillus subtilis", Nature vol. 390, no. 6657, pp.234-256, 1997.
-
(1997)
Nature
, vol.390
, Issue.6657
, pp. 234-256
-
-
Kunst, F.1
-
23
-
-
67650741685
-
From a consortium sequence to a unified sequence: The Bacillus subtilis 168 reference genome a decade later
-
Barbe, V., Cruveiller, S. Kunst, F., Lenoble, P., Meurice, G., Sekowska, A., Vallenet, D., Wang, T. Moszer, I., Médigue, C. & Danchin, A. "From a consortium sequence to a unified sequence: The Bacillus subtilis 168 reference genome a decade later", Microbiology vol. 155, pp.1758-1775, 2009.
-
(2009)
Microbiology
, vol.155
, pp. 1758-1775
-
-
Barbe, V.1
Cruveiller, S.2
Kunst, F.3
Lenoble, P.4
Meurice, G.5
Sekowska, A.6
Vallenet, D.7
Wang Moszer, T.I.8
Médigue, C.9
Danchin, A.10
-
25
-
-
0023022816
-
Characterization of a cloned Bacillus subtilis gene that inhibits sporulation in multiple copies
-
Gaur, N. K., Dubnau, E., and Smith, I. "Characterization of a cloned Bacillus subtilis gene that inhibits sporulation in multiple copies", Journal of Bacteriology vol. 168, no. 2, pp.860-869, 1986.
-
(1986)
Journal of Bacteriology
, vol.168
, Issue.2
, pp. 860-869
-
-
Gaur, N.K.1
Dubnau, E.2
Smith, I.3
-
26
-
-
0032514949
-
An evolutionary link between sporulation and prophage induction in the structure of a repressor:anti-repressor complex
-
DOI 10.1006/jmbi.1998.2163
-
Lewis, R. J., Brannigan, J. A., Offen, W. A., Smith, I., and Wilkinson, A. J. "An evolutionary link between sporulation and prophage induction in the structure of a repressor: anti-repressor complex", Journal of Molecular Biology vol. 283, pp.907-912, 1998. (Pubitemid 28515322)
-
(1998)
Journal of Molecular Biology
, vol.283
, Issue.5
, pp. 907-912
-
-
Lewis, R.J.1
Brannigan, J.A.2
Offen, W.A.3
Smith, I.4
Wilkinson, A.J.5
-
27
-
-
0027465228
-
Bacillus subtilis sporulation: Regulation of gene expression and control of morphogenesis
-
Errington, J. "Bacillus subtilis sporulation: regulation of gene expression and control of morphogenesis", Microbiological Reviews vol. 57, no. 1, pp.1-33, 1993.
-
(1993)
Microbiological Reviews
, vol.57
, Issue.1
, pp. 1-33
-
-
Errington, J.1
-
28
-
-
1242345225
-
Qualitative simulation of the initiation of sporulation in Bacillus subtilis
-
de Jong, H., Geiselman, J., Batt, G., Hernandez, C., and Page, M. "Qualitative simulation of the initiation of sporulation in Bacillus subtilis", Bulletin of Mathematical Biology vol. 66, pp.261-299, 2004
-
(2004)
Bulletin of Mathematical Biology
, vol.66
, pp. 261-299
-
-
De Jong, H.1
Geiselman, J.2
Batt, G.3
Hernandez, C.4
Page, M.5
-
29
-
-
35748955855
-
Model-based definition of population heterogeneity and its effects on metabolism in sporulating Bacillus subtilis
-
Morohashi, M., Ohashi, Y., Tani, S., Ishii, K., Itaya, M., Nanamiya, H., Kawamura, F., Tomita, M. & Soga, T. "Model-based definition of population heterogeneity and its effects on metabolism in sporulating Bacillus subtilis", Journal of Biochemistry vol. 142, no. 2, pp.183-191, 2007.
-
(2007)
Journal of Biochemistry
, vol.142
, Issue.2
, pp. 183-191
-
-
Morohashi, M.1
Ohashi, Y.2
Tani, S.3
Ishii, K.4
Itaya, M.5
Nanamiya, H.6
Kawamura, F.7
Tomita, M.8
Soga, T.9
-
30
-
-
33744976080
-
The mechanism of cell differentiation in Bacillus subtilis
-
Iber, D., Clarkson, J., Yudkin, M. D., and Campbell, I. D. "The mechanism of cell differentiation in Bacillus subtilis", Nature vol. 441, pp.371-374, 2006.
-
(2006)
Nature
, vol.441
, pp. 371-374
-
-
Iber, D.1
Clarkson, J.2
Yudkin, M.D.3
Campbell, I.D.4
-
31
-
-
41749107942
-
Stochasticity and cell fate
-
Losick, R., and Desplan, C. "Stochasticity and cell fate", Science vol. 320, pp.65-68, 2008.
-
(2008)
Science
, vol.320
, pp. 65-68
-
-
Losick, R.1
Desplan, C.2
-
32
-
-
33751204469
-
Optimization of a stochastically simulated gene network model via simulated annealing
-
Tomshine, J., and Kazneiss, Y. N. "Optimization of a stochastically simulated gene network model via simulated annealing", Biophysical Journal vol. 91, pp.3196-3205, 2006.
-
(2006)
Biophysical Journal
, vol.91
, pp. 3196-3205
-
-
Tomshine, J.1
Kazneiss, Y.N.2
-
33
-
-
0034688173
-
A synthetic oscillatory network of transcriptional regulators
-
Elowitz, M. B., and Leibler, S. "A synthetic oscillatory network of transcriptional regulators", Nature vol. 403, pp.335-338, 2000.
-
(2000)
Nature
, vol.403
, pp. 335-338
-
-
Elowitz, M.B.1
Leibler, S.2
-
34
-
-
0037165942
-
Combinatorial synthesis of gene networks
-
Guet, C. C., Elowitz, M. B., Hsing, W., and Leibler, S. "Combinatorial synthesis of gene networks", Science vol. 296, no. 5572, pp.1466-1470, 2002.
-
(2002)
Science
, vol.296
, Issue.5572
, pp. 1466-1470
-
-
Guet, C.C.1
Elowitz, M.B.2
Hsing, W.3
Leibler, S.4
-
35
-
-
0037041888
-
Synthetic gene networks for entraining and amplifying cellular oscillations
-
Hasty, J., Dolnik, M., Rottschafer, V., and Collins, J. J. "Synthetic gene networks for entraining and amplifying cellular oscillations", Physical Review Letters vol. 88, no. 14, pp.148101-1-148101-4, 2002.
-
(2002)
Physical Review Letters
, vol.88
, Issue.14
, pp. 1481011-1481014
-
-
Hasty, J.1
Dolnik, M.2
Rottschafer, V.3
Collins, J.J.4
-
36
-
-
5644236684
-
Preliminary studies on the in silico evolution of biochemical networks
-
Deckard, A., and Sauro, H. M. "Preliminary studies on the in silico evolution of biochemical networks", ChemBioChem vol. 5, pp.1423-1431, 2004.
-
(2004)
ChemBioChem
, vol.5
, pp. 1423-1431
-
-
Deckard, A.1
Sauro, H.M.2
-
37
-
-
33746593012
-
In silico evolution of functional modules in biochemical networks
-
Paladuqu, S.R., Chicarmane, V., Deckard, A., Frumkin, J. P., McCormack, M. & Sauro, H. M. "In silico evolution of functional modules in biochemical networks", Systems Biology (Stevenage) vol. 153, no. 4, pp.223-235, 2006.
-
(2006)
Systems Biology (Stevenage)
, vol.153
, Issue.4
, pp. 223-235
-
-
Paladuqu, S.R.1
Chicarmane, V.2
Deckard, A.3
Frumkin, J.P.4
McCormack, M.5
Sauro, H.M.6
-
39
-
-
0029096741
-
Genetic-algorithm selection of a regulatory structure that directs flux in a simple metabolic model
-
Gilman, A., and Ross, J. "Genetic-algorithm selection of a regulatory structure that directs flux in a simple metabolic model", Biophysical Journal vol. 69, no. 4, pp.1321, 1995.
-
(1995)
Biophysical Journal
, vol.69
, Issue.4
, pp. 1321
-
-
Gilman, A.1
Ross, J.2
-
40
-
-
0035953990
-
Application of genetic algorithm to chemical kinetics: Systematic determination of reaction mechanism and rate coefficients for a complex reaction network
-
Tsuchiya, M., and Ross, J. "Application of genetic algorithm to chemical kinetics: Systematic determination of reaction mechanism and rate coefficients for a complex reaction network", Journal of Physical Chemistry A vol. 105, no. 16, pp.4052-4058, 2001.
-
(2001)
Journal of Physical Chemistry A
, vol.105
, Issue.16
, pp. 4052-4058
-
-
Tsuchiya, M.1
Ross, J.2
-
41
-
-
5644270128
-
Evolutionary design of genetic circuits and cell-cell communications
-
Yokobayashi, Y., Collins, C. H., Leadbetter, J. R., Weiss, R., and Arnold, F. H. "Evolutionary design of genetic circuits and cell-cell communications.", Advances in Complex Systems vol. 6, no. 1, pp.1-9, 2003.
-
(2003)
Advances in Complex Systems
, vol.6
, Issue.1
, pp. 1-9
-
-
Yokobayashi, Y.1
Collins, C.H.2
Leadbetter, J.R.3
Weiss, R.4
Arnold, F.H.5
-
42
-
-
38049033443
-
Towards evolutionary network reconstruction tools for systems biology
-
Marchiori, E., Moore, J. H. & Rajapakse, J. C. (eds.)
-
Lenser, T., Hinze, T., Ibrahim, B., and Dittrich, P. "Towards evolutionary network reconstruction tools for systems biology", In Marchiori, E., Moore, J. H. & Rajapakse, J. C. (eds.) "EvoBio 2007, Lecture Notes in Computer Science 4447" : pp.132-142, 2007.
-
(2007)
EvoBio 2007, Lecture Notes in Computer Science
, vol.4447
, pp. 132-142
-
-
Lenser, T.1
Hinze, T.2
Ibrahim, B.3
Dittrich, P.4
-
43
-
-
50049100928
-
SlrR/SlrA controls the initiation of biofilm formation in Bacillus subtilis
-
Kobayashi, K. "SlrR/SlrA controls the initiation of biofilm formation in Bacillus subtilis", Molecular Microbiology vol. 69, no. 6, pp.1399-1410, 2008.
-
(2008)
Molecular Microbiology
, vol.69
, Issue.6
, pp. 1399-1410
-
-
Kobayashi, K.1
-
44
-
-
0037342537
-
The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models
-
Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C. et al."The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models", Bioinformatics vol. 19, pp.524-531, 2003.
-
(2003)
Bioinformatics
, vol.19
, pp. 524-531
-
-
Hucka, M.1
Finney, A.2
Sauro, H.M.3
Bolouri, H.4
Doyle, J.C.5
-
45
-
-
33845368513
-
COPASI-a complex pathway simulator
-
Hoops, S., Sahle, S., Guages, R., Lee, C., Pahle, J., Simus, N., Singhal, M., Xu, L., Mendes, P. & Kummer, U. "COPASI-a Complex PAthway SImulator", Bioinformatics vol. 22, no. 24, pp.3067-3074, 2006.
-
(2006)
Bioinformatics
, vol.22
, Issue.24
, pp. 3067-3074
-
-
Hoops, S.1
Sahle, S.2
Guages, R.3
Lee, C.4
Pahle, J.5
Simus, N.6
Singhal, M.7
Xu, L.8
Mendes, P.9
Kummer, U.10
-
46
-
-
37349100857
-
Bistability and biofilm formation in Bacillus subtilis
-
Chai, Y., Chu, F., Kolter, R., and Losick, R. "Bistability and biofilm formation in Bacillus subtilis", Molecular Microbiology vol. 67, no. 2, pp.254-263, 2008.
-
(2008)
Molecular Microbiology
, vol.67
, Issue.2
, pp. 254-263
-
-
Chai, Y.1
Chu, F.2
Kolter, R.3
Losick, R.4
-
47
-
-
1242274449
-
Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems
-
Angeli, D., Ferrell, J. E., and 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 vol. 101, no. 7, pp.1822-1827, 2004.
-
(2004)
Proceedings of the National Academy of Sciences of the USA
, vol.101
, Issue.7
, pp. 1822-1827
-
-
Angeli, D.1
Ferrell, J.E.2
Sontag, E.D.3
-
48
-
-
34249857117
-
Oscillation patterns in negative feedback loops
-
Pigolotti, S., Krishna, S., and Jensen, M. H. "Oscillation patterns in negative feedback loops", Proceedings of the National Academy of Sciences of the USA vol. 104, no. 16, pp.6533-6537, 2007.
-
(2007)
Proceedings of the National Academy of Sciences of the USA
, vol.104
, Issue.16
, pp. 6533-6537
-
-
Pigolotti, S.1
Krishna, S.2
Jensen, M.H.3
|