-
1
-
-
0014013196
-
Chemotaxis in bacteria
-
doi:10.1126/science.153.3737.708
-
Adler, J. 1966 Chemotaxis in bacteria. Science 153, 708-716. (doi:10.1126/science.153.3737.708)
-
(1966)
Science
, vol.153
, pp. 708-716
-
-
Adler, J.1
-
2
-
-
0033552946
-
Robustness in bacterial chemotaxis
-
doi:10.1038/16483
-
Alon, U., Surette, M., Barkai, N. & Leibler, S. 1999 Robustness in bacterial chemotaxis. Nature 397, 168-171. (doi:10.1038/16483)
-
(1999)
Nature
, vol.397
, pp. 168-171
-
-
Alon, U.1
Surette, M.2
Barkai, N.3
Leibler, S.4
-
3
-
-
0021724874
-
Two-state model for bacterial chemoreceptor proteins. The role of multiple methylation
-
doi:10.1016/0022-2836(84)90494-7
-
Asakura, S. & Honda, H. 1984 Two-state model for bacterial chemoreceptor proteins. The role of multiple methylation. J. Mol. Biol. 176, 349-367. (doi:10.1016/0022-2836(84)90494-7)
-
(1984)
J. Mol. Biol.
, vol.176
, pp. 349-367
-
-
Asakura, S.1
Honda, H.2
-
4
-
-
0030797355
-
Robustness in simple biochemical networks
-
doi:10.1038/43199
-
Barkai, N. & Leibler, S. 1997 Robustness in simple biochemical networks. Nature 387, 913-917. (doi:10.1038/43199)
-
(1997)
Nature
, vol.387
, pp. 913-917
-
-
Barkai, N.1
Leibler, S.2
-
5
-
-
0030804853
-
Flux analysis of underdetermined metabolic networks: The quest for the missing constraints
-
DOI 10.1016/S0167-7799(97)01067-6
-
Bonarius, H., Schmid, G. & Tramper, J. 1997 Flux analysis of underdetermined metabolic networks: the quest for the missing constraints. Trends Biotechnol. 15, 308-314. (doi:10.1016/S0167-7799(97)01067-6) (Pubitemid 27330626)
-
(1997)
Trends in Biotechnology
, vol.15
, Issue.8
, pp. 308-314
-
-
Bonarius, H.P.J.1
Schmid, G.2
Tramper, J.3
-
6
-
-
45749134288
-
Process algebras in systems biology
-
Formal methods for computational systems biology. New York, NY: Springer-Verlag
-
Ciocchetta, F. & Hillston, J. 2008 Process algebras in systems biology. In Formal methods for computational systems biology. Lecture Notes in Computer Science, no. 5016, pp. 265-312. New York, NY: Springer-Verlag.
-
(2008)
Lecture Notes in Computer Science
, vol.5016
, pp. 265-312
-
-
Ciocchetta, F.1
Hillston, J.2
-
7
-
-
0035393979
-
LSCs: Breathing life into message sequence charts
-
doi:10.1023/A:1011227529550
-
Damm, W. & Harel, D. 2001 LSCs: breathing life into message sequence charts. Formal Methods Syst. Des. 19, 45-80. (doi:10.1023/A:1011227529550)
-
(2001)
Formal Methods Syst. Des.
, vol.19
, pp. 45-80
-
-
Damm, W.1
Harel, D.2
-
8
-
-
0035125986
-
In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
-
doi:10.1038/84379
-
Edwards, J., Ibarra, R. & Palsson, B. 2001 In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat. Biotechnol. 19, 125-130. (doi:10.1038/84379)
-
(2001)
Nat. Biotechnol.
, vol.19
, pp. 125-130
-
-
Edwards, J.1
Ibarra, R.2
Palsson, B.3
-
9
-
-
33846542982
-
Emergent dynamics of thymocyte development and lineage determination
-
doi:10.1371/journal.pcbi.0030013
-
Efroni, S., Harel, D. & Cohen, I. 2007 Emergent dynamics of thymocyte development and lineage determination. PLoS Comput. Biol. 3, 3-13. (doi:10.1371/journal.pcbi.0030013)
-
(2007)
PLoS Comput. Biol.
, vol.3
, pp. 3-13
-
-
Efroni, S.1
Harel, D.2
Cohen, I.3
-
10
-
-
20744434856
-
AgentCell: A digital single-cell assay for bacterial chemotaxis
-
DOI 10.1093/bioinformatics/bti391
-
Emonet, T., Macal, C., North, M., Wickersham, C. & Cluzel, P. 2005 AgentCell: a digital single-cell assay for bacterial chemotaxis. Bioinformatics 21, 2714-2721. (doi:10.1093/bioinformatics/bti391) (Pubitemid 40852319)
-
(2005)
Bioinformatics
, vol.21
, Issue.11
, pp. 2714-2721
-
-
Emonet, T.1
Macal, C.M.2
North, M.J.3
Wickersham, C.E.4
Cluzel, P.5
-
11
-
-
34347332311
-
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
-
doi:10.1038/msb4100155
-
Feist, A., Henry, C., Reed, J., Krummenacker, M., Joyce, A., Karp, P., Broadbelt, L., Hatzimanikatis, V. & Palsson, B. 2007 A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol. Syst. Biol. 3, 121. (doi:10.1038/msb4100155)
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 121
-
-
Feist, A.1
Henry, C.2
Reed, J.3
Krummenacker, M.4
Joyce, A.5
Karp, P.6
Broadbelt, L.7
Hatzimanikatis, V.8
Palsson, B.9
-
12
-
-
9444266171
-
CellDesigner: A process diagram editor for gene-regulatory and biochemical networks
-
doi:10.1016/S1478-5382(03)02370-9
-
Funahashi, A., Morohashi, M., Kitano, H. & Tanimura, N. 2003 CellDesigner: a process diagram editor for gene-regulatory and biochemical networks. BIOSILICO 1, 159-162. (doi:10.1016/S1478-5382(03)02370-9)
-
(2003)
Biosilico
, vol.1
, pp. 159-162
-
-
Funahashi, A.1
Morohashi, M.2
Kitano, H.3
Tanimura, N.4
-
13
-
-
0023365727
-
Statecharts: A visual formalism for complex systems
-
doi:10.1016/0167-6423(87)90035-9
-
Harel, D. 1987 Statecharts: a visual formalism for complex systems. Sci. Comput. Program. 8, 231-274. (doi:10.1016/0167-6423(87)90035-9)
-
(1987)
Sci. Comput. Program.
, vol.8
, pp. 231-274
-
-
Harel, D.1
-
14
-
-
0031187475
-
Executable object modeling with statecharts
-
doi:10.1109/2.596624
-
Harel, D. & Gery, E. 1997 Executable object modeling with statecharts. Computer 30, 31-42. (doi:10.1109/2.596624)
-
(1997)
Computer
, vol.30
, pp. 31-42
-
-
Harel, D.1
Gery, E.2
-
15
-
-
35048831026
-
The RHAPSODY semantics of statecharts (or, on the executable core of the UML)
-
Integration of software specification techniques for application in engineering. New York, NY: Springer-Verlag
-
Harel, D. & Kugler, H. 2004 The RHAPSODY semantics of statecharts (or, On the executable core of the UML). In Integration of software specification techniques for application in engineering. Lecture Notes in Computer Science, no. 3147, pp. 325-354. New York, NY: Springer-Verlag.
-
(2004)
Lecture Notes in Computer Science
, vol.3147
, pp. 325-354
-
-
Harel, D.1
Kugler, H.2
-
16
-
-
53849108096
-
A scenario-based approach to modeling development: A prototype model of C. elegans vulval fate specification
-
doi:10.1016/j.ydbio.2008.07.030
-
Kam, N., Kugler, H., Marelly, R., Appleby, L., Fisher, J., Pnueli, A., Harel, D., Stern, M. & Hubbard, E. 2008 A scenario-based approach to modeling development: a prototype model of C. elegans vulval fate specification. Dev. Biol. 323, 1-5. (doi:10.1016/j.ydbio.2008.07.030)
-
(2008)
Dev. Biol.
, vol.323
, pp. 1-5
-
-
Kam, N.1
Kugler, H.2
Marelly, R.3
Appleby, L.4
Fisher, J.5
Pnueli, A.6
Harel, D.7
Stern, M.8
Hubbard, E.9
-
17
-
-
23444439817
-
Using process diagrams for the graphical representation of biological networks
-
doi:10.1038/nbt1111
-
Kitano, H., Funahashi, A., Matsuoka, Y. & Oda, K. 2005 Using process diagrams for the graphical representation of biological networks. Nat. Biotechnol. 23, 961-966. (doi:10.1038/nbt1111)
-
(2005)
Nat. Biotechnol.
, vol.23
, pp. 961-966
-
-
Kitano, H.1
Funahashi, A.2
Matsuoka, Y.3
Oda, K.4
-
18
-
-
33745435987
-
Circuit diagrams for biological networks
-
doi:10.1038/msb4100044
-
Kohn, K. & Aladjem, M. 2006 Circuit diagrams for biological networks. Mol. Syst. Biol. 2, 2006.0002. (doi:10.1038/msb4100044)
-
(2006)
Mol. Syst. Biol.
, vol.2
-
-
Kohn, K.1
Aladjem, M.2
-
19
-
-
33750735728
-
Depicting combinatorial complexity with the molecular interaction map notation
-
doi:10.1038/msb4100088
-
Kohn, K., Aladjem, M., Kim, S., Weinstein, J. & Pommier, Y. 2006 Depicting combinatorial complexity with the molecular interaction map notation. Mol. Syst. Biol. 2, 51. (doi:10.1038/msb4100088)
-
(2006)
Mol. Syst. Biol.
, vol.2
, pp. 51
-
-
Kohn, K.1
Aladjem, M.2
Kim, S.3
Weinstein, J.4
Pommier, Y.5
-
21
-
-
0031982512
-
Origins of individual swimming behavior in bacteria
-
Levin, M., Morton-Firth, C., Abouhamad, W., Bourret, R. & Bray, D. 1998 Origins of individual swimming behavior in bacteria. Biophys. J. 74, 175-181. (doi:10.1016/S0006-3495(98)77777-X) (Pubitemid 28041747)
-
(1998)
Biophysical Journal
, vol.74
, Issue.1
, pp. 175-181
-
-
Levin, M.D.1
Morton-Firth, C.J.2
Abouhamad, W.N.3
Bourret, R.B.4
Bray, D.5
-
22
-
-
0036708443
-
Dynamic Flux Balance Analysis of diauxic growth in Escherichia coli
-
Mahadevan, R., Edwards, J. & Doyle, F. 2002 Dynamic flux balance analysis of diauxic growth in Escherichia coli. Biophys. J. 83, 1331-1340. (doi:10.1016/S0006-3495(02)73903-9) (Pubitemid 34977706)
-
(2002)
Biophysical Journal
, vol.83
, Issue.3
, pp. 1331-1340
-
-
Mahadevan, R.1
Edwards, J.S.2
Doyle III, F.J.3
-
23
-
-
0032492834
-
Predicting temporal fluctuations in an intracellular signalling pathway
-
doi:10.1006/jtbi.1997.0651
-
Morton-Firth, C. & Bray, D. 1998 Predicting temporal fluctuations in an intracellular signalling pathway. J. Theor. Biol. 192, 117-128. (doi:10.1006/jtbi.1997.0651)
-
(1998)
J. Theor. Biol.
, vol.192
, pp. 117-128
-
-
Morton-Firth, C.1
Bray, D.2
-
24
-
-
0033525474
-
A free-energy-based stochastic simulation of the Tar receptor complex
-
doi:10.1006/jmbi.1999.2535
-
Morton-Firth, C., Shimizu, T. & Bray, D. 1999 A free-energy-based stochastic simulation of the Tar receptor complex. J. Mol. Biol. 286, 1059-1074. (doi:10.1006/jmbi.1999.2535)
-
(1999)
J. Mol. Biol.
, vol.286
, pp. 1059-1074
-
-
Morton-Firth, C.1
Shimizu, T.2
Bray, D.3
-
25
-
-
85020789103
-
-
MSF08 See
-
MSF08 2008 Microsoft Solver Foundation. See http://code. msdn.microsoft.com/solverfoundation.
-
(2008)
-
-
-
26
-
-
0034961694
-
STOCHSIM: Modelling of stochastic biomolecular processes
-
Novère, N. L. & Shimizu, T. 2001 StochSim: modelling of stochastic biomolecular processes. Bioinformatics 17, 575-576. (doi:10.1093/bioinformatics/17.6.575) (Pubitemid 32600510)
-
(2001)
Bioinformatics
, vol.17
, Issue.6
, pp. 575-576
-
-
Le Novere, N.1
Shimizu, T.S.2
-
27
-
-
68449103579
-
The systems biology graphical notation
-
doi:10.1038/nbt.1558
-
Novère, N. L. et al. 2009 The systems biology graphical notation. Nat. Biotechnol. 27, 735-741. (doi:10.1038/nbt.1558)
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 735-741
-
-
Novère, N.L.1
-
28
-
-
33746889808
-
A comprehensive pathway map of epidermal growth factor receptor signaling
-
doi:10. 1038/msb4100014
-
Oda, K., Matsuoka, Y., Funahashi, A. & Kitano, H. 2005 A comprehensive pathway map of epidermal growth factor receptor signaling. Mol. Syst. Biol. 1, 2005.0010. (doi:10. 1038/msb4100014)
-
(2005)
Mol. Syst. Biol.
, vol.1
, Issue.2005
, pp. 0010
-
-
Oda, K.1
Matsuoka, Y.2
Funahashi, A.3
Kitano, H.4
-
29
-
-
0030026495
-
Qualitative analysis of biochemical reaction systems
-
doi:10.1016/0010-4825(95)00042-9
-
Reddy, V., Liebman, M. & Mavrovouniotis, M. 1996 Qualitative analysis of biochemical reaction systems. Comput. Biol. Med. 26, 9-24. (doi:10.1016/0010-4825(95)00042-9)
-
(1996)
Comput. Biol. Med.
, vol.26
, pp. 9-24
-
-
Reddy, V.1
Liebman, M.2
Mavrovouniotis, M.3
-
30
-
-
0035235039
-
Representation and simulation of biochemical processes using the pi-calculus process algebra
-
Singapore: World Scientific
-
Regev, A., Silverman, W. & Shapiro, E. 2001 Representation and simulation of biochemical processes using the pi-calculus process algebra. In Pacific Symp. on Biocomputing, pp. 459-470. Singapore: World Scientific.
-
(2001)
Pacific Symp. on Biocomputing
, pp. 459-470
-
-
Regev, A.1
Silverman, W.2
Shapiro, E.3
-
31
-
-
0017585044
-
Resolution of the multiplicity of the glutamate and aspartate transport systems of Escherichia coli
-
Schellenberg, G. & Furlong, C. 1977 Resolution of the multiplicity of the glutamate and aspartate transport systems of Escherichia coli. J. Biol. Chem. 252, 9055-9064.
-
(1977)
J. Biol. Chem.
, vol.252
, pp. 9055-9064
-
-
Schellenberg, G.1
Furlong, C.2
-
32
-
-
34447523907
-
Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
-
doi:10. 1038/msb4100162
-
Schuetz, R., Kuepfer, L. & Sauer, U. 2007 Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol. Syst. Biol. 3, 119. (doi:10. 1038/msb4100162)
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 119
-
-
Schuetz, R.1
Kuepfer, L.2
Sauer, U.3
-
33
-
-
58149511982
-
Four-dimensional realistic modeling of pancreatic organogenesis
-
doi:10. 1073/pnas.0808725105
-
Setty, Y., Cohen, I., Dor, Y. & Harel, D. 2008 Four-dimensional realistic modeling of pancreatic organogenesis. Proc. Natl Acad. Sci. USA 105, 20 374-20 379. (doi:10. 1073/pnas.0808725105)
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, pp. 20374-20379
-
-
Setty, Y.1
Cohen, I.2
Dor, Y.3
Harel, D.4
-
34
-
-
48449102329
-
Over-view of mathematical approaches used to model bacterial chemotaxis II: Bacterial populations
-
doi:10.1007/s11538-008-9322-5
-
Tindall, M., Maini, P., Porter, S. & Armitage, J. 2008a Over-view of mathematical approaches used to model bacterial chemotaxis II: bacterial populations. Bull. Math. Biol. 70, 1570-1607. (doi:10.1007/s11538-008-9322-5)
-
(2008)
Bull. Math. Biol.
, vol.70
, pp. 1570-1607
-
-
Tindall, M.1
Maini, P.2
Porter, S.3
Armitage, J.4
-
35
-
-
48449104873
-
Overview of mathematical approaches used to model bacterial chemotaxis I: The single cell
-
doi:10.1007/s11538-008-9321-6
-
Tindall, M., Porter, S., Maini, P., Gaglia, G. & Armitage, J. 2008b Overview of mathematical approaches used to model bacterial chemotaxis I: the single cell. Bull. Math. Biol. 70, 1525-1569. (doi:10.1007/s11538-008-9321-6)
-
(2008)
Bull. Math. Biol.
, vol.70
, pp. 1525-1569
-
-
Tindall, M.1
Porter, S.2
Maini, P.3
Gaglia, G.4
Armitage, J.5
-
36
-
-
0028146781
-
Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W311
-
Varma, A. & Palsson, B. O. 1994 Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W311. Appl. Environ. Microbiol. 60, 3724-3731.
-
(1994)
Appl. Environ. Microbiol.
, vol.60
, pp. 3724-3731
-
-
Varma, A.1
Palsson, B.O.2
-
37
-
-
10044252242
-
Making sense of it all: Bacterial chemotaxis
-
doi:10.1038/nrm1524
-
Wadhams, G. & Armitage, J. 2004 Making sense of it all: bacterial chemotaxis. Nat. Rev. Mol. Cell Biol. 12, 1024-1037. (doi:10.1038/nrm1524)
-
(2004)
Nat. Rev. Mol. Cell Biol.
, vol.12
, pp. 1024-1037
-
-
Wadhams, G.1
Armitage, J.2
-
38
-
-
0025157012
-
Chemotaxis in Escherichia coli proceeds efficiently from different initial tumble frequencies
-
Weis, R. & Koshland, D. 1990 Chemotaxis in Escherichia coli proceeds efficiently from different initial tumble frequencies. J. Bacteriol. 172, 1099-1105. (Pubitemid 20070425)
-
(1990)
Journal of Bacteriology
, vol.172
, Issue.2
, pp. 1099-1105
-
-
Weis, R.M.1
Koshland Jr., D.E.2
-
39
-
-
0031105797
-
Mathematical model of the lac operon: Inducer exclusion, catabolite repression, and diauxic growth on glucose and lactose
-
doi:10.1021/bp970003o
-
Wong, P., Gladney, S. & Keasling, J. D. 1997 Mathematical model of the lac operon: inducer exclusion, catabolite repression, and diauxic growth on glucose and lactose. Biotechnol. Prog. 13, 132-143. (doi:10.1021/bp970003o)
-
(1997)
Biotechnol. Prog.
, vol.13
, pp. 132-143
-
-
Wong, P.1
Gladney, S.2
Keasling, J.D.3
|