-
1
-
-
69249126551
-
Bacterial cell division: Assembly, maintenance and disassembly of the Z ring
-
Adams DW, Errington J (2009) Bacterial cell division: assembly, maintenance and disassembly of the Z ring. Nat Rev Microbiol 7(9): 642-653.
-
(2009)
Nat Rev Microbiol
, vol.7
, Issue.9
, pp. 642-653
-
-
Adams, D.W.1
Errington, J.2
-
2
-
-
14844328879
-
SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: Analysis of simple networks
-
Ander M, Beltrao P, Ventura BD, Ferkinghoff-Borg J, Foglierini M, Kaplan A, Lemerle C, Tomas-Oliveira I, Serrano L (2004) SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks. Syst Biol 1(1): 129-138.
-
(2004)
Syst Biol
, vol.1
, Issue.1
, pp. 129-138
-
-
Ander, M.1
Beltrao, P.2
Ventura, B.D.3
Ferkinghoff-Borg, J.4
Foglierini, M.5
Kaplan, A.6
Lemerle, C.7
Tomas-Oliveira, I.8
Serrano, L.9
-
3
-
-
33748520215
-
Stochastic simulation of chemical reactions with spatial resolution and single molecule detail
-
Andrews SS, Bray D (2004) Stochastic simulation of chemical reactions with spatial resolution and single molecule detail. Phys Biol 1(3-4): 137-151.
-
(2004)
Phys Biol
, vol.1
, Issue.3-4
, pp. 137-151
-
-
Andrews, S.S.1
Bray, D.2
-
4
-
-
76149108865
-
A guide to modeling reaction-diffusion of molecules with the E-Cell System
-
In: Arjunan SNV, Dhar PK, Tomita M (eds), Landes Bioscience and Springer Science+Business Media (in press)
-
Arjunan SNV (2009a) A guide to modeling reaction-diffusion of molecules with the E-Cell System. In: Arjunan SNV, Dhar PK, Tomita M (eds) E-Cell System: basic concepts and applications. Landes Bioscience and Springer Science+Business Media (in press).
-
(2009)
E-Cell System: Basic Concepts and Applications
-
-
Arjunan, S.N.V.1
-
6
-
-
76149141642
-
Modeling reaction-diffusion of molecules on surface and in volume spaces with the E-Cell System
-
Arjunan SNV, Tomita M (2009) Modeling reaction-diffusion of molecules on surface and in volume spaces with the E-Cell System. Int J Comput Sci Inf Secur 3(1): 211-216.
-
(2009)
Int J Comput Sci Inf Secur
, vol.3
, Issue.1
, pp. 211-216
-
-
Arjunan, S.N.V.1
Tomita, M.2
-
7
-
-
0029000513
-
Transport effects on the kinetics of protein-surface binding
-
Balgi G, Leckb D, Nitsche J (1995) Transport effects on the kinetics of protein-surface binding. Biophys J 68(6): 2251-2260.
-
(1995)
Biophys J
, vol.68
, Issue.6
, pp. 2251-2260
-
-
Balgi, G.1
Leckb, D.2
Nitsche, J.3
-
8
-
-
19444386428
-
SlmA, a nucleoid-associated, FtsZ binding protein required for blocking septal ring assembly over chromosomes in E. coli
-
Bernhardt TG, de Boer PAJ (2005) SlmA, a nucleoid-associated, FtsZ binding protein required for blocking septal ring assembly over chromosomes in E. coli. Mol Cell 18(5): 555-564.
-
(2005)
Mol Cell
, vol.18
, Issue.5
, pp. 555-564
-
-
Bernhardt, T.G.1
de Boer, P.A.J.2
-
9
-
-
70350215725
-
Predictions from a stochastic polymer model for the MinDE protein dynamics in Escherichia coli
-
Borowski P, Cytrynbaum EN (2009) Predictions from a stochastic polymer model for the MinDE protein dynamics in Escherichia coli. Phys Rev E 80(4): 041916.
-
(2009)
Phys Rev E
, vol.80
, Issue.4
, pp. 041916
-
-
Borowski, P.1
Cytrynbaum, E.N.2
-
10
-
-
50149096614
-
GridCell: A stochastic particle-based biological system simulator
-
Boulianne L, Assaad SA, Dumontier M, Gross W (2008) GridCell: a stochastic particle-based biological system simulator. BMC Syst Biol 2(1): 66.
-
(2008)
BMC Syst Biol
, vol.2
, Issue.1
, pp. 66
-
-
Boulianne, L.1
Assaad, S.A.2
Dumontier, M.3
Gross, W.4
-
11
-
-
49849103199
-
Decoding the quantitative nature of TGF-beta/Smad signaling
-
Clarke DC, Liu X (2008) Decoding the quantitative nature of TGF-beta/Smad signaling. Trends Cell Biol 18(9): 430-442.
-
(2008)
Trends Cell Biol
, vol.18
, Issue.9
, pp. 430-442
-
-
Clarke, D.C.1
Liu, X.2
-
12
-
-
0141902430
-
Diffusion-controlled reaction rates
-
Collins FC, Kimball GE (1949) Diffusion-controlled reaction rates. J Colloid Sci 4(4): 425-437.
-
(1949)
J Colloid Sci
, vol.4
, Issue.4
, pp. 425-437
-
-
Collins, F.C.1
Kimball, G.E.2
-
13
-
-
34548255900
-
A multistranded polymer model explains MinDE dynamics in E. coli cell division
-
Cytrynbaum EN, Marshall BDL (2007) A multistranded polymer model explains MinDE dynamics in E. coli cell division. Biophys J 93(4): 1134-1150.
-
(2007)
Biophys J
, vol.93
, Issue.4
, pp. 1134-1150
-
-
Cytrynbaum, E.N.1
Marshall, B.D.L.2
-
14
-
-
68949091841
-
Self-organization of the MinE protein ring in subcellular Min oscillations
-
Derr J, Hopper JT, Sain A, Rutenberg AD (2009) Self-organization of the MinE protein ring in subcellular Min oscillations. Phys Rev E 80(1 Pt 1): 011922.
-
(2009)
Phys Rev E
, vol.80
, Issue.1 PART 1
, pp. 011922
-
-
Derr, J.1
Hopper, J.T.2
Sain, A.3
Rutenberg, A.D.4
-
15
-
-
48249124302
-
Crowding effects on diffusion in solutions and cells
-
Dix JA, Verkman AS (2008) Crowding effects on diffusion in solutions and cells. Annu Rev Biophys 37: 247-263.
-
(2008)
Annu Rev Biophys
, vol.37
, pp. 247-263
-
-
Dix, J.A.1
Verkman, A.S.2
-
16
-
-
17844384217
-
A polymerization-depolymerization model that accurately generates the self-sustained oscillatory system involved in bacterial division site placement
-
Drew DA, Osborn MJ, Rothfield LI (2005) A polymerization-depolymerization model that accurately generates the self-sustained oscillatory system involved in bacterial division site placement. Proc Natl Acad Sci USA 102(17): 6114-6118.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, Issue.17
, pp. 6114-6118
-
-
Drew, D.A.1
Osborn, M.J.2
Rothfield, L.I.3
-
17
-
-
42949117368
-
Protein area occupancy at the center of the red blood cell membrane
-
Dupuy AD, Engelman DM (2008) Protein area occupancy at the center of the red blood cell membrane. Proc Natl Acad Sci USA 105(8): 2848-2852.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, Issue.8
, pp. 2848-2852
-
-
Dupuy, A.D.1
Engelman, D.M.2
-
18
-
-
20844455677
-
Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases
-
Elf J, Ehrenberg M (2004) Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases. Syst Biol 1(2): 230-236.
-
(2004)
Syst Biol
, vol.1
, Issue.2
, pp. 230-236
-
-
Elf, J.1
Ehrenberg, M.2
-
19
-
-
0035478585
-
Macromolecular crowding: Obvious but underappreciated
-
Ellis RJ (2001) Macromolecular crowding: obvious but underappreciated. Trends Biochem Sci 26(10): 597-604.
-
(2001)
Trends Biochem Sci
, vol.26
, Issue.10
, pp. 597-604
-
-
Ellis, R.J.1
-
20
-
-
33745591124
-
Noise-induced Min phenotypes in E. coli
-
Fange D, Elf J (2006) Noise-induced Min phenotypes in E. coli. PLoS Comput Biol 2(6): e80.
-
(2006)
PLoS Comput Biol
, vol.2
, Issue.6
-
-
Fange, D.1
Elf, J.2
-
21
-
-
56749104130
-
Fluorescent probes for super-resolution imaging in living cells
-
Fernandez-Suarez M, Ting AY (2008) Fluorescent probes for super-resolution imaging in living cells. Nat Rev Mol Cell Biol 9(12): 929-943.
-
(2008)
Nat Rev Mol Cell Biol
, vol.9
, Issue.12
, pp. 929-943
-
-
Fernandez-Suarez, M.1
Ting, A.Y.2
-
22
-
-
0001144902
-
Efficient exact stochastic simulation of chemical systems with many species and many channels
-
Gibson M, Bruck J (2000) Efficient exact stochastic simulation of chemical systems with many species and many channels. J Phys Chem A 104(9): 1876-1889.
-
(2000)
J Phys Chem A
, vol.104
, Issue.9
, pp. 1876-1889
-
-
Gibson, M.1
Bruck, J.2
-
23
-
-
0017030517
-
A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
-
Gillespie DT (1976) A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J Comput Phys 22(4): 403-434.
-
(1976)
J Comput Phys
, vol.22
, Issue.4
, pp. 403-434
-
-
Gillespie, D.T.1
-
24
-
-
33645429016
-
Exact stochastic simulation of coupled chemical reactions
-
Gillespie DT (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81(25): 2340-2361.
-
(1977)
J Phys Chem
, vol.81
, Issue.25
, pp. 2340-2361
-
-
Gillespie, D.T.1
-
25
-
-
33846250352
-
Mass fluctuation kinetics: Capturing stochastic effects in systems of chemical reactions through coupled mean-variance computations
-
Gomez-Uribe CA, Verghese GC (2007) Mass fluctuation kinetics: capturing stochastic effects in systems of chemical reactions through coupled mean-variance computations. J Chem Phys 126(2): 024109.
-
(2007)
J Chem Phys
, vol.126
, Issue.2
, pp. 024109
-
-
Gomez-Uribe, C.A.1
Verghese, G.C.2
-
26
-
-
67649922591
-
Self-organization of the Escherichia coli chemotaxis network imaged with super-resolution light microscopy
-
Greenfield D, McEvoy AL, Shroff H, Crooks GE, Wingreen NS, Betzig E, Liphardt J (2009) Self-organization of the Escherichia coli chemotaxis network imaged with super-resolution light microscopy. PLoS Biol 7(6): e1000137.
-
(2009)
PLoS Biol
, vol.7
, Issue.6
-
-
Greenfield, D.1
McEvoy, A.L.2
Shroff, H.3
Crooks, G.E.4
Wingreen, N.S.5
Betzig, E.6
Liphardt, J.7
-
27
-
-
0041931122
-
Macromolecular crowding: Qualitative and semiquantitative successes, quantitative challenges
-
Hall D, Minton A(2003) Macromolecular crowding: qualitative and semiquantitative successes, quantitative challenges. Biochim Biophys Acta 1649(2): 127-139.
-
(2003)
Biochim Biophys Acta
, vol.1649
, Issue.2
, pp. 127-139
-
-
Hall, D.1
Minton, A.2
-
28
-
-
38949210309
-
Chemotaxis in Escherichia coli: A molecular model for robust precise adaptation
-
Hansen CH, Endres RG, Wingreen NS (2008) Chemotaxis in Escherichia coli: a molecular model for robust precise adaptation. PLoS Comput Biol 4(1): e1.
-
(2008)
PLoS Comput Biol
, vol.4
, Issue.1
-
-
Hansen, C.H.1
Endres, R.G.2
Wingreen, N.S.3
-
29
-
-
20844432892
-
Stochastic reaction-diffusion simulation with MesoRD
-
Hattne J, Fange D, Elf J (2005) Stochastic reaction-diffusion simulation with MesoRD. Bioinformatics 21(12): 2923-2924.
-
(2005)
Bioinformatics
, vol.21
, Issue.12
, pp. 2923-2924
-
-
Hattne, J.1
Fange, D.2
Elf, J.3
-
30
-
-
0038050464
-
Pattern formation inside bacteria: Fluctuations due to the low copy number of proteins
-
Howard M, Rutenberg AD (2003) Pattern formation inside bacteria: fluctuations due to the low copy number of proteins. Phys Rev Lett 90(12): 128102.
-
(2003)
Phys Rev Lett
, vol.90
, Issue.12
, pp. 128102
-
-
Howard, M.1
Rutenberg, A.D.2
-
31
-
-
16744362844
-
Dynamic compartmentalization of bacteria: Accurate division in E. coli
-
Howard M, Rutenberg AD, de Vet S (2001) Dynamic compartmentalization of bacteria: accurate division in E. coli. Phys Rev Lett 87(27 Pt 1): 278102.
-
(2001)
Phys Rev Lett
, vol.87
, Issue.27 PART 1
, pp. 278102
-
-
Howard, M.1
Rutenberg, A.D.2
de vet, S.3
-
32
-
-
0032846485
-
Topological regulation of cell division in Escherichia coli involves rapid pole to pole oscillation of the division inhibitor MinC under the control of MinD and MinE
-
Hu Z, Lutkenhaus J (1999) Topological regulation of cell division in Escherichia coli involves rapid pole to pole oscillation of the division inhibitor MinC under the control of MinD and MinE. Mol Microbiol 34(1): 82-90.
-
(1999)
Mol Microbiol
, vol.34
, Issue.1
, pp. 82-90
-
-
Hu, Z.1
Lutkenhaus, J.2
-
33
-
-
0034964370
-
Topological regulation of cell division in E. coli. spatiotemporal oscillation of MinD requires stimulation of its ATPase by MinE and phospholipid
-
Hu Z, Lutkenhaus J (2001) Topological regulation of cell division in E. coli. spatiotemporal oscillation of MinD requires stimulation of its ATPase by MinE and phospholipid. Mol Cell 7(6): 1337-1343.
-
(2001)
Mol Cell
, vol.7
, Issue.6
, pp. 1337-1343
-
-
Hu, Z.1
Lutkenhaus, J.2
-
34
-
-
0033592949
-
The MinC component of the division site selection system in Escherichia coli interacts with FtsZ to prevent polymerization
-
Hu Z, Mukherjee A, Pichoff S, Lutkenhaus J (1999) The MinC component of the division site selection system in Escherichia coli interacts with FtsZ to prevent polymerization. Proc Natl Acad Sci USA 96(26): 14819-14824.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, Issue.26
, pp. 14819-14824
-
-
Hu, Z.1
Mukherjee, A.2
Pichoff, S.3
Lutkenhaus, J.4
-
35
-
-
0037215535
-
Recruitment of MinC, an inhibitor of Z-ring formation, to the membrane in Escherichia coli: Role of MinD and MinE
-
Hu Z, Saez C, Lutkenhaus J (2003) Recruitment of MinC, an inhibitor of Z-ring formation, to the membrane in Escherichia coli: role of MinD and MinE. J Bacteriol 185(1): 196-203.
-
(2003)
J Bacteriol
, vol.185
, Issue.1
, pp. 196-203
-
-
Hu, Z.1
Saez, C.2
Lutkenhaus, J.3
-
36
-
-
67650762824
-
Super-resolution fluorescence microscopy
-
Huang B, Bates M, Zhuang X (2009) Super-resolution fluorescence microscopy. Annu Rev Biochem 78: 993-1016.
-
(2009)
Annu Rev Biochem
, vol.78
, pp. 993-1016
-
-
Huang, B.1
Bates, M.2
Zhuang, X.3
-
37
-
-
0242268448
-
Dynamic structures in Escherichia coli: Spontaneous formation of MinE rings and MinD polar zones
-
Huang KC, Meir Y, Wingreen NS (2003) Dynamic structures in Escherichia coli: spontaneous formation of MinE rings and MinD polar zones. Proc Natl Acad Sci USA 100(22): 12724-12728.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, Issue.22
, pp. 12724-12728
-
-
Huang, K.C.1
Meir, Y.2
Wingreen, N.S.3
-
38
-
-
0037716676
-
Building with a scaffold: Emerging strategies for high- to low-level cellular modeling
-
Ideker T, Lauffenburger D (2003) Building with a scaffold: emerging strategies for high- to low-level cellular modeling. Trends Biotechnol 21(6): 255-262.
-
(2003)
Trends Biotechnol
, vol.21
, Issue.6
, pp. 255-262
-
-
Ideker, T.1
Lauffenburger, D.2
-
39
-
-
65549088576
-
Advances in the speed and resolution of light microscopy
-
Ji N, Shroff H, Zhong H, Betzig E (2008) Advances in the speed and resolution of light microscopy. Curr Opin Neurobiol 18(6): 605-616.
-
(2008)
Curr Opin Neurobiol
, vol.18
, Issue.6
, pp. 605-616
-
-
Ji, N.1
Shroff, H.2
Zhong, H.3
Betzig, E.4
-
40
-
-
31044441342
-
Division accuracy in a stochastic model of Min oscillations in Escherichia coli
-
Kerr RA, Levine H, Sejnowski TJ, Rappel W (2006) Division accuracy in a stochastic model of Min oscillations in Escherichia coli. Proc Natl Acad Sci USA 103(2): 347-352.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, Issue.2
, pp. 347-352
-
-
Kerr, R.A.1
Levine, H.2
Sejnowski, T.J.3
Rappel, W.4
-
41
-
-
0033038056
-
The dimerization and topological specificity functions of MinE reside in a structurally autonomous C-terminal domain
-
King GF, Rowland SL, Pan B, Mackay JP, Mullen GP, Rothfield LI (1999) The dimerization and topological specificity functions of MinE reside in a structurally autonomous C-terminal domain. Mol Microbiol 31(4): 1161-1169.
-
(1999)
Mol Microbiol
, vol.31
, Issue.4
, pp. 1161-1169
-
-
King, G.F.1
Rowland, S.L.2
Pan, B.3
Mackay, J.P.4
Mullen, G.P.5
Rothfield, L.I.6
-
42
-
-
0033756302
-
Structural basis for the topological specificity function of MinE
-
King GF, Shih YL, Maciejewski MW, Bains NP, Pan B, Rowland SL, Mullen GP, Rothfield LI (2000) Structural basis for the topological specificity function of MinE. Nat Struct Biol 7(11): 1013-1017.
-
(2000)
Nat Struct Biol
, vol.7
, Issue.11
, pp. 1013-1017
-
-
King, G.F.1
Shih, Y.L.2
Maciejewski, M.W.3
Bains, N.P.4
Pan, B.5
Rowland, S.L.6
Mullen, G.P.7
Rothfield, L.I.8
-
43
-
-
68949103682
-
Stochastic simulation of signal transduction: Impact of the cellular architecture on diffusion
-
Klann MT, Lapin A, Reuss M (2009) Stochastic simulation of signal transduction: impact of the cellular architecture on diffusion. Biophys J 96(12): 5122-5129.
-
(2009)
Biophys J
, vol.96
, Issue.12
, pp. 5122-5129
-
-
Klann, M.T.1
Lapin, A.2
Reuss, M.3
-
44
-
-
0036154068
-
A dynamic model for determining the middle of Escherichia coli
-
Kruse K (2002) A dynamic model for determining the middle of Escherichia coli. Biophys J 82(2): 618-627.
-
(2002)
Biophys J
, vol.82
, Issue.2
, pp. 618-627
-
-
Kruse, K.1
-
45
-
-
44049091101
-
Spatial regulators for bacterial cell division self-organize into surface waves in vitro
-
Loose M, Fischer-Friedrich E, Ries J, Kruse K, Schwille P (2008) Spatial regulators for bacterial cell division self-organize into surface waves in vitro. Science 320(5877): 789-792.
-
(2008)
Science
, vol.320
, Issue.5877
, pp. 789-792
-
-
Loose, M.1
Fischer-Friedrich, E.2
Ries, J.3
Kruse, K.4
Schwille, P.5
-
46
-
-
34548630230
-
Assembly dynamics of the bacterial MinCDE system and spatial regulation of the Z ring
-
Lutkenhaus J (2007) Assembly dynamics of the bacterial MinCDE system and spatial regulation of the Z ring. Annu Rev Biochem 76: 539-562.
-
(2007)
Annu Rev Biochem
, vol.76
, pp. 539-562
-
-
Lutkenhaus, J.1
-
47
-
-
0041530044
-
Mapping the MinE site involved in interaction with the MinD division site selection protein of Escherichia coli
-
Ma L, King G, Rothfield L (2003) Mapping the MinE site involved in interaction with the MinD division site selection protein of Escherichia coli. J Bacteriol 185(16): 4948-4955.
-
(2003)
J Bacteriol
, vol.185
, Issue.16
, pp. 4948-4955
-
-
Ma, L.1
King, G.2
Rothfield, L.3
-
48
-
-
22244444522
-
Min-oscillations in Escherichia coli induced by interactions of membrane-bound proteins
-
Meacci G, Kruse K (2005) Min-oscillations in Escherichia coli induced by interactions of membrane-bound proteins. Phys Biol 2(2): 89-97.
-
(2005)
Phys Biol
, vol.2
, Issue.2
, pp. 89-97
-
-
Meacci, G.1
Kruse, K.2
-
49
-
-
33846998421
-
Mobility of Min- proteins in Escherichia coli measured by fluorescence correlation spectroscopy
-
Meacci G, Ries J, Fischer-Friedrich E, Kahya N, Schwille P, Kruse K (2006) Mobility of Min- proteins in Escherichia coli measured by fluorescence correlation spectroscopy. Phys Biol 3(4): 255-263.
-
(2006)
Phys Biol
, vol.3
, Issue.4
, pp. 255-263
-
-
Meacci, G.1
Ries, J.2
Fischer-Friedrich, E.3
Kahya, N.4
Schwille, P.5
Kruse, K.6
-
50
-
-
0035807879
-
Pattern formation in Escherichia coli: A model for the pole-to-pole oscillations of Min proteins and the localization of the division site
-
Meinhardt H, de Boer PA (2001) Pattern formation in Escherichia coli: a model for the pole-to-pole oscillations of Min proteins and the localization of the division site. Proc Natl Acad Sci USA 98(25): 14202-14207.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, Issue.25
, pp. 14202-14207
-
-
Meinhardt, H.1
de Boer, P.A.2
-
51
-
-
0035815743
-
The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media
-
Minton A (2001) The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media. J Biol Chem 276(14): 10577-10580.
-
(2001)
J Biol Chem
, vol.276
, Issue.14
, pp. 10577-10580
-
-
Minton, A.1
-
52
-
-
50649105102
-
Toward a biomechanical understanding of whole bacterial cells
-
Morris DM, Jensen GJ (2008) Toward a biomechanical understanding of whole bacterial cells. Annu Rev Biochem 77: 583-613.
-
(2008)
Annu Rev Biochem
, vol.77
, pp. 583-613
-
-
Morris, D.M.1
Jensen, G.J.2
-
53
-
-
65549085736
-
Models of spatially restricted biochemical reaction systems
-
Neves SR, Iyengar R (2009) Models of spatially restricted biochemical reaction systems. J Biol Chem 284(9): 5445-5449.
-
(2009)
J Biol Chem
, vol.284
, Issue.9
, pp. 5445-5449
-
-
Neves, S.R.1
Iyengar, R.2
-
54
-
-
43049156015
-
Cell shape and negative links in regulatory motifs together control spatial information flow in signaling networks
-
Neves SR, Tsokas P, Sarkar A, Grace EA, Rangamani P, Taubenfeld SM, Alberini CM, Schaff JC, Blitzer RD, Moraru II, Iyengar R (2008) Cell shape and negative links in regulatory motifs together control spatial information flow in signaling networks. Cell 133(4): 666-680.
-
(2008)
Cell
, vol.133
, Issue.4
, pp. 666-680
-
-
Neves, S.R.1
Tsokas, P.2
Sarkar, A.3
Grace, E.A.4
Rangamani, P.5
Taubenfeld, S.M.6
Alberini, C.M.7
Schaff, J.C.8
Blitzer, R.D.9
Moraru, I.I.10
Iyengar, R.11
-
55
-
-
33344473476
-
Min-protein oscillations in Escherichia coli with spontaneous formation of two-stranded filaments in a three-dimensional stochastic reaction-diffusion model
-
Pavin N, Paljetak HC, Krstict V (2006) Min-protein oscillations in Escherichia coli with spontaneous formation of two-stranded filaments in a three-dimensional stochastic reaction-diffusion model. Phys Rev E 73(2 Pt 1): 021904.
-
(2006)
Phys Rev E
, vol.73
, Issue.2 PART 1
, pp. 021904
-
-
Pavin, N.1
Paljetak, H.C.2
Krstict, V.3
-
56
-
-
0028784405
-
Deletion analysis of gene minE which encodes the topological specificity factor of cell division in Escherichia coli
-
Pichoff S, Vollrath B, Touriol C, Bouche JP (1995) Deletion analysis of gene minE which encodes the topological specificity factor of cell division in Escherichia coli. Mol Microbiol 18(2): 321-329.
-
(1995)
Mol Microbiol
, vol.18
, Issue.2
, pp. 321-329
-
-
Pichoff, S.1
Vollrath, B.2
Touriol, C.3
Bouche, J.P.4
-
57
-
-
0035890437
-
Three-dimensional simulations of reversible bimolecular reactions: The simple target problem
-
Popov AV, Agmon N (2001) Three-dimensional simulations of reversible bimolecular reactions: The simple target problem. J Chem Phys 115(19): 8921-8932.
-
(2001)
J Chem Phys
, vol.115
, Issue.19
, pp. 8921-8932
-
-
Popov, A.V.1
Agmon, N.2
-
58
-
-
0037159085
-
Exact solution for the geminate ABCD reaction
-
Popov AV, Agmon N (2002) Exact solution for the geminate ABCD reaction. J Chem Phys 117(12): 5770-5779.
-
(2002)
J Chem Phys
, vol.117
, Issue.12
, pp. 5770-5779
-
-
Popov, A.V.1
Agmon, N.2
-
59
-
-
33645678291
-
Conformation of the cell division regulator MinE: Evidence for interactions between the topological specificity and anti-MinCD domains
-
Ramos D, Ducat T, Cheng J, Eng NF, Dillon JR, Goto NK (2006) Conformation of the cell division regulator MinE: evidence for interactions between the topological specificity and anti-MinCD domains. Biochemistry 45(14): 4593-4601.
-
(2006)
Biochemistry
, vol.45
, Issue.14
, pp. 4593-4601
-
-
Ramos, D.1
Ducat, T.2
Cheng, J.3
Eng, N.F.4
Dillon, J.R.5
Goto, N.K.6
-
60
-
-
58149237830
-
Modelling cellular signalling systems
-
Rangamani P, Iyengar R (2008) Modelling cellular signalling systems. Essays Biochem 45: 83-94.
-
(2008)
Essays Biochem
, vol.45
, pp. 83-94
-
-
Rangamani, P.1
Iyengar, R.2
-
61
-
-
67651207661
-
The molecular basis of excitation and adaptation during chemotactic sensory transduction in bacteria
-
Rao CV, Ordal GW (2009) The molecular basis of excitation and adaptation during chemotactic sensory transduction in bacteria. Contrib Microbiol 16: 33-64.
-
(2009)
Contrib Microbiol
, vol.16
, pp. 33-64
-
-
Rao, C.V.1
Ordal, G.W.2
-
62
-
-
0030780085
-
The MinE ring: An FtsZ-independent cell structure required for selection of the correct division site in E. coli
-
Raskin DM, de Boer PA (1997) The MinE ring: an FtsZ-independent cell structure required for selection of the correct division site in E. coli. Cell 91(5): 685-694.
-
(1997)
Cell
, vol.91
, Issue.5
, pp. 685-694
-
-
Raskin, D.M.1
de Boer, P.A.2
-
63
-
-
0033609139
-
Rapid pole-to-pole oscillation of a protein required for directing division to the middle of Escherichia coli
-
Raskin DM, de Boer PA (1999) Rapid pole-to-pole oscillation of a protein required for directing division to the middle of Escherichia coli. Proc Natl Acad Sci USA 96(9): 4971-4976.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, Issue.9
, pp. 4971-4976
-
-
Raskin, D.M.1
de Boer, P.A.2
-
64
-
-
50849104529
-
Quantum dots versus organic dyes as fluorescent labels
-
Resch-Genger U, Grabolle M, Cavaliere-Jaricot S, Nitschke R, Nann T (2008) Quantum dots versus organic dyes as fluorescent labels. Nat Methods 5(9): 763-775.
-
(2008)
Nat Methods
, vol.5
, Issue.9
, pp. 763-775
-
-
Resch-Genger, U.1
Grabolle, M.2
Cavaliere-Jaricot, S.3
Nitschke, R.4
Nann, T.5
-
65
-
-
33748972985
-
Accommodating space, time and randomness in network simulation
-
Ridgway D, Broderick G, Ellison MJ (2006) Accommodating space, time and randomness in network simulation. Curr Opin Biotechnol 17(5): 493-498.
-
(2006)
Curr Opin Biotechnol
, vol.17
, Issue.5
, pp. 493-498
-
-
Ridgway, D.1
Broderick, G.2
Ellison, M.J.3
-
66
-
-
43849103490
-
Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm
-
Ridgway D, Broderick G, Lopez-Campistrous A, Ru'aini M, Winter P, Hamilton M, Boulanger P, Kovalenko A, Ellison MJ (2008) Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm. Biophys J 94(10): 3748-3759.
-
(2008)
Biophys J
, vol.94
, Issue.10
, pp. 3748-3759
-
-
Ridgway, D.1
Broderick, G.2
Lopez-Campistrous, A.3
Ru'aini, M.4
Winter, P.5
Hamilton, M.6
Boulanger, P.7
Kovalenko, A.8
Ellison, M.J.9
-
67
-
-
33747829956
-
Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli
-
Rodriguez JV, Kaandorp JA, Dobrzyki M, Blom JG (2006) Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli. Bioinformatics 22(15): 1895-1901.
-
(2006)
Bioinformatics
, vol.22
, Issue.15
, pp. 1895-1901
-
-
Rodriguez, J.V.1
Kaandorp, J.A.2
Dobrzyki, M.3
Blom, J.G.4
-
68
-
-
0033983163
-
Membrane redistribution of the Escherichia coli MinD protein induced by MinE
-
Rowland SL, Fu X, Sayed MA, Zhang Y, Cook WR, Rothfield LI (2000) Membrane redistribution of the Escherichia coli MinD protein induced by MinE. J Bacteriol 182(3): 613-619.
-
(2000)
J Bacteriol
, vol.182
, Issue.3
, pp. 613-619
-
-
Rowland, S.L.1
Fu, X.2
Sayed, M.A.3
Zhang, Y.4
Cook, W.R.5
Rothfield, L.I.6
-
69
-
-
33751377585
-
Cell++-simulating biochemical pathways
-
Sanford C, Yip MLK, White C, Parkinson J (2006) Cell++-simulating biochemical pathways. Bioinformatics 22(23): 2918-2925.
-
(2006)
Bioinformatics
, vol.22
, Issue.23
, pp. 2918-2925
-
-
Sanford, C.1
Yip, M.L.K.2
White, C.3
Parkinson, J.4
-
70
-
-
0347057016
-
Analysis of nonlinear dynamics on arbitrary geometries with the Virtual Cell
-
Schaff JC, Slepchenko BM, Choi Y, Wagner J, Resasco D, Loew LM (2001) Analysis of nonlinear dynamics on arbitrary geometries with the Virtual Cell. Chaos 11(1): 115-131.
-
(2001)
Chaos
, vol.11
, Issue.1
, pp. 115-131
-
-
Schaff, J.C.1
Slepchenko, B.M.2
Choi, Y.3
Wagner, J.4
Resasco, D.5
Loew, L.M.6
-
71
-
-
34249028789
-
Analysis of actin filament network organization in lamellipodia by comparing experimental and simulated images
-
Schaub S, Meister J, Verkhovsky AB (2007) Analysis of actin filament network organization in lamellipodia by comparing experimental and simulated images. J Cell Sci 120(Pt 8): 1491-1500.
-
(2007)
J Cell Sci
, vol.120
, Issue.PART 8
, pp. 1491-1500
-
-
Schaub, S.1
Meister, J.2
Verkhovsky, A.B.3
-
72
-
-
0036646101
-
Division site placement in E. coli: Mutations that prevent formation of the MinE ring lead to loss of the normal midcell arrest of growth of polar MinD membrane domains
-
Shih Y, Fu X, King GF, Le T, Rothfield L (2002) Division site placement in E. coli: mutations that prevent formation of the MinE ring lead to loss of the normal midcell arrest of growth of polar MinD membrane domains. EMBO J 21(13): 3347-3357.
-
(2002)
EMBO J
, vol.21
, Issue.13
, pp. 3347-3357
-
-
Shih, Y.1
Fu, X.2
King, G.F.3
Le, T.4
Rothfield, L.5
-
73
-
-
0037699937
-
Division site selection in Escherichia coli involves dynamic redistribution of Min proteins within coiled structures that extend between the two cell poles
-
Shih Y, Le T, Rothfield L (2003) Division site selection in Escherichia coli involves dynamic redistribution of Min proteins within coiled structures that extend between the two cell poles. Proc Natl Acad Sci USA 100(13): 7865-7870.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, Issue.13
, pp. 7865-7870
-
-
Shih, Y.1
Le, T.2
Rothfield, L.3
-
74
-
-
49449096617
-
An allosteric model of calmodulin explains differential activation of PP2B and CaMKII
-
Stefan MI, Edelstein SJ, Novere NL (2008) An allosteric model of calmodulin explains differential activation of PP2B and CaMKII. Proc Natl Acad Sci USA 105(31): 10768-10773.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, Issue.31
, pp. 10768-10773
-
-
Stefan, M.I.1
Edelstein, S.J.2
Novere, N.L.3
-
75
-
-
85057660342
-
Monte Carlo methods for simulating realistic synaptic microphysiology using MCell
-
In: Schutter ED (ed), CRC Press, Boca Raton
-
Stiles JR, Bartol TM (2001) Monte Carlo methods for simulating realistic synaptic microphysiology using MCell. In: Schutter ED (ed) Computational neuroscience: realistic modeling for experimentalists, CRC Press, Boca Raton, pp 87-127.
-
(2001)
Computational Neuroscience: Realistic Modeling for Experimentalists
, pp. 87-127
-
-
Stiles, J.R.1
Bartol, T.M.2
-
76
-
-
0004491955
-
Nonequilibrium distribution function formalism for diffusion-influenced bimolecular reactions: Beyond the superposition approximation
-
Sung J, Lee S (1999) Nonequilibrium distribution function formalism for diffusion-influenced bimolecular reactions: Beyond the superposition approximation. J Chem Phys 111(3): 796-803.
-
(1999)
J Chem Phys
, vol.111
, Issue.3
, pp. 796-803
-
-
Sung, J.1
Lee, S.2
-
77
-
-
0000553448
-
Theory of diffusion-influenced fluorescence quenching
-
Szabo A (1989) Theory of diffusion-influenced fluorescence quenching. J Phys Chem 93(19): 6929-6939.
-
(1989)
J Phys Chem
, vol.93
, Issue.19
, pp. 6929-6939
-
-
Szabo, A.1
-
79
-
-
1542400036
-
A multi-algorithm, multi-timescale method for cell simulation
-
Takahashi K, Kaizu K, Hu B, Tomita M (2004) A multi-algorithm, multi-timescale method for cell simulation. Bioinformatics 20(4): 538-546.
-
(2004)
Bioinformatics
, vol.20
, Issue.4
, pp. 538-546
-
-
Takahashi, K.1
Kaizu, K.2
Hu, B.3
Tomita, M.4
-
80
-
-
14844321288
-
Space in systems biology of signaling pathways-towards intracellular molecular crowding in silico
-
Takahashi K, Arjunan SNV, Tomita M (2005) Space in systems biology of signaling pathways-towards intracellular molecular crowding in silico. FEBS Lett 579(8): 1783-1788.
-
(2005)
FEBS Lett
, vol.579
, Issue.8
, pp. 1783-1788
-
-
Takahashi, K.1
Arjunan, S.N.V.2
Tomita, M.3
-
81
-
-
76149105004
-
Spatio-temporal correlations can drastically change the response of a MAPK pathway
-
(in press)
-
Takahashi K, Tanase-Nicola S, ten Wolde PR (2009) Spatio-temporal correlations can drastically change the response of a MAPK pathway. Proc Natl Acad Sci USA (in press).
-
(2009)
Proc Natl Acad Sci USA
-
-
Takahashi, K.1
Tanase-Nicola, S.2
ten Wolde, P.R.3
-
82
-
-
33645549945
-
A stochastic model of Min oscillations in Escherichia coli and Min protein segregation during cell division
-
Tostevin F, Howard M (2006) A stochastic model of Min oscillations in Escherichia coli and Min protein segregation during cell division. Phys Biol 3(1): 1-12.
-
(2006)
Phys Biol
, vol.3
, Issue.1
, pp. 1-12
-
-
Tostevin, F.1
Howard, M.2
-
83
-
-
34548041173
-
Mechanistic insight into lymphocyte activation through quantitative imaging and theoretical modelling
-
Treanor B, Batista FD (2007) Mechanistic insight into lymphocyte activation through quantitative imaging and theoretical modelling. Curr Opin Immunol 19(4): 476-483.
-
(2007)
Curr Opin Immunol
, vol.19
, Issue.4
, pp. 476-483
-
-
Treanor, B.1
Batista, F.D.2
-
84
-
-
67149133373
-
Differential affinity and catalytic activity of CheZ in E. coli chemotaxis
-
van Albada SB, ten Wolde PR (2009) Differential affinity and catalytic activity of CheZ in E. coli chemotaxis. PLoS Comput Biol 5(5): e1000378.
-
(2009)
PLoS Comput Biol
, vol.5
, Issue.5
-
-
van Albada, S.B.1
ten Wolde, P.R.2
-
85
-
-
29244454300
-
Green's-function reaction dynamics: A particle based approach for simulating biochemical networks in time and space
-
van Zon JS, ten Wolde PR (2005) Green's-function reaction dynamics: a particle based approach for simulating biochemical networks in time and space. J Chem Phys 123(23): 234910.
-
(2005)
J Chem Phys
, vol.123
, Issue.23
, pp. 234910
-
-
van Zon, J.S.1
ten Wolde, P.R.2
-
86
-
-
70350493966
-
The dynamic nature of the bacterial cytoskeleton
-
Vats P, Yu J, Rothfield L (2009) The dynamic nature of the bacterial cytoskeleton. Cell Mol Life Sci 66(20): 3353-3362.
-
(2009)
Cell Mol Life Sci
, vol.66
, Issue.20
, pp. 3353-3362
-
-
Vats, P.1
Yu, J.2
Rothfield, L.3
-
87
-
-
0000267310
-
Versuch einer mathematischen Theorie der Koagulationskinetik kolloider Lsungen
-
von Smoluchowski M (1917) Versuch einer mathematischen Theorie der Koagulationskinetik kolloider Lsungen. Z Phys Chem, Stoechiom Verwandtschaftsl 92: 129-168.
-
(1917)
Z Phys Chem, Stoechiom Verwandtschaftsl
, vol.92
, pp. 129-168
-
-
von Smoluchowski, M.1
-
88
-
-
77950545445
-
STEPS: Modeling and simulating complex reaction-diffusion systems with Python
-
Wils S, Schutter ED (2009) STEPS: modeling and simulating complex reaction-diffusion systems with Python. Front Neuroinformatics 3: 15.
-
(2009)
Front Neuroinformatics
, vol.3
, pp. 15
-
-
Wils, S.1
Schutter, E.D.2
-
89
-
-
0025098776
-
Role of the nucleoid in the toporegulation of division
-
Woldringh CL, Mulder E, Valkenburg JA, Wientjes FB, Zaritsky A, Nanninga N (1990) Role of the nucleoid in the toporegulation of division. Res Microbiol 141(1): 39-49.
-
(1990)
Res Microbiol
, vol.141
, Issue.1
, pp. 39-49
-
-
Woldringh, C.L.1
Mulder, E.2
Valkenburg, J.A.3
Wientjes, F.B.4
Zaritsky, A.5
Nanninga, N.6
-
90
-
-
0025813235
-
Toporegulation of bacterial division according to the nucleoid occlusion model
-
Woldringh CL, Mulder E, Huls PG, Vischer N (1991) Toporegulation of bacterial division according to the nucleoid occlusion model. Res Microbiol 142(2-3): 309-320.
-
(1991)
Res Microbiol
, vol.142
, Issue.2-3
, pp. 309-320
-
-
Woldringh, C.L.1
Mulder, E.2
Huls, P.G.3
Vischer, N.4
-
91
-
-
0031753463
-
The relationship between hetero-oligomer formation and function of the topological specificity domain of the Escherichia coli MinE protein
-
Zhang Y, Rowland S, King G, Braswell E, Rothfield L (1998) The relationship between hetero-oligomer formation and function of the topological specificity domain of the Escherichia coli MinE protein. Mol Microbiol 30(2): 265-273.
-
(1998)
Mol Microbiol
, vol.30
, Issue.2
, pp. 265-273
-
-
Zhang, Y.1
Rowland, S.2
King, G.3
Braswell, E.4
Rothfield, L.5
-
92
-
-
67649314133
-
Crowding Effects of Membrane Proteins
-
Zhou H (2009) Crowding Effects of Membrane Proteins. J Phys Chem B 113(23): 7995-8005.
-
(2009)
J Phys Chem B
, vol.113
, Issue.23
, pp. 7995-8005
-
-
Zhou, H.1
-
93
-
-
1342346602
-
The switch I and II regions of MinD are required for binding and activating MinC
-
Zhou H, Lutkenhaus J (2004) The switch I and II regions of MinD are required for binding and activating MinC. J Bacteriol 186(5): 1546-1555.
-
(2004)
J Bacteriol
, vol.186
, Issue.5
, pp. 1546-1555
-
-
Zhou, H.1
Lutkenhaus, J.2
-
94
-
-
11844251354
-
Analysis of MinD mutations reveals residues required for MinE stimulation of the MinD ATPase and residues required for MinC interaction
-
Zhou H, Schulze R, Cox S, Saez C, Hu Z, Lutkenhaus J (2005) Analysis of MinD mutations reveals residues required for MinE stimulation of the MinD ATPase and residues required for MinC interaction. J Bacteriol 187(2): 629-638.
-
(2005)
J Bacteriol
, vol.187
, Issue.2
, pp. 629-638
-
-
Zhou, H.1
Schulze, R.2
Cox, S.3
Saez, C.4
Hu, Z.5
Lutkenhaus, J.6
-
95
-
-
0026344818
-
Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli
-
Zimmerman S, Trach S (1991) Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli. J Mol Biol 222(3): 599-620.
-
(1991)
J Mol Biol
, vol.222
, Issue.3
, pp. 599-620
-
-
Zimmerman, S.1
Trach, S.2
|