-
1
-
-
38149049951
-
Models for synthetic biology
-
Y.N. Kaznessis, "Models for Synthetic Biology," BMC Systems Biology, vol.1, p. 47, 2007.
-
(2007)
BMC Systems Biology
, vol.1
, pp. 47
-
-
Kaznessis, Y.N.1
-
2
-
-
19544379881
-
Stochasticity in gene expression: From theories to phenotypes
-
DOI 10.1038/nrg1615
-
M. Kaern, T.C. Elston, W.J. Blake, and J.J. Collins, "Stochasticity in Gene Expression: From Theories to Phenotypes," Nature Rev. Genetics, vol.6, pp. 451-464, 2005. (Pubitemid 40733890)
-
(2005)
Nature Reviews Genetics
, vol.6
, Issue.6
, pp. 451-464
-
-
Kaern, M.1
Elston, T.C.2
Blake, W.J.3
Collins, J.J.4
-
3
-
-
27844576653
-
Multi-scale models for gene network engineering
-
Y.N. Kaznessis, "Multi-Scale Models for Gene Network Engineering," Chemical Eng. Science, vol.61, pp. 940-953, 2006.
-
(2006)
Chemical Eng. Science
, vol.61
, pp. 940-953
-
-
Kaznessis, Y.N.1
-
4
-
-
0036405165
-
Fifteen minutes of fim: Control of type 1 pili expression in E. coli
-
D.M. Wolf and A.P. Arkin, "Fifteen Minutes of Fim: Control of Type 1 Pili Expression in E. coli," Omics, vol.6, pp. 91-114, 2002.
-
(2002)
Omics
, vol.6
, pp. 91-114
-
-
Wolf, D.M.1
Arkin, A.P.2
-
5
-
-
15744378289
-
Numerical simulation of stochastic gene circuits
-
DOI 10.1016/j.compchemeng.2004.08.017, PII S0098135404002467, Computational Challenges in Biology
-
H. Salis and Y. Kaznessis, "Numerical Simulation of Stochastic Gene Circuits," Computers and Chemical Eng., vol.29, pp. 577-588, 2005. (Pubitemid 40417804)
-
(2005)
Computers and Chemical Engineering
, vol.29
, Issue.3
, pp. 577-588
-
-
Salis, H.1
Kaznessis, Y.2
-
6
-
-
27844563625
-
Model-driven designs of an oscillating gene network
-
DOI 10.1529/biophysj.105.064204
-
L. Tuttle, H. Salis, J. Tomshine, and Y.N. Kaznessis, "Model- Driven Designs of an Oscillating Gene Network," Biophysical J., vol.89, no.6, pp. 3873-3883, Dec. 2005. (Pubitemid 41725609)
-
(2005)
Biophysical Journal
, vol.89
, Issue.6
, pp. 3873-3883
-
-
Tuttle, L.M.1
Salis, H.2
Tomshine, J.3
Kaznessis, Y.N.4
-
7
-
-
34447518290
-
Synthetic tetracycline inducible regulatory networks: Computer-aided design of dynamic phenotypes
-
V. Sotiropoulos and Y. Kaznessis, "Synthetic Tetracycline Inducible Regulatory Networks: Computer-Aided Design of Dynamic Phenotypes," BMC Systems Biology, vol.1, p. 7, 2007.
-
(2007)
BMC Systems Biology
, vol.1
, pp. 7
-
-
Sotiropoulos, V.1
Kaznessis, Y.2
-
8
-
-
34247517470
-
Computer-aided design of modular protein devices: Boolean AND gene activation
-
DOI 10.1088/1478-3975/3/4/007, PII S1478397506253391, 007
-
H. Salis and Y.N. Kaznessis, "Computer-Aided Design of Modular Protein Devices: Boolean AND Gene Activation," Physical Biology, vol.3, pp. 295-310, 2006. (Pubitemid 46646260)
-
(2006)
Physical Biology
, vol.3
, Issue.4
, pp. 295-310
-
-
Salis, H.1
Kaznessis, Y.N.2
-
9
-
-
0037119587
-
Stochastic gene expression in a single cell
-
DOI 10.1126/science.1070919
-
M.B. Elowitz, A.J. Levine, E.D. Siggia, and P.S. Swain, "Stochastic Gene Expression in a Single Cell," Science, vol.297, pp. 1183-1186, 2002. (Pubitemid 36193353)
-
(2002)
Science
, vol.297
, Issue.5584
, pp. 1183-1186
-
-
Elowitz, M.B.1
Levine, A.J.2
Siggia, E.D.3
Swain, P.S.4
-
10
-
-
0017030517
-
A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
-
D.T. Gillespie, "A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions," J. Computational Physics, vol.22, pp. 403-434, 1976.
-
(1976)
J. Computational Physics
, vol.22
, pp. 403-434
-
-
Gillespie, D.T.1
-
11
-
-
33645429016
-
Exact stochastic simulation of coupled chemical reactions
-
D.T. Gillespie, "Exact Stochastic Simulation of Coupled Chemical Reactions," J. Physical Chemistry, vol.81, pp. 2340-2361, 1977.
-
(1977)
J. Physical Chemistry
, vol.81
, pp. 2340-2361
-
-
Gillespie, D.T.1
-
12
-
-
0001144902
-
Efficient exact stochastic simulation of chemical systems with many species and many channels
-
M.A. Gibson and J. Bruck, "Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels," J. Physical Chemistry A, vol.104, pp. 1876-1889, 2000.
-
(2000)
J. Physical Chemistry A
, vol.104
, pp. 1876-1889
-
-
Gibson, M.A.1
Bruck, J.2
-
13
-
-
0035933994
-
Approximate accelerated stochastic simulation of chemically reacting systems
-
D.T. Gillespie, "Approximate Accelerated Stochastic Simulation of Chemically Reacting Systems," J. Chemical Physics, vol.115, pp. 1716-1733, 2001.
-
(2001)
J. Chemical Physics
, vol.115
, pp. 1716-1733
-
-
Gillespie, D.T.1
-
14
-
-
0037444724
-
Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the gillespie algorithm
-
C.V. Rao and A.P. Arkin, "Stochastic Chemical Kinetics and the Quasi-Steady-State Assumption: Application to the Gillespie Algorithm," J. Chemical Physics, vol.118, pp. 4999-5010, 2003.
-
(2003)
J. Chemical Physics
, vol.118
, pp. 4999-5010
-
-
Rao, C.V.1
Arkin, A.P.2
-
15
-
-
33645463036
-
An equation-free probabilistic steady-state approximation: Dynamic application to the stochastic simulation of biochemical reaction networks
-
H. Salis and Y.N. Kaznessis, "An Equation-Free Probabilistic Steady-State Approximation: Dynamic Application to the Stochastic Simulation of Biochemical Reaction Networks," J. Chemical Physics, vol.123, p. 214106, 2005.
-
(2005)
J. Chemical Physics
, vol.123
, pp. 214106
-
-
Salis, H.1
Kaznessis, Y.N.2
-
16
-
-
22944451159
-
Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions
-
DOI 10.1063/1.1835951, 054103
-
H. Salis and Y. Kaznessis, "Accurate Hybrid Stochastic Simulation of a System of Coupled Chemical or Biochemical Reactions," J. Chemical Physics, vol.122, p. 54103, 2005. (Pubitemid 41047527)
-
(2005)
Journal of Chemical Physics
, vol.122
, Issue.5
, pp. 1-13
-
-
Salis, H.1
Kaznessis, Y.2
-
17
-
-
26944450876
-
Overcoming stiffness in stochastic simulation stemming from partial equilibrium: A multiscale Monte Carlo algorithm
-
DOI 10.1063/1.2046628, 144114
-
A. Samant and D.G. Vlachos, "Overcoming Stiffness in Stochastic Simulation Stemming from Partial Equilibrium: A Multiscale Monte Carlo Algorithm," J. Chemical Physics, vol.123, p. 144114, 2005. (Pubitemid 41476710)
-
(2005)
Journal of Chemical Physics
, vol.123
, Issue.14
, pp. 1-8
-
-
Samant, A.1
Vlachos, D.G.2
-
18
-
-
22944477377
-
The numerical stability of leaping methods for stochastic simulation of chemically reacting systems
-
DOI 10.1063/1.1823412
-
Y. Cao, H. Li, and L. Petzold, "Efficient Formulation of the Stochastic Simulation Algorithm for Chemically Reacting Systems," J. Chemical Physics, vol.121, pp. 4059-4067, 2004. (Pubitemid 41041575)
-
(2004)
Journal of Chemical Physics
, vol.121
, Issue.24
, pp. 12169-12178
-
-
Cao, Y.1
Petzold, L.R.2
Rathinam, M.3
Gillespie, D.T.4
-
19
-
-
22944480262
-
The slow-scale stochastic simulation algorithm
-
DOI 10.1063/1.1824902, 014116
-
Y. Cao, D.T. Gillespie, and L.R. Petzold, "The Slow-Scale Stochastic Simulation Algorithm," J. Chemical Physics, vol.122, p. 014116, 2005. (Pubitemid 41047759)
-
(2005)
Journal of Chemical Physics
, vol.122
, Issue.1
, pp. 1-18
-
-
Cao, Y.1
Gillespie, D.T.2
Petzold, L.R.3
-
20
-
-
3142543968
-
Binomial leap methods for simulating stochastic chemical kinetics
-
DOI 10.1063/1.1810475
-
T. Tian and K. Burrage, "Binomial Leap Methods for Simulating Stochastic Chemical Kinetics," J. Chemical Physics, vol.121, pp. 10356-10364, 2004. (Pubitemid 40001577)
-
(2004)
Journal of Chemical Physics
, vol.121
, Issue.21
, pp. 10356-10364
-
-
Tian, T.1
Burrage, K.2
-
21
-
-
27744516835
-
Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates
-
W.E, L. Di, and E.V. Eijnden, "Nested Stochastic Simulation Algorithm for Chemical Kinetic Systems with Disparate Rates," J. Chemical Physics, vol.123, p. 194107, 2005.
-
(2005)
J. Chemical Physics
, vol.123
, pp. 194107
-
-
W, E.1
Di, L.2
Eijnden, E.V.3
-
22
-
-
33751347484
-
The finite state projection algorithm for the solution of the chemical master equation
-
DOI 10.1063/1.2145882, 044104
-
B. Munsky and M. Khammash, "The Finite State Projection Algorithm for the Solution of the Chemical Master Equation," J. Chemical Physics, vol.124, p. 044104, 2006. (Pubitemid 43166302)
-
(2006)
Journal of Chemical Physics
, vol.124
, Issue.4
, pp. 1-13
-
-
Munsky, B.1
Khammash, M.2
-
23
-
-
0034225547
-
The chemical langevin equation
-
D.T. Gillespie, "The Chemical Langevin Equation," J. Chemical Physics, vol.113, pp. 297-306, 2000.
-
(2000)
J.Chemical Physics
, vol.113
, pp. 297-306
-
-
Gillespie, D.T.1
-
24
-
-
38049035399
-
An adaptive time step scheme for a system of stochastic differential equations with multiple multiplicative noise: Chemical langevin equation, a proof of concept
-
V. Sotiropoulos and Y.N. Kaznessis, "An Adaptive Time Step Scheme for a System of Stochastic Differential Equations with Multiple Multiplicative Noise: Chemical Langevin Equation, a Proof of Concept," J. Chemical Physics, vol.128, p. 014103, 2008.
-
(2008)
J. Chemical Physics
, vol.128
, pp. 014103
-
-
Sotiropoulos, V.1
Kaznessis, Y.N.2
-
25
-
-
0032025439
-
Simplification of mathematical models of chemical reaction systems
-
M.S. Okino and M.L. Mavrovouniotis, "Simplification of Mathematical Models of Chemical Reaction Systems," Chemical Rev., vol.98, pp. 391-408, 1998. (Pubitemid 128631432)
-
(1998)
Chemical Reviews
, vol.98
, Issue.2
, pp. 391-408
-
-
Okino, M.S.1
Mavrovouniotis, M.L.2
-
26
-
-
0005541614
-
Nonlinear model reduction of chemical reaction systems
-
DOI 10.1002/aic.690471016
-
P.D.N. Vora, "Nonlinear Model Reduction of Chemical Reaction Systems," AIChE J., vol.47, pp. 2320-2332, 2001. (Pubitemid 36858785)
-
(2001)
AIChE Journal
, vol.47
, Issue.10
, pp. 2320-2332
-
-
Vora, N.1
Daoutidis, P.2
-
27
-
-
2342567053
-
Non-linear reduction for kinetic models of metabolic reaction networks
-
DOI 10.1016/j.ymben.2003.11.003
-
Z.P. Gerdtzen, P. Daoutidis, and W.S. Hu, "Non-Linear Reduction for Kinetic Models of Metabolic Reaction Networks," Metabolic Eng., vol.6, pp. 140-154, 2004. (Pubitemid 38601067)
-
(2004)
Metabolic Engineering
, vol.6
, Issue.2
, pp. 140-154
-
-
Gerdtzen, Z.P.1
Daoutidis, P.2
Hu, W.-S.3
-
28
-
-
31144447003
-
Reduced-order modelling of biochemical networks: Application to the GTPase-cycle signalling module
-
DOI 10.1049/ip-syb:20050014
-
M.R. Maurya, S.J. Bornheimer, V. Venkatasubramanian, and S. Subramaniam, "Reduced-Order Modelling of Biochemical Networks: Application to the GTpase-Cycle Signalling Module," Systems Biology, IEE Proc., vol.152, no.4, pp. 229-242, Dec. 2005. (Pubitemid 43125141)
-
(2005)
IEE Proceedings Systems Biology
, vol.152
, Issue.4
, pp. 229-242
-
-
Maurya, M.R.1
Bornheimer, S.J.2
Venkatasubramanian, V.3
Subramaniam, S.4
-
29
-
-
0038311902
-
The convex basis of the left null space of the stoichiometric matrix leads to the definition of metabolically meaningful pools
-
I. Famili and B.O. Palsson, "The Convex Basis of the Left Null Space of the Stoichiometric Matrix Leads to the Definition of Metabolically Meaningful Pools," Biophysical J., vol.85, pp. 16-26, 2003. (Pubitemid 36753613)
-
(2003)
Biophysical Journal
, vol.85
, Issue.1
, pp. 16-26
-
-
Famili, I.1
Palsson, B.O.2
-
30
-
-
11244341009
-
Elucidation and structural analysis of conserved pools for genome-scale metabolic reconstructions
-
E.V. Nikolaev, A.P. Burgard, and C.D. Maranas, "Elucidation and Structural Analysis of Conserved Pools for Genome-Scale Metabolic Reconstructions," Biophysical J., vol.88, pp. 37-49, 2005.
-
(2005)
Biophysical J.
, vol.88
, pp. 37-49
-
-
Nikolaev, E.V.1
Burgard, A.P.2
Maranas, C.D.3
-
31
-
-
0002582794
-
The elimination of fast variables in complex chemical reactions. II. mesoscopic level (reducible case)
-
J.A.M. Janssen, "The Elimination of Fast Variables in Complex Chemical Reactions. II. Mesoscopic Level (Reducible Case)," J. Statistical Physics, vol.57, pp. 171-185, 1989.
-
(1989)
J. Statistical Physics
, vol.57
, pp. 171-185
-
-
Janssen, J.A.M.1
-
32
-
-
0011500833
-
The elimination of fast variables in complex chemical reactions. III. mesoscopic level (irreducible case)
-
J.A.M. Janssen, "The Elimination of Fast Variables in Complex Chemical Reactions. III. Mesoscopic Level (Irreducible Case)," J. Statistical Physics, vol.57, pp. 187-198, 1989.
-
(1989)
J. Statistical Physics
, vol.57
, pp. 187-198
-
-
Janssen, J.A.M.1
-
33
-
-
0142116225
-
Reducing the master equations for noisy chemical reactions
-
T. Shibata, "Reducing the Master Equations for Noisy Chemical Reactions," J. Chemical Physics, vol.119, pp. 6629-6634, 2003.
-
(2003)
J. Chemical Physics
, vol.119
, pp. 6629-6634
-
-
Shibata, T.1
-
34
-
-
33751347484
-
The finite state projection algorithm for the solution of the chemical master equation
-
DOI 10.1063/1.2145882, 044104
-
S. Peles, B. Munsky, and M. Khammash, "Reduction and Solution of the Chemical Master Equation Using Time Scale Separation and Finite State Projection," J. Chemical Physics, vol.125, p. 204104, 2006. (Pubitemid 43166302)
-
(2006)
Journal of Chemical Physics
, vol.124
, Issue.4
, pp. 1-13
-
-
Munsky, B.1
Khammash, M.2
-
35
-
-
18844402156
-
Quasiequilibrium approximation of fast reaction kinetics in stochastic biochemical systems
-
J. Goutsias, "Quasiequilibrium Approximation of Fast Reaction Kinetics in Stochastic Biochemical Systems," J. Chemical Physics, vol.122, p. 184102, 2005.
-
(2005)
J. Chemical Physics
, vol.122
, pp. 184102
-
-
Goutsias, J.1
-
36
-
-
34748883671
-
Simplification of stochastic chemical reaction models with fast and slow dynamics
-
DOI 10.1007/s10867-007-9043-2
-
G. Dong, L. Jakobowski, M. Iafolla, and D. McMillen, "Simplification of Stochastic Chemical Reaction Models with Fast and Slow Dynamics," J. Biological Physics, vol.33, pp. 67-95, 2007. (Pubitemid 47476586)
-
(2007)
Journal of Biological Physics
, vol.33
, Issue.1
, pp. 67-95
-
-
Dong, G.Q.1
Jakobowski, L.2
Iafolla, M.A.J.3
McMillen, D.R.4
-
38
-
-
34047202219
-
Decoupling of fast and slow variables in chemical Langevin equations with fast and slow reactions
-
1655396, Proceedings of the 2006 American Control Conference
-
M.N. Contou-Carrere and P. Daoutidis, "Decoupling of Fast and Slow Variables in Chemical Langevin Equations with Fast and Slow Reactions," Proc. Am. Control Conf., 2006. (Pubitemid 46530851)
-
(2006)
Proceedings of the American Control Conference
, vol.2006
, pp. 442-447
-
-
Contou-Carrere, M.-N.1
Daoutidis, P.2
-
40
-
-
33645465102
-
Multiscale hy3s: Hybrid stochastic simulation for supercomputers
-
H. Salis, V. Sotiropoulos, and Y.N. Kaznessis, "Multiscale Hy3S: Hybrid Stochastic Simulation for Supercomputers," BMC Bioinfor- matics, vol.7, p. 93, 2006.
-
(2006)
BMC Bioinfor- Matics
, vol.7
, pp. 93
-
-
Salis, H.1
Sotiropoulos, V.2
Kaznessis, Y.N.3
-
41
-
-
54949133752
-
Synbioss: The synthetic biology modeling suite
-
A.D. Hill, J.R. Tomshine, E.M.B. Weeding, V. Sotiropoulos, and Y.N. Kaznessis, "SynBioSS: The Synthetic Biology Modeling Suite," Bioinformatics, vol.24, pp. 2551-2553, 2008.
-
(2008)
Bioinformatics
, vol.24
, pp. 2551-2553
-
-
Hill, A.D.1
Tomshine, J.R.2
Weeding, E.M.B.3
Sotiropoulos, V.4
Kaznessis, Y.N.5
-
43
-
-
0031569865
-
Sorbitol dehydrogenase from bovine lens: Purification and properties
-
DOI 10.1006/abbi.1997.9882
-
I. Marini, L. Bucchioni, P. Borella, A.D. Corso, and U. Mura, "Sorbitol Dehydrogenase from Bovine Lens: Purification and Properties," Archives Biochemistry and Biophysics, vol.340, pp. 383-391, 1997. (Pubitemid 27200549)
-
(1997)
Archives of Biochemistry and Biophysics
, vol.340
, Issue.2
, pp. 383-391
-
-
Marini, I.1
Bucchioni, L.2
Borella, P.3
Corso, A.D.4
Mura, U.5
|