相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。Discreteness-induced concentration inversion in mesoscopic chemical systems
Rajesh Ramaswamy et al.
NATURE COMMUNICATIONS (2012)
The Moderately Efficient Enzyme: Evolutionary and Physicochemical Trends Shaping Enzyme Parameters
Arren Bar-Even et al.
BIOCHEMISTRY (2011)
StochKit2: software for discrete stochastic simulation of biochemical systems with events
Kevin R. Sanft et al.
BIOINFORMATICS (2011)
Efficient Formulations for Exact Stochastic Simulation of Chemical Systems
Sean Mauch et al.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2011)
How accurate are the nonlinear chemical Fokker-Planck and chemical Langevin equations?
Ramon Grima et al.
JOURNAL OF CHEMICAL PHYSICS (2011)
Intrinsic noise alters the frequency spectrum of mesoscopic oscillatory chemical reaction systems
Rajesh Ramaswamy et al.
SCIENTIFIC REPORTS (2011)
CellMC-a multiplatform model compiler for the Cell Broadband Engine and x86
Emmet Caulfield et al.
BIOINFORMATICS (2010)
Elucidating Cytochrome c Release from Mitochondria: Insights from an In Silico Three-Dimensional Model
Zhi Yang Tam et al.
BIOPHYSICAL JOURNAL (2010)
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
Chen Li et al.
BMC SYSTEMS BIOLOGY (2010)
Stochastic theory of large-scale enzyme-reaction networks: Finite copy number corrections to rate equation models
Philipp Thomas et al.
JOURNAL OF CHEMICAL PHYSICS (2010)
An effective rate equation approach to reaction kinetics in small volumes: Theory and application to biochemical reactions in nonequilibrium steady-state conditions
R. Grima
JOURNAL OF CHEMICAL PHYSICS (2010)
Functional roles for noise in genetic circuits
Avigdor Eldar et al.
NATURE (2010)
Detailed Simulations of Cell Biology with Smoldyn 2.1
Steven S. Andrews et al.
PLOS COMPUTATIONAL BIOLOGY (2010)
Investigating the robustness of the classical enzyme kinetic equations in small intracellular compartments
Ramon Grima
BMC SYSTEMS BIOLOGY (2009)
Mesoscopic statistical properties of multistep enzyme-mediated reactions
W. H. de Ronde et al.
IET SYSTEMS BIOLOGY (2009)
Moment-closure approximations for mass-action models
C. S. Gillespie
IET SYSTEMS BIOLOGY (2009)
A diffusional bimolecular propensity function
Daniel T. Gillespie
JOURNAL OF CHEMICAL PHYSICS (2009)
The challenge of lipid rafts
Linda J. Pike
JOURNAL OF LIPID RESEARCH (2009)
Noise-Induced Breakdown of the Michaelis-Menten Equation in Steady-State Conditions
R. Grima
PHYSICAL REVIEW LETTERS (2009)
Quantification of Circadian Rhythms in Single Cells
Pal O. Westermark et al.
PLOS COMPUTATIONAL BIOLOGY (2009)
LibSBML: an API library for SBML
Benjamin J. Bornstein et al.
BIOINFORMATICS (2008)
The stochastic nature of biochemical networks
Vahid Shahrezaei et al.
CURRENT OPINION IN BIOTECHNOLOGY (2008)
Modelling reaction kinetics inside cells
Ramon Grima et al.
ESSAYS IN BIOCHEMISTRY: SYSTEMS BIOLOGY, VOL 45 (2008)
CellDesigner 3.5: A versatile modeling tool for biochemical networks
Akira Funahashi et al.
PROCEEDINGS OF THE IEEE (2008)
FAST MONTE CARLO SIMULATION METHODS FOR BIOLOGICAL REACTION-DIFFUSION SYSTEMS IN SOLUTION AND ON SURFACES
Rex A. Kerr et al.
SIAM JOURNAL ON SCIENTIFIC COMPUTING (2008)
Modeling and simulating chemical reactions
Desmond J. Higham
SIAM REVIEW (2008)
Amplified biochemical oscillations in cellular systems
A. J. McKane et al.
JOURNAL OF STATISTICAL PHYSICS (2007)
SBMLeditor:: effective creation of models in the Systems Biology Markup Language (SBML)
Nicolas Rodriguez et al.
BMC BIOINFORMATICS (2007)
Stochastic simulation of chemical kinetics
Daniel T. Gillespie
ANNUAL REVIEW OF PHYSICAL CHEMISTRY (2007)
The SBML ODE Solver Library:: a native API for symbolic and fast numerical analysis of reaction networks
Rainer Machne et al.
BIOINFORMATICS (2006)
Predicting stochastic gene expression dynamics in single cells
Jerome T. Mettetal et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Feedback repression is required for mammalian circadian clock function
TK Sato et al.
NATURE GENETICS (2006)
Tools for the SBML community
CS Gillespie et al.
BIOINFORMATICS (2006)
Conservation analysis of large biochemical networks
RR Vallabhajosyula et al.
BIOINFORMATICS (2006)
The finite state projection algorithm for the solution of the chemical master equation
B Munsky et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Optimal observability of sustained stochastic competitive inhibition oscillations at organellar volumes
KL Davis et al.
FEBS JOURNAL (2006)
Green's-function reaction dynamics: A particle-based approach for simulating biochemical networks in time and space
JS van Zon et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
Stochastic reaction-diffusion simulation with MesoRD
J Hattne et al.
BIOINFORMATICS (2005)
Modelling genetic networks with noisy and varied experimental data:: the circadian clock in Arabidopsis thaliana
JCW Locke et al.
JOURNAL OF THEORETICAL BIOLOGY (2005)
Modelling cellular systems with PySCeS
BG Olivier et al.
BIOINFORMATICS (2005)
Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks
D Adalsteinsson et al.
BMC BIOINFORMATICS (2004)
Efficient formulation of the stochastic simulation algorithm for chemically reacting systems
Y Cao et al.
JOURNAL OF CHEMICAL PHYSICS (2004)
Bioluminescence imaging of individual fibroblasts reveals persistent, independently phased circadian rhythms of clock gene expression
DK Welsh et al.
CURRENT BIOLOGY (2004)
Stochastic approaches for modelling in vivo reactions
TE Turner et al.
COMPUTATIONAL BIOLOGY AND CHEMISTRY (2004)
The linear noise approximation for molecular fluctuations within cells
F Hayot et al.
PHYSICAL BIOLOGY (2004)
Fast evaluation of fluctuations in biochemical networks with the linear noise approximation
J Elf et al.
GENOME RESEARCH (2003)
Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm
CV Rao et al.
JOURNAL OF CHEMICAL PHYSICS (2003)
Computational approaches to cellular rhythms
A Goldbeter
NATURE (2002)
Atypical kinetic profiles in drug metabolism reactions
JM Hutzler et al.
DRUG METABOLISM AND DISPOSITION (2002)
Introduction to the GiNaC framework for symbolic computation within the C++ programming language
C Bauer et al.
JOURNAL OF SYMBOLIC COMPUTATION (2002)
Intrinsic noise in gene regulatory networks
M Thattai et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)