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Tag biorefs [65 articles]

Recent papers classified by the tag biorefs.
  • Bayesian Inference for Stochastic Kinetic Models Using a Diffusion Approximation
    Biometrics, Vol. 61, No. 3. (2005), pp. 781-788.
    by A Golightly, DJ Wilkinson
    posted to biorefs by cottrell on 2007-01-20 21:42:14 as ** along with 1 person petermilner
  • Temporal acceleration of spatially distributed kinetic Monte Carlo simulations
    Journal of Computational Physics, Vol. 211, No. 2. (20 January 2006), pp. 596-615.
    by Abhijit Chatterjee, Dionisios G Vlachos
    posted to biorefs reaction-diffusion by cottrell on 2007-07-03 16:56:02 as **
  • A modified Next Reaction Method for simulating systems with time varying rate constants and systems with delays
    (2 Aug 2007)
    by David F Anderson
    posted to biorefs next-reaction-method simulation by cottrell on 2007-08-03 14:37:22 as **
  • Systematic analysis of the multivariate master equation for a reaction-diffusion system
    Journal of Statistical Physics, Vol. 22, No. 4. (1 April 1980), pp. 495-512.
    by G Nicolis, M Malek-Mansour
    posted to biorefs master-equation reaction-diffusion by cottrell on 2007-08-02 20:19:26 as **
  • Gene expression and the myth of the average cell
    Trends in Cell Biology, Vol. 13, No. 1. (January 2003), pp. 4-6.
    by Jeffrey M Levsky, Robert H Singer
    posted to biorefs gene_expression by cottrell on 2006-07-12 19:01:19 as **
  • Fluctuations in a coupled population model
    Journal of Physics A: Mathematical and General, Vol. 38, No. 29. (22 July 2005), pp. 6447-6461.
    by E Jakeman, KI Hopcraft, JO Matthews
    posted to biorefs networks by cottrell on 2006-09-08 20:24:51 as ****
  • Perfect Sampling of the Chemical Master Equation for Gene Regulatory Networks
    (27 Oct 2006)
    by Martin Hemberg, Mauricio Barahona
    posted to ssa sampling biorefs by cottrell on 2007-01-20 22:15:53 as **
  • Stepping Stone Models for Population Growth
    Journal of Applied Probability, Vol. 11, No. 1. (1974), pp. 16-31.
    by E Renshaw
    posted to biorefs modeling population by cottrell on 2006-08-04 22:34:21 as **
  • Particle Systems and Reaction-Diffusion Equations
    The Annals of Probability, Vol. 22, No. 1. (1994), pp. 289-333.
    by R Durrett, C Neuhauser
    posted to biorefs reaction-diffusion by cottrell on 2007-08-02 21:05:42 as **
  • An accurate and efficient tau-leaping procedure for the simulation of chemical reaction systems
    (2 Aug 2007)
    by David F Anderson
    posted to biorefs reaction simulation tau-leaping by cottrell on 2007-08-03 14:36:50 as ** along with 1 person margaritis
  • Bridging genetic networks and queueing theory
    Physica A: Statistical Mechanics and its Applications, Vol. 332 (1 February 2004), pp. 585-616.
    by Arnon Arazi, Eshel Ben-Jacob, Uri Yechiali
    posted to biorefs networks queing by cottrell on 2006-07-12 18:24:02 as ***
  • Stochastic Models for Second-Order Chemical Reaction Kinetics. The Equilibrium State
    The Journal of Chemical Physics, Vol. 45, No. 6. (1966), pp. 2145-2155.
    by IG Darvey, BW Ninham, PJ Staff
    posted to biorefs networks by cottrell on 2006-07-12 18:40:40 as ***
  • Integrating heterogeneous knowledges for understanding biological behaviors: a probabilistic approach
    (23 Dec 2007)
    by Jérémie Bourdon, Damien Eveillard, Samuel Gabillard, Theo Merle
    posted to biomath biorefs by cottrell on 2008-01-02 19:41:48 as **
  • Particle-Based Stochastic Simulation in Systems Biology
    Current Bioinformatics, Vol. 1, No. 3. (August 2006), pp. 315-320.
    by P Tolle, Dominic, Le Novere, Nicolas
    posted to simulation particle-based biorefs by cottrell on 2007-01-20 22:16:24 as ** along with 1 person csanford
  • Transcriptional stochasticity in gene expression
    Journal of Theoretical Biology, Vol. 238, No. 2. (21 January 2006), pp. 348-367.
    by Tomasz Lipniacki, Pawel Paszek, Anna Marciniak-Czochra, Allan R Brasier, Marek Kimmel
    posted to biorefs gene_expression by cottrell on 2006-07-12 19:48:07 as ** along with 5 people jjray bayesian bh2 balabu klo
  • Interacting Particle Systems (Classics in Mathematics)
    (22 December 2004)
    by Thomas M Liggett
    posted to biorefs interacting-diffusion interacting-particles by cottrell on 2007-07-27 22:05:59 as **
  • Spatial Epidemics: Critical Behavior in One Dimension
    (25 Jul 2007)
    by Steven P Lalley
    posted to biorefs interacting-particles spatial stochastic by cottrell on 2007-07-27 23:04:05 as **
  • On a Fourier space master equation for Navier-Stokes turbulence
    Zeitschrift für Physik B Condensed Matter, Vol. V100, No. 3. (17 June 1996), pp. 461-468.
    by Heinz-Peter Breuer, Francesco Petruccione, Frithjof Weber
    posted to stochastic navier-stokes master-equation biorefs by cottrell on 2007-01-25 17:17:44 as **
  • Modeling transcription factor binding events to DNA using a random walker/jumper representation on a 1D/2D lattice with different affinity sites
    (9 Aug 2007)
    by Vahid Rezania, Jack Tuszynski, Michael Hendzel
    posted to binding biorefs spatial-simulation by cottrell on 2007-08-31 00:38:25 as **
  • Scaling limit, noise, stability
    Vol. 1840 (2004), pp. 1-106.
    by Boris Tsirelson
    posted to biorefs limits networks scaling by cottrell on 2006-08-30 18:37:52 as **
  • A Reaction-Diffusion Model to Study RNA Motion by Quantitative Fluorescence Recovery after Photobleaching
    Biophys. J., Vol. 92, No. 8. (15 April 2007), pp. 2694-2703.
    by Jose Braga, James G Mcnally, Maria Carmo-Fonseca
    posted to biorefs by cottrell on 2007-04-19 21:39:43 as **
  • Reaction volume statistics for rate processes in disordered systems. Thermodynamic analogies and extracting information from experimental data
    Chemical Physics, Vol. 243, No. 3. (15 May 1999), pp. 273-294.
    by Marcel O Vlad, John Ross, Andrzej Plonka
    posted to biorefs reaction-diffusion by cottrell on 2006-10-06 01:45:07 as **
  • Enzyme localization can drastically affect signal amplification in signal transduction pathways
    (27 Aug 2007)
    by Siebe B van Albada, Pieter
    posted to biorefs enzyme gene_expression localization by cottrell on 2007-08-28 15:09:20 as **
  • The role of proofreading in signal transduction specificity.
    Biophys J, Vol. 82, No. 6. (June 2002), pp. 2928-2933.
    by PS Swain, ED Siggia
    posted to biorefs gene_expression by cottrell on 2006-10-02 19:00:28 as **
  • Stochastics in Finite and Infinite Dimensions (Trends in Mathematics)
    (15 October 2000)
    by Takeyuki Hida
    posted to biorefs book process stochastic by cottrell on 2006-10-30 19:39:44 as **
  • An analytical solution of the stochastic master equation for reversible bimolecular reaction kinetics
    The Journal of Chemical Physics, Vol. 113, No. 8. (2000), pp. 3315-3322.
    by Ian J Laurenzi
    posted to biorefs networks by cottrell on 2006-07-12 18:46:14 as ** along with 1 person dah
  • Viscosity solutions for quasilinear degenerate parabolic equations of porous medium type
    Indiana Univ. Math. J., Vol. 54, No. 3. (2005), pp. 817-860.
    by Cristina Brändle, Juan L Vázquez
    posted to biorefs medium pde porous by cottrell on 2006-09-12 23:11:10 as **
  • Statistical Modeling and Analysis for Complex Data Problems (Gerad 25th Anniversary Series)
    (01 January 2005)
    by P Duchesne, B Remillard
    posted to biorefs book process stochastic by cottrell on 2006-10-30 19:43:14 as **
  • Microscopic spatial correlations induced by external noise in a reaction-diffusion system
    Physica A: Statistical and Theoretical Physics, Vol. 188, No. 1-3. (1 September 1992), pp. 386-403.
    by Charles R Doering
    posted to biorefs reaction-diffusion by cottrell on 2006-10-06 01:41:16 as **
  • Discrete Green's functions for products of regular graphs
    (8 Sep 2003)
    by Robert B Ellis
    posted to torus random-walk hitting-time graph biorefs by cottrell on 2007-01-21 06:54:26 as **
  • Toward large-scale modeling of the microbial cell for computer simulation.
    J Biotechnol, Vol. 113, No. 1-3. (30 September 2004), pp. 281-294.
    by N Ishii, M Robert, Y Nakayama, A Kanai, M Tomita
    posted to biorefs by cottrell on 2006-05-07 23:53:18 as *** along with 8 people and 3 groups csanford eldan wnpx Doug livingthingdan josepe fishtank roland_ewald livingthing dIEMoSIRIS MoSi-Rostock
  • Nonlinear Stochastic PDE's: Hydrodynamic Limit and Burgers' Turbulence (The IMA Volumes in Mathematics and its Applications)
    (01 December 1995)
    by Tadahisa Funaki, Wojbor A Woyczynski
    posted to biorefs reaction-diffusion spde by cottrell on 2007-07-27 19:48:27 as **
  • Stochastic fluctuations in gene expression far from equilibrium: Omega expansion and linear noise approximation
    The Journal of Chemical Physics, Vol. 122, No. 12. (2005)
    by Yi Tao, Yuting Jia, Gregory T Dewey
    posted to biorefs by cottrell on 2006-05-07 23:13:53 as **
  • Stochastic Interacting Systems: Contact, Voter and Exclusion Processes (Grundlehren der mathematischen Wissenschaften)
    (15 November 1999)
    by Thomas M Liggett
    posted to biorefs interacting-diffusion interacting-particles by cottrell on 2007-07-27 22:06:41 as **
  • Bridging from molecular simulation to biochemical networks
    Current Opinion in Structural Biology, Vol. 17, No. 2. (April 2007), pp. 166-172.
    by Matthias Stein, Razif R Gabdoulline, Rebecca C Wade
    posted to biorefs simulation by cottrell on 2007-06-08 17:52:39 as read
  • Open First-Order Stochastic Processes
    The Journal of Chemical Physics, Vol. 33, No. 3. (1960), pp. 691-694.
    by Paul J Gans
    posted to biorefs networks queing by cottrell on 2006-07-18 16:11:22 as ***
  • Microbial cell modeling via reacting diffusive particles
    Journal of Physics: Conference Series, Vol. 16, No. 1. (2005), 305.
    by Steven J Plimpton, Alex Slepoy
    posted to biorefs by cottrell on 2006-08-22 19:07:33 as *****
  • notes Theoretical analysis of internal fluctuations and bistability in CO oxidation on nanoscale surfaces
    The Journal of Chemical Physics, Vol. 124, No. 4. (2006)
    by M Pineda, R Imbihl, Schimansky L Geier, Ch
    posted to biorefs by cottrell on 2006-05-07 22:53:08 as *
  • A general method for the computation of probabilities in systems of first order chemical reactions
    The Journal of Chemical Physics, Vol. 122, No. 10. (2005)
    by Xueying Zhang, Katrien De Cock, Monica F Bugallo, Petar M Djuric
    posted to biorefs by cottrell on 2007-01-20 21:43:25 as **
  • Noise in eukaryotic gene expression.
    Nature, Vol. 422, No. 6932. (10 April 2003), pp. 633-637.
    by WJ Blake, M KAErn, CR Cantor, JJ Collins
    posted to biorefs gene_expression by cottrell on 2006-07-12 18:29:59 as ** along with 6 people rklancer dbikard margaritis mjoach jiny klo
  • Coarse-grained stochastic processes and Monte Carlo simulations in lattice systems
    Journal of Computational Physics, Vol. 186, No. 1. (20 March 2003), pp. 250-278.
    by Markos A Katsoulakis, Andrew J Majda, Dionisios G Vlachos
    posted to biorefs reaction-diffusion by cottrell on 2007-07-03 16:56:15 as **
  • Viscosity solutions for the porous medium equation
    Vol. 65 (1999), pp. 13-26.
    by Luis Caffarelli, Juan L Vazquez
    posted to biorefs medium pde porous by cottrell on 2006-09-13 19:24:46 as **
  • Stochastic gene expression in a single cell.
    Science, Vol. 297, No. 5584. (16 August 2002), pp. 1183-1186.
    by MB Elowitz, AJ Levine, ED Siggia, PS Swain
    posted to biorefs gene_expression by cottrell on 2006-10-02 19:01:54 as ** along with 16 people and 3 groups wilvc madhadron mmt litam mhucka timflutre margaritis roland_ewald ptupper mjoach tvdbulck jiny balicea dylanwalker jjray austin UWNICU dIEMoSIRIS MoSi-Rostock
  • Fluctuations and correlations in a diffusion-reaction system: Exact hydrodynamics
    Journal of Statistical Physics, Vol. V65, No. 5. (1 December 1991), pp. 953-970.
    by Charles R Doering, Martin A Burschka, Werner Horsthemke
    posted to biorefs reaction-diffusion by cottrell on 2006-10-06 01:30:32 as **
  • Stochastic mRNA Synthesis in Mammalian Cells
    PLoS Biology, Vol. 4, No. 10. (1 October 2006), e309.
    by Arjun Raj, Charles S Peskin, Daniel Tranchina, Diana Y Vargas, Sanjay Tyagi
    posted to biorefs by cottrell on 2007-04-19 19:30:45 as ** along with 7 people jjray nirfriedman madhadron balabu qfwills johncumbers margaritis
  • Coarse-graining approximation for simulating surface reaction kinetics in particulate systems
    Computational Materials Science, Vol. 38, No. 2. (December 2006), pp. 369-373.
    by Jeffrey W Bullard
    posted to biorefs coarse_graining reaction_rates by cottrell on 2007-06-08 17:41:10 as **
  • Grand canonical Markov model: A stochastic theory for open nonequilibrium biochemical networks
    The Journal of Chemical Physics, Vol. 124, No. 4. (2006)
    by William J Heuett, Hong Qian
    posted to biorefs by cottrell on 2006-08-22 19:36:30 as **
  • Mesoscopic reaction-diffusion in intracellular signaling
    Fluctuations and Noise in Biological, Biophysical, and Biomedical Systems, Vol. 5110, No. 1. (2003), pp. 114-124.
    by Johan Elf, Andreas Doncic, Mans Ehrenberg
    edited by Sergey M Bezrukov, Hans Frauenfelder, Frank Moss
    posted to biorefs reaction-diffusion by cottrell on 2007-06-26 20:23:22 as **
  • Pullback attractors and extremal complete trajectories for non-autonomous reaction-diffusion problems
    Journal of Differential Equations, Vol. 238, No. 2. (15 July 2007), pp. 289-337.
    by James C Robinson, Anibal Rodriguez-Bernal, Alejandro Vidal-Lopez
    posted to biorefs reaction-diffusion by cottrell on 2007-06-26 17:54:18 as *****
  • Localization in lattice and continuum models of reinforced random walks
    Applied Mathematics Letters, Vol. 16, No. 3. (April 2003), pp. 375-381.
    by KJ Painter, D Horstmann, HG Othmer
    posted to biorefs by cottrell on 2006-05-08 00:04:29 as **
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