Citations to MesoRD and NSM

[1] David Fange and Johan Elf (2006) Noise induced Min phenotypes in E. coli. PLoS Comp. Biol. link

[2] Johan Hattne, David Fange and Johan Elf (2005) Stochastic reaction-diffusion simulation with MesoRD Bioinfomatics pdf.

[1] Alves R, Antunes F, Salvador A.(2006) Tools for kinetic modeling of biochemical networks. Nat Biotechnol. 24:667-72.

[2] F. J. Bruggeman and H. V. Westerhoff (2006) Approaches to Biosimulation of Cellular Processes. Journal Journal of Biological Physics 32:273-288.

[3] Wayne Materi and David S. Wishart (2007) Computational systems biology in drug discovery and development: methods and applications. Drug Discovery Today 12:295-303.

[4] Tolle, Dominic P.; Le Novere, Nicolas (2006) Particle-Based Stochastic Simulation in Systems Biology. Current Bioinformatics 1:315-320

[5] Radek Erban, S. Jonathan Chapman, and Philip K. Maini. (2007) A Practical Guide to Stochastic Simulations of Reaction-Diffusion Processes. arXiv:0704.1908v1

[6] Steven S. Andrews and Adam P. Arkin (2006) Simulating cell biology Current Biology 16: R523-R527

[7] Douglas Ridgway, Gordon Broderick and Michael J Ellison (2006) Accommodating space, time and randomness in network simulation Current Opinion in Biotechnology 17: 493-498

[8] Alexander L Tournier, Paul W Fitzjohn, and Paul A Batescorresponding (2006) Probability-based model of protein-protein interactions on biological timescales Algorithms Mol Biol. 1: 25.

[9] Steven J Plimpton et al (2005) Microbial cell modeling via reacting diffusive particles J. Phys.: Conf. Ser. 16:305-309

[10] Radek Erban, S. Jonathan Chapman (2006) What is the time scale of random sequential adsorption? arXiv:physics 0611252v1

[11] Radek Erban, S. Jonathan Chapman (2006) Realistic boundary conditions for stochastic simulations of reaction-diffusion processes arXiv:physics 0611251v1

[12] Mats H. M. Olsson, and Arieh (2006) Warshel Monte Carlo simulations of proton pumps: On the working principles of the biological valve that controls proton pumping in cytochrome c oxidase PNAS 103:6500-6505

[13] J. Vidal Rodríguez, Jaap A. Kaandorp, Maciej Dobrzynski and Joke G. Blom (2006) Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli Bioinformatics 22:1895-1901

[14] Chris Sanford, Matthew L.K. Yip, Carl White and John Parkinson (2006) Cell++-simulating biochemical pathways Bioinformatics 22:2918-2925

[15] Yann Dublanche, Konstantinos Michalodimitrakis, Nico Kümmerer, Mathilde Foglierini & Luis Serrano (2006) Noise in transcription negative feedback loops: simulation and experimental analysis Molecular Systems Biology 2:41

[16] Jeroen S. van Zon, Marco J. Morelli, Sorin Tanase-Nicola and Pieter Rein ten Wolde (2006) Diffusion of Transcription Factors Can Drastically Enhance the Noise in Gene Expression Biophysical Journal 91:4350-4367

[17] Matthew Scott, Brian Ingalls & Mads Kaern. (2006) Estimations of intrinsic and extrinsic noise in models of nonlinear genetic networks. Chaos 16:026107