Selected studies where MesoRD have been used

  1. Mahmutovic, Anel, et al. "Lost in presumption: stochastic reactions in spatial models." Nature methods 9.12 (2012): 1163-1166.
  2. Di Ventura, Barbara, and Victor Sourjik. "Self-organized partitioning of dynamically localized proteins in bacterial cell division." Molecular systems biology 7.1 (2011).
  3. Holloway, David M., et al. "Gene expression noise in spatial patterning: hunchback promoter structure affects noise amplitude and distribution in Drosophila segmentation." PLoS computational biology 7.2 (2011): e1001069.
  4. Wu, Yu Feng. "Computational Systems Analysis of Deterministic Pair Rule Gene Network and Stochastic Bicoid Morphogen Gradient in Drosophila melanogaster. (2011)"
  5. David Fange and Johan Elf (2006) Noise induced Min phenotypes in E. coli. PLoS Comp. Biol.
  6. Johan Hattne, David Fange and Johan Elf (2005) Stochastic reaction-diffusion simulation with MesoRD Bioinfomatics.

Citations to MesoRD and NSM

  1. Hellander, Stefan. "Single molecule simulations in complex geometries with embedded dynamic one-dimensional structures." arXiv preprint arXiv:1303.2696(2013).
  2. Blackwell, K. T. "Approaches and tools for modeling signaling pathways and calcium dynamics in neurons." Journal of neuroscience methods (2013).
  3. Agbanusi, Ikemefuna C., and Samuel A. Isaacson. "A comparison of bimolecular reaction models for stochastic reaction diffusion models." arXiv preprint arXiv:1301.0547 (2013).
  4. Choi, TaiJung. Stochastic Modeling of Advection-Diffusion-Reaction Processes in Biological Systems. Diss. University of California, San Diego, 2013.
  5. Schöneberg, Johannes, and Frank Noé. "ReaDDy-A Software for Particle-Based Reaction-Diffusion Dynamics in Crowded Cellular Environments." PloS one 8.9 (2013): e74261.
  6. Erban, Radek, Mark B. Flegg, and Garegin A. Papoian. "Multiscale Stochastic Reaction–Diffusion Modeling: Application to Actin Dynamics in Filopodia."Bulletin of mathematical biology (2013): 1-20.
  7. Kühn, Clemens, and Peter Gennemark. "MODELING YEAST OSMOADAPTATION AT DIFFERENT LEVELS OF RESOLUTION." Journal of bioinformatics and computational biology 11.02 (2013).
  8. Flegg, Mark B., et al. "Analysis of the two-regime method on square meshes."arXiv preprint arXiv:1304.5487 (2013).
  9. Roberts, Elijah, John E. Stone, and Zaida Luthey-Schulten. "Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation." Journal of Computational Chemistry 34.3 (2013): 245-255.
  10. Liu, Wei. Machine learning approaches to modelling bicoid morphogen in Drosophila melanogaster. Diss. University of Southampton, 2013.
  11. Flegg, Mark B., Stefan Hellander, and Radek Erban. "Convergence of methods for coupling of microscopic and mesoscopic reaction-diffusion simulations."arXiv preprint arXiv:1304.7393 (2013).
  12. Wu, Wei, and Jin Wang. "Landscape Framework and Global Stability for Stochastic Reaction Diffusion and General Spatially Extended Systems with Intrinsic Fluctuations." The Journal of Physical Chemistry B (2013).
  13. Zhang, Yong, et al. "Evaluation and linking of effective parameters in particle-based models and continuum models for mixing-limited bimolecular reactions."Water Resources Research (2013).
  14. Fange, David, Anel Mahmutovic, and Johan Elf. "MesoRD 1.0: Stochastic reaction-diffusion simulations in the microscopic limit." Bioinformatics 28.23 (2012): 3155-3157.
  15. Chen, Weiliang, and Erik de Schutter. "STEPS: efficient simulation of stochastic reaction-diffusion models in realistic morphologies." (2012).
  16. Drawert, Brian, Stefan Engblom, and Andreas Hellander. "URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries." BMC systems biology 6.1 (2012): 76.
  17. Mahmutovic, Anel, et al. "Lost in presumption: stochastic reactions in spatial models." Nature methods 9.12 (2012): 1163-1166.
  18. Chakrabarti, Anirikh, et al. "Multiscale models of breast cancer progression."Annals of biomedical engineering 40.11 (2012): 2488-2500.
  19. Cowan, Ann E., et al. "Spatial modeling of cell signaling networks." Methods in cell biology 110 (2012): 195.
  20. Lloyd-Price, Jason, Abhishekh Gupta, and Andre S. Ribeiro. "SGNS2: a compartmentalized stochastic chemical kinetics simulator for dynamic cell populations." Bioinformatics 28.22 (2012): 3004-3005.
  21. Blackwell, K. T. "Approaches and tools for modeling signaling pathways and calcium dynamics in neurons." Journal of neuroscience methods (2013).
  22. Flegg, Mark B., S. Jonathan Chapman, and Radek Erban. "The two-regime method for optimizing stochastic reaction–diffusion simulations." Journal of the Royal Society Interface 9.70 (2012): 859-868.
  23. Klann, Michael, and Heinz Koeppl. "Spatial Simulations in Systems Biology: From Molecules to Cells." International journal of molecular sciences 13.6 (2012): 7798-7827.
  24. Thomas, Philipp, Hannes Matuschek, and Ramon Grima. "Intrinsic noise analyzer: A software package for the exploration of stochastic biochemical kinetics using the system size expansion." PloS one 7.6 (2012): e38518.
  25. Santamaria, Fidel, Gabriela Antunes, and Erik De Schutter. "Breakdown of Mass-Action Laws in Biochemical Computation." Computational Systems Neurobiology. Springer Netherlands, 2012. 119-132.
  26. Sokolowski, Thomas R., Thorsten Erdmann, and Pieter Rein ten Wolde. "Mutual repression enhances the steepness and precision of gene expression boundaries." PLoS computational biology 8.8 (2012): e1002654.
  27. Flegg, Mark B., et al. "Analysis of the two-regime method on square meshes."arXiv preprint arXiv:1304.5487 (2013).
  28. Beste, Michael T., et al. "An integrated stochastic model of “inside-out” integrin activation and selective T-lymphocyte recruitment." Langmuir 28.4 (2012): 2225-2237.
  29. Vigelius, Matthias, and Bernd Meyer. "Multi-Dimensional, Mesoscopic Monte Carlo Simulations of Inhomogeneous Reaction-Drift-Diffusion Systems on Graphics-Processing Units." PloS one 7.4 (2012): e33384.
  30. Montagna, Sara, and Mirko Viroli. "A Computational Framework for Multilevel Morphologies." Morphogenetic Engineering. Springer Berlin Heidelberg, 2012. 383-405.
  31. Yang, Chang-li, and Ai-lin Zhu. "A closed form solution to one dimensional robin boundary problems." Acta Mathematicae Applicatae Sinica, English Series28.3 (2012): 549-556.
  32. Mugler, Andrew, and Pieter Rein ten Wolde. "The macroscopic effects of microscopic heterogeneity." arXiv preprint arXiv:1210.0104 (2012).
  33. Wang, Siyang, et al. "Stochastic reaction–diffusion processes with embedded lower dimensional structures." (2012).
  34. Oliveira, Rodrigo F., MyungSook Kim, and Kim T. Blackwell. "Subcellular location of PKA controls striatal plasticity: stochastic simulations in spiny dendrites." PLoS computational biology 8.2 (2012): e1002383.
  35. Hellander, Andreas, Stefan Hellander, and Per Lo¨tstedt. "Coupled mesoscopic and microscopic simulation of stochastic reaction-diffusion processes in mixed dimensions." Multiscale Modeling & Simulation 10.2 (2012): 585-611.
  36. Franz, Benjamin, et al. "Multiscale reaction-diffusion algorithms: PDE-assisted Brownian dynamics." arXiv preprint arXiv:1206.5860 (2012).
  37. Vigelius, Matthias, Aidan Lane, and Bernd Meyer. "Accelerating reaction–diffusion simulations with general-purpose graphics processing units."Bioinformatics 27.2 (2011): 288-290.
  38. Lis, Mieszko, et al. "Efficient stochastic simulation of reaction–diffusion processes via direct compilation." Bioinformatics 25.17 (2009): 2289-2291.
  39. Chen, Weiliang, Iain Hepburn, and Erik De Schutter. "Tetrahedral mesh generation and visualization for stochastic reaction-diffusion simulation." BMC Neuroscience 11.Suppl 1 (2010): P70.
  40. Ghosh, Preetam, et al. "Holding time estimation for reactions in stochastic event-based simulation of complex biological systems." Simulation Modelling Practice and Theory 16.10 (2008): 1615-1639.
  41. Holloway, David M., and Alexander V. Spirov. "Gene expression noise in embryonic spatial patterning: Reliable formation of the head-to-tail axis in the fruit fly." Noise and Fluctuations (ICNF), 2011 21st International Conference on. IEEE, 2011.
  42. Artyomov, Maxim N., et al. "CD4 and CD8 binding to MHC molecules primarily acts to enhance Lck delivery." Proceedings of the National Academy of Sciences 107.39 (2010): 16916-16921.
  43. Elfverson, Daniel, and Emil Kieri. "Spatial stochastic simulation of cellular reaction networks." (2010).
  44. Ogawa, Makoto, et al. "Development of a particle simulator on cancer cell signaling network with PC cluster system." Control Automation and Systems (ICCAS), 2010 International Conference on. IEEE, 2010.
  45. Grima, Ramon, and Santiago Schnell. "Modelling reaction kinetics inside cells."Essays Biochem 45 (2008): 41-56.
  46. Burrage, Kevin, et al. "Stochastic simulation for spatial modelling of dynamic processes in a living cell." Design and Analysis of Biomolecular Circuits. Springer New York, 2011. 43-62.
  47. Stoma, Szymon, et al. "STSE: Spatio-temporal simulation environment dedicated to biology." BMC bioinformatics 12.1 (2011): 126.
  48. Arjunan, Satya Nanda Vel, and Masaru Tomita. "Modeling reaction-diffusion of molecules on surface and in volume spaces with the E-Cell System." IJCSIS3.1 (2009): 211-216.
  49. Sjoberg, Paul, Otto G. Berg, and Johan Elf. "Taking the reaction-diffusion master equation to the microscopic limit." arXiv preprint arXiv:0905.4629(2009).
  50. Leier, André, T. T. Marquez-Lago, and K. Burrage. "Probability distributed time delays: integrating spatial effects into temporal models."
  51. Wils, Stefan, and Erik De Schutter. "STEPS: modeling and simulating complex reaction-diffusion systems with Python." Frontiers in neuroinformatics 3 (2009).
  52. Chandren, Muniyandi Ravie, and Mohd Zin Abdullah. "Simulation strategy of membrane computing to characterize the structure and non-deterministic behavior of biological systems: a case study with ligand-receptor network of protein TGF-ß." Visual Informatics: Sustaining Research and Innovations. Springer Berlin Heidelberg, 2011. 56-66.
  53. Ghosh, S., et al. "A Discrete Event Based Stochastic Simulation Platform for ‘In silico’Study of Molecular-level Cellular Dynamics." J Biotechnol Biomaterial S 6 (2011): 2.
  54. Orsi, G., et al. "HEMETß: improvement of hepatocyte metabolism mathematical model." Computer methods in biomechanics and biomedical engineering 14.10 (2011): 837-851.
  55. Klingbeil, Guido, et al. "STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB." Bioinformatics 27.8 (2011): 1170-1171.
  56. Klipp, Edda, and Falko Krause. "Computational Tools for Systems Biology."Cancer Systems Biology, Bioinformatics and Medicine. Springer Netherlands, 2011. 213-243.
  57. Twycross, Jamie, Malcolm Bennett, and Natalio Krasnogor. "A High-Performance Multicompartment Stochastic Simulator for Executable Biology."
  58. Boulianne, Laurier, et al. "GridCell: a stochastic particle-based biological system simulator." BMC systems biology 2.1 (2008): 66.
  59. Engblom, Stefan, et al. "Simulation of stochastic reaction-diffusion processes on unstructured meshes." SIAM Journal on Scientific Computing 31.3 (2009): 1774-1797.
  60. Kenmochi, Ryusuke, et al. "Particle simulation of epidermal growth factor receptor in prostate cancer cells." World Congress. Vol. 18. No. 1. 2011.
  61. Ramaswamy, Rajesh, and Ivo F. Sbalzarini. "Exact on-lattice stochastic reaction-diffusion simulations using partial-propensity methods." The Journal of chemical physics 135.24 (2011): 244103-244103.
  62. Oliveira, Rodrigo F., et al. "The role of type 4 phosphodiesterases in generating microdomains of cAMP: large scale stochastic simulations." PloS one 5.7 (2010): e11725.
  63. Anderson, James B., Louise E. Anderson, and Jörg Kussmann. "Monte Carlo simulations of single-and multistep enzyme-catalyzed reaction sequences: Effects of diffusion, cell size, enzyme fluctuations, colocalization, and segregation." The Journal of chemical physics 133 (2010): 034104.
  64. Fange, David, et al. "Stochastic reaction-diffusion kinetics in the microscopic limit." Proceedings of the National Academy of Sciences 107.46 (2010): 19820-19825.
  65. Hellander, Andreas. Numerical simulation of well stirred biochemical reaction networks governed by the master equation. Diss. Department of Information Technology, Uppsala University, 2008.
  66. Kowald, Axel, and Christoph Wierling. "Standards, Tools, and Databases for the Analysis of Yeast ‘Omics Data." Yeast Systems Biology. Humana Press, 2011. 345-365.
  67. Erban, Radek, and S. Jonathan Chapman. "Stochastic modelling of reaction–diffusion processes: algorithms for bimolecular reactions." Physical biology 6.4 (2009): 046001.
  68. Resat, Haluk, Linda Petzold, and Michel F. Pettigrew. "Kinetic modeling of biological systems." Computational Systems Biology. Humana Press, 2009. 311-335.
  69. Beck, Martin, et al. "Exploring the spatial and temporal organization of a cell’s proteome." Journal of structural biology 173.3 (2011): 483-496.
  70. Krause, Falko, et al. "Sustainable model building the role of standards and biological semantics." Methods Enzymol 500 (2011): 371-395.
  71. Rodríguez, Jordi Vidal. "Signal Transduction Pathways."
  72. Mosca, Ettore, et al. "Modelling spatial heterogeneity and macromolecular crowding with membrane systems." Membrane Computing. Springer Berlin Heidelberg, 2011. 285-304.
  73. Kim, Jongrae, Xuerong Mao, and Pat Heslop-Harrison. "Noise from spatial heterogeneity changes signal amplification magnitude and increases the variability in dose responses." (2008).
  74. Gruenert, Gerd, et al. "Rule-based spatial modeling with diffusing, geometrically constrained molecules." BMC bioinformatics 11.1 (2010): 307.
  75. Mavelli, Fabio, and Kepa Ruiz-Mirazo. "ENVIRONMENT: a computational platform to stochastically simulate reacting and self-reproducing lipid compartments." Physical biology 7.3 (2010): 036002.
  76. Wallden, Mats, and Johan Elf. "Studying transcriptional interactions in single cells at sufficient resolution." Current Opinion in Biotechnology 22.1 (2011): 81-86.
  77. Hellander, Stefan, and Per Lötstedt. "Flexible single molecule simulation of reaction–diffusion processes." Journal of Computational Physics 230.10 (2011): 3948-3965.
  78. Modchang, Charin, et al. "A comparison of deterministic and stochastic simulations of neuronal vesicle release models." Physical biology 7.2 (2010): 026008.
  79. Arjunan, Satya Nanda Vel, and Masaru Tomita. "A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation." Systems and synthetic biology 4.1 (2010): 35-53.
  80. Meier-Schellersheim, Martin, Iain DC Fraser, and Frederick Klauschen. "Multiscale modeling for biologists." Wiley Interdisciplinary Reviews: Systems Biology and Medicine 1.1 (2009): 4-14.
  81. Hellander, Andreas, and Per Lötstedt. "Incorporating active transport of cellular cargo in stochastic mesoscopic models of living cells." Multiscale Modeling & Simulation 8.5 (2010): 1691-1714.
  82. Wang, Bing, et al. "Abstract Next Subvolume Method: A logical process-based approach for spatial stochastic simulation of chemical reactions."Computational Biology and Chemistry 35.3 (2011): 193-198.
  83. Montagna, Sara, and Mirko Viroli. "A framework for modelling and simulating networks of cells." Electronic Notes in Theoretical Computer Science 268 (2010): 115-129.
  84. Byrne, Michael J., M. Neal Waxham, and Yoshihisa Kubota. "Cellular dynamic simulator: an event driven molecular simulation environment for cellular physiology." Neuroinformatics 8.2 (2010): 63-82.
  85. Tolle, Dominic P., and Nicolas Le Novère. "Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes."BMC systems biology 4.1 (2010): 24.
  86. Andrews, Steven S., et al. "Detailed simulations of cell biology with Smoldyn 2.1." PLoS computational biology 6.3 (2010): e1000705.
  87. Islam, Ahmad Ehteshamul, and Muhammad Ashraful Alam. "Analyzing the distribution of threshold voltage degradation in nanoscale transistors by using reaction-diffusion and percolation theory." Journal of computational electronics10.4 (2011): 341-351.
  88. Arjunan, Satya Nanda Vel. Modeling three dimensional spatial regulation of bacterial cell division. Diss. PhD Thesis, Keio University, 2009.
  89. Schluttig, Jakob. "Stochastic dynamics of protein assembly." (2009).
  90. Tian, T. "Effective Stochastic Simulation Methods for Chemical Reaction Systems." Journal of Numerical Mathematics and Stochastics 1.1 (2009): 85-101.
  91. Lipková, Jana, et al. "Analysis of Brownian dynamics simulations of reversible bimolecular reactions." SIAM Journal on Applied Mathematics 71.3 (2011): 714-730.
  92. Kotaleski, Jeanette Hellgren, and Kim T. Blackwell. "Modelling the molecular mechanisms of synaptic plasticity using systems biology approaches." Nature Reviews Neuroscience 11.4 (2010): 239-251.
  93. Shimoni, Yishai, et al. "Multi-scale stochastic simulation of diffusion-coupled agents and its application to cell culture simulation." PloS one 6.12 (2011): e29298.
  94. Marquez-Lago, Tatiana, André Leier, and Kevin Burrage. "Probability distributed time delays: integrating spatial effects into temporal models." BMC systems biology 4.1 (2010): 19.
  96. Artomov, Maksym. Stochastic processes in biological systems: selected problems. Diss. Massachusetts Institute of Technology, 2009.
  97. Chakraborty, Arup K., and Andrej Košmrlj. "Statistical mechanical concepts in immunology." Annual review of physical chemistry 61 (2010): 283-303.
  98. Barrio, Manuel, et al. "Computational approaches for modelling intrinsic noise and delays in genetic regulatory networks." Handbook of Research on Computational Methodologies in Gene Regulatory Networks (2010): 169-197.
  99. Kim, Myungsook, et al. "Colocalization of protein kinase A with adenylyl cyclase enhances protein kinase A activity during induction of long-lasting long-term-potentiation." PLoS computational biology 7.6 (2011): e1002084.
  100. Li, Isaac TS, Evan Mills, and Kevin Truong. "A computational tool for monte carlo simulations of biomolecular reaction networks modeled on physical principles." NanoBioscience, IEEE Transactions on 9.1 (2010): 24-30.
  101. Sauro, Herbert M., and Frank T. Bergmann. "Software Tools for Systems Biology." Systems Biomedicine: Concepts and Perspectives (2009): 289.
  102. Roberts, Elijah, et al. "Noise contributions in an inducible genetic switch: a whole-cell simulation study." PLoS computational biology 7.3 (2011): e1002010.
  103. Garcia-Ojalvo, Jordi. "Physical approaches to the dynamics of genetic circuits: a tutorial." Contemporary Physics 52.5 (2011): 439-464.
  104. Koumoutsakos, Petros, et al. "Particle simulations of morphogenesis."Mathematical Models and Methods in Applied Sciences 21.supp01 (2011): 955-1006.
  105. Germain, Ronald N., et al. "Systems Biology in Immunology–A Computational Modeling Perspective." Annual review of immunology 29 (2011): 527.
  106. Mazloom, Amin Reza. "EukaSimBioSys: A Stochastic Discrete Event-based Simulation Software For In-silico Study Of Insulin Signaling And Metabolism In Cardiac Myocytes." (2008).
  107. Baker, Ruth E., Christian A. Yates, and Radek Erban. "From microscopic to macroscopic descriptions of cell migration on growing domains." Bulletin of mathematical biology 72.3 (2010): 719-762.
  108. Alves R, Antunes F, Salvador A.(2006) Tools for kinetic modeling of biochemical networks. Nat Biotechnol. 24:667-72.
  109. F. J. Bruggeman and H. V. Westerhoff (2006) Approaches to Biosimulation of Cellular Processes. Journal Journal of Biological Physics 32:273-288.
  110. Wayne Materi and David S. Wishart (2007) Computational systems biology in drug discovery and development: methods and applications. Drug Discovery Today 12:295-303.
  111. Tolle, Dominic P.; Le Novere, Nicolas (2006) Particle-Based Stochastic Simulation in Systems Biology. Current Bioinformatics 1:315-320
  112. Radek Erban, S. Jonathan Chapman, and Philip K. Maini. (2007) A Practical Guide to Stochastic Simulations of Reaction-Diffusion Processes. arXiv:0704.1908v1
  113. Steven S. Andrews and Adam P. Arkin (2006) Simulating cell biology Current Biology 16: R523-R527
  114. Douglas Ridgway, Gordon Broderick and Michael J Ellison (2006) Accommodating space, time and randomness in network simulation Current Opinion in Biotechnology 17: 493-498
  115. 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.
  116. Steven J Plimpton et al (2005) Microbial cell modeling via reacting diffusive particles J. Phys.: Conf. Ser. 16:305-309
  117. Radek Erban, S. Jonathan Chapman (2006) What is the time scale of random sequential adsorption? arXiv:physics 0611252v1
  118. Radek Erban, S. Jonathan Chapman (2006) Realistic boundary conditions for stochastic simulations of reaction-diffusion processes arXiv:physics 0611251v1
  119. 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
  120. 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
  121. Chris Sanford, Matthew L.K. Yip, Carl White and John Parkinson (2006) Cell++-simulating biochemical pathways Bioinformatics 22:2918-2925
  122. 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
  123. 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
  124. Matthew Scott, Brian Ingalls & Mads Kaern. (2006) Estimations of intrinsic and extrinsic noise in models of nonlinear genetic networks. Chaos 16:026107