Literature DB >> 23223170

Lost in presumption: stochastic reactions in spatial models.

Anel Mahmutovic1, David Fange, Otto G Berg, Johan Elf.   

Abstract

Physical modeling is increasingly important for generating insights into intracellular processes. We describe situations in which combined spatial and stochastic aspects of chemical reactions are needed to capture the relevant dynamics of biochemical systems.

Mesh：

Year:  2012        PMID： 23223170     DOI： 10.1038/nmeth.2253

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  13 in total

1.  Summing up the noise in gene networks.

Authors:  Johan Paulsson
Journal:  Nature       Date:  2004-01-29       Impact factor: 49.962

2.  Finding the center reliably: robust patterns of developmental gene expression.

Authors:  Martin Howard; Pieter Rein ten Wolde
Journal:  Phys Rev Lett       Date:  2005-11-09       Impact factor: 9.161

3.  Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases.

Authors:  J Elf; M Ehrenberg
Journal:  Syst Biol (Stevenage)       Date:  2004-12

4.  Spatio-temporal correlations can drastically change the response of a MAPK pathway.

Authors:  Koichi Takahashi; Sorin Tanase-Nicola; Pieter Rein ten Wolde
Journal:  Proc Natl Acad Sci U S A       Date:  2010-01-25       Impact factor: 11.205

5.  A model for the statistical fluctuations of protein numbers in a microbial population.

Authors:  O G Berg
Journal:  J Theor Biol       Date:  1978-04-20       Impact factor: 2.691

6.  MesoRD 1.0: Stochastic reaction-diffusion simulations in the microscopic limit.

Authors:  David Fange; Anel Mahmutovic; Johan Elf
Journal:  Bioinformatics       Date:  2012-10-07       Impact factor: 6.937

7.  Detailed simulations of cell biology with Smoldyn 2.1.

Authors:  Steven S Andrews; Nathan J Addy; Roger Brent; Adam P Arkin
Journal:  PLoS Comput Biol       Date:  2010-03-12       Impact factor: 4.475

8.  Fast rebinding increases dwell time of Src homology 2 (SH2)-containing proteins near the plasma membrane.

Authors:  Dongmyung Oh; Mari Ogiue-Ikeda; Joshua A Jadwin; Kazuya Machida; Bruce J Mayer; Ji Yu
Journal:  Proc Natl Acad Sci U S A       Date:  2012-08-10       Impact factor: 11.205

9.  Computational modeling of cellular signaling processes embedded into dynamic spatial contexts.

Authors:  Bastian R Angermann; Frederick Klauschen; Alex D Garcia; Thorsten Prustel; Fengkai Zhang; Ronald N Germain; Martin Meier-Schellersheim
Journal:  Nat Methods       Date:  2012-01-29       Impact factor: 28.547

10.  Noise-induced Min phenotypes in E. coli.

Authors:  David Fange; Johan Elf
Journal:  PLoS Comput Biol       Date:  2006-05-18       Impact factor: 4.475
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  15 in total

1.  Accuracy of the Michaelis-Menten approximation when analysing effects of molecular noise.

Authors:  Michael J Lawson; Linda Petzold; Andreas Hellander
Journal:  J R Soc Interface       Date:  2015-05-06       Impact factor: 4.118

2.  Extracting intracellular diffusive states and transition rates from single-molecule tracking data.

Authors:  Fredrik Persson; Martin Lindén; Cecilia Unoson; Johan Elf
Journal:  Nat Methods       Date:  2013-02-10       Impact factor: 28.547

3.  Mesoscopic-microscopic spatial stochastic simulation with automatic system partitioning.

Authors:  Stefan Hellander; Andreas Hellander; Linda Petzold
Journal:  J Chem Phys       Date:  2017-12-21       Impact factor: 3.488

4.  Toward a Whole-Cell Model of Ribosome Biogenesis: Kinetic Modeling of SSU Assembly.

Authors:  Tyler M Earnest; Jonathan Lai; Ke Chen; Michael J Hallock; James R Williamson; Zaida Luthey-Schulten
Journal:  Biophys J       Date:  2015-08-30       Impact factor: 4.033

5.  A unified framework for analysis of individual-based models in ecology and beyond.

Authors:  Stephen J Cornell; Yevhen F Suprunenko; Dmitri Finkelshtein; Panu Somervuo; Otso Ovaskainen
Journal:  Nat Commun       Date:  2019-10-17       Impact factor: 14.919

6.  Ratiometric GPCR signaling enables directional sensing in yeast.

Authors:  Nicholas T Henderson; Michael Pablo; Debraj Ghose; Manuella R Clark-Cotton; Trevin R Zyla; James Nolen; Timothy C Elston; Daniel J Lew
Journal:  PLoS Biol       Date:  2019-10-17       Impact factor: 8.029

7.  A general mechanism for competitor-induced dissociation of molecular complexes.

Authors:  Thayaparan Paramanathan; Daniel Reeves; Larry J Friedman; Jane Kondev; Jeff Gelles
Journal:  Nat Commun       Date:  2014-10-24       Impact factor: 14.919

8.  Multi-level kinetic model of mRNA delivery via transfection of lipoplexes.

Authors:  Thomas S Ligon; Carolin Leonhardt; Joachim O Rädler
Journal:  PLoS One       Date:  2014-09-19       Impact factor: 3.240

9.  Particle-based simulations of polarity establishment reveal stochastic promotion of Turing pattern formation.

Authors:  Michael Pablo; Samuel A Ramirez; Timothy C Elston
Journal:  PLoS Comput Biol       Date:  2018-03-12       Impact factor: 4.475

10.  Cox process representation and inference for stochastic reaction-diffusion processes.

Authors:  David Schnoerr; Ramon Grima; Guido Sanguinetti
Journal:  Nat Commun       Date:  2016-05-25       Impact factor: 14.919
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