| Year |
Citation |
Score |
| 2023 |
Öcal K, Sanguinetti G, Grima R. Model reduction for the Chemical Master Equation: An information-theoretic approach. The Journal of Chemical Physics. 158: 114113. PMID 36948813 DOI: 10.1063/5.0131445 |
0.32 |
|
| 2021 |
Sukys A, Grima R. MomentClosure.jl: automated moment closure approximations in Julia. Bioinformatics (Oxford, England). PMID 34170295 DOI: 10.1093/bioinformatics/btab469 |
0.359 |
|
| 2020 |
Cao Z, Filatova T, Oyarzún DA, Grima R. A Stochastic Model of Gene Expression with Polymerase Recruitment and Pause Release. Biophysical Journal. PMID 32814062 DOI: 10.1016/J.Bpj.2020.07.020 |
0.347 |
|
| 2020 |
Perez-Carrasco R, Beentjes C, Grima R. Effects of cell cycle variability on lineage and population measurements of messenger RNA abundance. Journal of the Royal Society, Interface. 17: 20200360. PMID 32634365 DOI: 10.1098/Rsif.2020.0360 |
0.322 |
|
| 2020 |
Jia C, Grima R. Dynamical phase diagram of an auto-regulating gene in fast switching conditions. The Journal of Chemical Physics. 152: 174110. PMID 32384856 DOI: 10.1063/5.0007221 |
0.365 |
|
| 2020 |
Beentjes CHL, Perez-Carrasco R, Grima R. Exact solution of stochastic gene expression models with bursting, cell cycle and replication dynamics. Physical Review. E. 101: 032403. PMID 32290003 DOI: 10.1103/Physreve.101.032403 |
0.417 |
|
| 2020 |
Holehouse J, Cao Z, Grima R. Stochastic Modeling of Autoregulatory Genetic Feedback Loops: A Review and Comparative Study. Biophysical Journal. PMID 32155410 DOI: 10.1016/J.Bpj.2020.02.016 |
0.361 |
|
| 2020 |
Jia C, Grima R. Small protein number effects in stochastic models of autoregulated bursty gene expression. The Journal of Chemical Physics. 152: 084115. PMID 32113345 DOI: 10.1063/1.5144578 |
0.35 |
|
| 2020 |
Cao Z, Grima R. Analytical distributions for detailed models of stochastic gene expression in eukaryotic cells. Proceedings of the National Academy of Sciences of the United States of America. PMID 32071224 DOI: 10.1073/Pnas.1910888117 |
0.361 |
|
| 2020 |
Holehouse J, Gupta A, Grima R. Steady-state fluctuations of a genetic feedback loop with fluctuating rate parameters using the unified colored noise approximation Journal of Physics A. DOI: 10.1088/1751-8121/Aba4D0 |
0.316 |
|
| 2020 |
Öcal K, Grima R, Sanguinetti G. Parameter estimation for biochemical reaction networks using Wasserstein distances Journal of Physics A. 53: 34002. DOI: 10.1088/1751-8121/Ab5877 |
0.35 |
|
| 2019 |
Holehouse J, Grima R. Revisiting the Reduction of Stochastic Models of Genetic Feedback Loops with Fast Promoter Switching. Biophysical Journal. PMID 31540707 DOI: 10.1016/J.Bpj.2019.08.021 |
0.388 |
|
| 2019 |
Keizer EM, Bastian B, Smith RW, Grima R, Fleck C. Extending the linear-noise approximation to biochemical systems influenced by intrinsic noise and slow lognormally distributed extrinsic noise. Physical Review. E. 99: 052417. PMID 31212540 DOI: 10.1103/Physreve.99.052417 |
0.354 |
|
| 2019 |
Cao Z, Grima R. Accuracy of parameter estimation for auto-regulatory transcriptional feedback loops from noisy data. Journal of the Royal Society, Interface. 16: 20180967. PMID 30940028 DOI: 10.1098/Rsif.2018.0967 |
0.353 |
|
| 2019 |
Moraki E, Grima R, Painter KJ. A stochastic model of corneal epithelium maintenance and recovery following perturbation Journal of Mathematical Biology. 78: 1245-1276. PMID 30478759 DOI: 10.1007/S00285-018-1308-9 |
0.385 |
|
| 2018 |
Cao Z, Grima R. Linear mapping approximation of gene regulatory networks with stochastic dynamics. Nature Communications. 9: 3305. PMID 30120244 DOI: 10.1038/S41467-018-05822-0 |
0.386 |
|
| 2018 |
Smith S, Grima R. Spatial Stochastic Intracellular Kinetics: A Review of Modelling Approaches. Bulletin of Mathematical Biology. PMID 29785521 DOI: 10.1007/S11538-018-0443-1 |
0.435 |
|
| 2018 |
Smith S, Grima R. Single-cell variability in multicellular organisms. Nature Communications. 9: 345. PMID 29367605 DOI: 10.1038/S41467-017-02710-X |
0.348 |
|
| 2017 |
Schnoerr D, Cseke B, Grima R, Sanguinetti G. Efficient Low-Order Approximation of First-Passage Time Distributions. Physical Review Letters. 119: 210601. PMID 29219406 DOI: 10.1103/Physrevlett.119.210601 |
0.4 |
|
| 2017 |
Cianci C, Smith S, Grima R. Capturing Brownian dynamics with an on-lattice model of hard-sphere diffusion. Physical Review. E. 95: 052118. PMID 28618561 DOI: 10.1103/Physreve.95.052118 |
0.426 |
|
| 2017 |
Smith S, Cianci C, Grima R. Macromolecular crowding directs the motion of small molecules inside cells. Journal of the Royal Society, Interface. 14. PMID 28615492 DOI: 10.1098/Rsif.2017.0047 |
0.383 |
|
| 2017 |
Smith S, Grima R. Fast simulation of Brownian dynamics in a crowded environment. The Journal of Chemical Physics. 146: 024105. PMID 28088138 DOI: 10.1063/1.4973606 |
0.355 |
|
| 2017 |
Cianci C, Schnoerr D, Piehler A, Grima R. An alternative route to the system-size expansion Journal of Physics a: Mathematical and Theoretical. 50: 395003. DOI: 10.1088/1751-8121/Aa85Aa |
0.394 |
|
| 2017 |
Schnoerr D, Sanguinetti G, Grima R. Approximation and inference methods for stochastic biochemical kinetics—a tutorial review Journal of Physics a: Mathematical and Theoretical. 50: 093001. DOI: 10.1088/1751-8121/Aa54D9 |
0.428 |
|
| 2016 |
Grima R, Leier A. Exact Product Formation Rates for Stochastic Enzyme Kinetics. The Journal of Physical Chemistry. B. PMID 27959536 DOI: 10.1021/Acs.Jpcb.6B08891 |
0.344 |
|
| 2016 |
Fröhlich F, Thomas P, Kazeroonian A, Theis FJ, Grima R, Hasenauer J. Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion. Plos Computational Biology. 12: e1005030. PMID 27447730 DOI: 10.1371/Journal.Pcbi.1005030 |
0.414 |
|
| 2016 |
Smith S, Grima R. Breakdown of the reaction-diffusion master equation with nonelementary rates. Physical Review. E. 93: 052135. PMID 27300857 DOI: 10.1103/Physreve.93.052135 |
0.448 |
|
| 2016 |
Voliotis M, Thomas P, Grima R, Bowsher CG. Stochastic Simulation of Biomolecular Networks in Dynamic Environments. Plos Computational Biology. 12: e1004923. PMID 27248512 DOI: 10.1371/Journal.Pcbi.1004923 |
0.383 |
|
| 2016 |
Schnoerr D, Grima R, Sanguinetti G. Cox process representation and inference for stochastic reaction-diffusion processes. Nature Communications. 7: 11729. PMID 27222432 DOI: 10.1038/Ncomms11729 |
0.39 |
|
| 2016 |
Smith S, Cianci C, Grima R. Analytical approximations for spatial stochastic gene expression in single cells and tissues. Journal of the Royal Society, Interface / the Royal Society. 13. PMID 27146686 DOI: 10.1098/Rsif.2015.1051 |
0.439 |
|
| 2016 |
Cianci C, Smith S, Grima R. Molecular finite-size effects in stochastic models of equilibrium chemical systems. The Journal of Chemical Physics. 144: 084101. PMID 26931675 DOI: 10.1063/1.4941583 |
0.471 |
|
| 2016 |
Smith S, Grima R. Breakdown of the reaction-diffusion master equation with nonelementary rates Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 93. DOI: 10.1103/PhysRevE.93.052135 |
0.346 |
|
| 2015 |
Smith S, Cianci C, Grima R. Model reduction for stochastic chemical systems with abundant species. The Journal of Chemical Physics. 143: 214105. PMID 26646867 DOI: 10.1063/1.4936394 |
0.388 |
|
| 2015 |
Schnoerr D, Sanguinetti G, Grima R. Comparison of different moment-closure approximations for stochastic chemical kinetics. The Journal of Chemical Physics. 143: 185101. PMID 26567686 DOI: 10.1063/1.4934990 |
0.413 |
|
| 2015 |
Grima R. Linear-noise approximation and the chemical master equation agree up to second-order moments for a class of chemical systems. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 92: 042124. PMID 26565185 DOI: 10.1103/Physreve.92.042124 |
0.408 |
|
| 2015 |
Thomas P, Grima R. Approximate probability distributions of the master equation. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 92: 012120. PMID 26274137 DOI: 10.1103/Physreve.92.012120 |
0.424 |
|
| 2015 |
Duncan A, Liao S, Vejchodský T, Erban R, Grima R. Noise-induced multistability in chemical systems: Discrete versus continuum modeling. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 91: 042111. PMID 25974443 DOI: 10.1103/Physreve.91.042111 |
0.4 |
|
| 2014 |
Schnoerr D, Sanguinetti G, Grima R. Validity conditions for moment closure approximations in stochastic chemical kinetics. The Journal of Chemical Physics. 141: 084103. PMID 25173001 DOI: 10.1063/1.4892838 |
0.443 |
|
| 2014 |
Schnoerr D, Sanguinetti G, Grima R. The complex chemical Langevin equation. The Journal of Chemical Physics. 141: 024103. PMID 25027995 DOI: 10.1063/1.4885345 |
0.436 |
|
| 2014 |
Middleton AM, Fleck C, Grima R. A continuum approximation to an off-lattice individual-cell based model of cell migration and adhesion. Journal of Theoretical Biology. 359: 220-32. PMID 24972155 DOI: 10.1016/J.Jtbi.2014.06.011 |
0.369 |
|
| 2014 |
Thomas P, Popović N, Grima R. Phenotypic switching in gene regulatory networks. Proceedings of the National Academy of Sciences of the United States of America. 111: 6994-9. PMID 24782538 DOI: 10.1073/Pnas.1400049111 |
0.345 |
|
| 2014 |
Grima R. Anomalous fluctuation scaling laws in stochastic enzyme kinetics: increase of noise strength with the mean concentration. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 89: 012710. PMID 24580260 DOI: 10.1103/Physreve.89.012710 |
0.326 |
|
| 2014 |
Grima R, Walter NG, Schnell S. Single-molecule enzymology à la Michaelis-Menten. The Febs Journal. 281: 518-30. PMID 24289171 DOI: 10.1111/Febs.12663 |
0.401 |
|
| 2014 |
Toner DL, Grima R. Effects of bursty protein production on the noisy oscillatory properties of downstream pathways. Scientific Reports. 3: 2438. PMID 23942456 DOI: 10.1038/Srep02438 |
0.312 |
|
| 2014 |
Thomas P, Fleck C, Grima R, Popović N. System size expansion using Feynman rules and diagrams Journal of Physics a: Mathematical and Theoretical. 47. DOI: 10.1088/1751-8113/47/45/455007 |
0.421 |
|
| 2013 |
Thomas P, Matuschek H, Grima R. How reliable is the linear noise approximation of gene regulatory networks? Bmc Genomics. 14: S5. PMID 24266939 DOI: 10.1186/1471-2164-14-S4-S5 |
0.374 |
|
| 2013 |
Thomas P, Straube AV, Timmer J, Fleck C, Grima R. Signatures of nonlinearity in single cell noise-induced oscillations. Journal of Theoretical Biology. 335: 222-34. PMID 23831270 DOI: 10.1016/J.Jtbi.2013.06.021 |
0.339 |
|
| 2013 |
Basile R, Grima R, Popović N. A graph-based approach for the approximate solution of the chemical master equation. Bulletin of Mathematical Biology. 75: 1653-96. PMID 23797789 DOI: 10.1007/S11538-013-9864-Z |
0.442 |
|
| 2013 |
Toner DL, Grima R. Molecular noise induces concentration oscillations in chemical systems with stable node steady states. The Journal of Chemical Physics. 138: 055101. PMID 23406149 DOI: 10.1063/1.4788979 |
0.336 |
|
| 2012 |
Thomas P, Grima R, Straube AV. Rigorous elimination of fast stochastic variables from the linear noise approximation using projection operators. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 86: 041110. PMID 23214532 DOI: 10.1103/Physreve.86.041110 |
0.356 |
|
| 2012 |
Grima R, Kim J. Modelling noise in biochemical reaction networks Iet Systems Biology. 6: 101-101. PMID 23039690 DOI: 10.1049/Iet-Syb.2012.0039 |
0.371 |
|
| 2012 |
Grima R, Schmidt DR, Newman TJ. Steady-state fluctuations of a genetic feedback loop: an exact solution. The Journal of Chemical Physics. 137: 035104. PMID 22830733 DOI: 10.1063/1.4736721 |
0.661 |
|
| 2012 |
Thomas P, Matuschek H, Grima R. Intrinsic noise analyzer: a software package for the exploration of stochastic biochemical kinetics using the system size expansion. Plos One. 7: e38518. PMID 22723865 DOI: 10.1371/Journal.Pone.0038518 |
0.446 |
|
| 2012 |
Thomas P, Straube AV, Grima R. The slow-scale linear noise approximation: an accurate, reduced stochastic description of biochemical networks under timescale separation conditions. Bmc Systems Biology. 6: 39. PMID 22583770 DOI: 10.1186/1752-0509-6-39 |
0.389 |
|
| 2012 |
Grima R. A study of the accuracy of moment-closure approximations for stochastic chemical kinetics. The Journal of Chemical Physics. 136: 154105. PMID 22519313 DOI: 10.1063/1.3702848 |
0.445 |
|
| 2012 |
Ramaswamy R, González-Segredo N, Sbalzarini IF, Grima R. Discreteness-induced concentration inversion in mesoscopic chemical systems. Nature Communications. 3: 779. PMID 22491327 DOI: 10.1038/Ncomms1775 |
0.425 |
|
| 2011 |
Grima R. Construction and accuracy of partial differential equation approximations to the chemical master equation. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 84: 056109. PMID 22181475 DOI: 10.1103/Physreve.84.056109 |
0.396 |
|
| 2011 |
Thomas P, Straube AV, Grima R. Communication: limitations of the stochastic quasi-steady-state approximation in open biochemical reaction networks. The Journal of Chemical Physics. 135: 181103. PMID 22088045 DOI: 10.1063/1.3661156 |
0.44 |
|
| 2011 |
Grima R, Thomas P, Straube AV. How accurate are the nonlinear chemical Fokker-Planck and chemical Langevin equations? The Journal of Chemical Physics. 135: 084103. PMID 21895155 DOI: 10.1063/1.3625958 |
0.425 |
|
| 2010 |
Thomas P, Straube AV, Grima R. Stochastic theory of large-scale enzyme-reaction networks: finite copy number corrections to rate equation models. The Journal of Chemical Physics. 133: 195101. PMID 21090871 DOI: 10.1063/1.3505552 |
0.435 |
|
| 2010 |
Grima R. An effective rate equation approach to reaction kinetics in small volumes: Theory and application to biochemical reactions in nonequilibrium steady-state conditions Journal of Chemical Physics. 133: 35101-35101. PMID 20649359 DOI: 10.1063/1.3454685 |
0.466 |
|
| 2010 |
Grima R, Yaliraki SN, Barahona M. Crowding-induced anisotropic transport modulates reaction kinetics in nanoscale porous media. The Journal of Physical Chemistry. B. 114: 5380-5. PMID 20369856 DOI: 10.1021/Jp9025865 |
0.371 |
|
| 2010 |
Grima R. Intrinsic biochemical noise in crowded intracellular conditions The Journal of Chemical Physics. 132: 185102. DOI: 10.1063/1.3427244 |
0.443 |
|
| 2009 |
Grima R. Investigating the robustness of the classical enzyme kinetic equations in small intracellular compartments. Bmc Systems Biology. 3: 101. PMID 19814817 DOI: 10.1186/1752-0509-3-101 |
0.382 |
|
| 2009 |
Grima R. Noise-induced breakdown of the Michaelis-Menten equation in steady-state conditions. Physical Review Letters. 102: 218103. PMID 19519139 DOI: 10.1103/PhysRevLett.102.218103 |
0.329 |
|
| 2008 |
Grima R, Schnell S. Modelling reaction kinetics inside cells. Essays in Biochemistry. 45: 41-56. PMID 18793122 DOI: 10.1042/Bse0450041 |
0.391 |
|
| 2008 |
Grima R. Multiscale modeling of biological pattern formation. Current Topics in Developmental Biology. 81: 435-60. PMID 18023737 DOI: 10.1016/S0070-2153(07)81015-5 |
0.345 |
|
| 2007 |
Grima R, Schnell S. A mesoscopic simulation approach for modeling intracellular reactions Journal of Statistical Physics. 128: 139-164. DOI: 10.1007/S10955-006-9202-Z |
0.346 |
|
| 2006 |
Grima R, Schnell S. A systematic investigation of the rate laws valid in intracellular environments Biophysical Chemistry. 124: 1-10. PMID 16781049 DOI: 10.1016/J.Bpc.2006.04.019 |
0.363 |
|
| 2006 |
Grima R, Schnell S. How reaction kinetics with time-dependent rate coefficients differs from generalized mass action. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 7: 1422-4. PMID 16755640 DOI: 10.1002/Cphc.200600081 |
0.371 |
|
| 2005 |
Grima R. Strong-coupling dynamics of a multicellular chemotactic system. Physical Review Letters. 95: 128103. PMID 16197116 DOI: 10.1103/Physrevlett.95.128103 |
0.409 |
|
| 2004 |
Newman TJ, Grima R. Many-body theory of chemotactic cell-cell interactions. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 70: 051916. PMID 15600665 DOI: 10.1103/Physreve.70.051916 |
0.655 |
|
| 2004 |
Grima R, Newman TJ. Accurate discretization of advection-diffusion equations. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 70: 036703. PMID 15524671 DOI: 10.1103/Physreve.70.036703 |
0.656 |
|
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