Ramon Grima
Contact details
- Tel: +44 (0)131 651 651 9060
- Email: Ramon.Grima@ed.ac.uk
- Web: Group Website
Address
- Street
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Rm. 3.03, Waddington Building
- City
- Post code
Background
2000 B. Sc (Hons), Physics and Pure Mathematics, University of Malta, Malta
2002 M.A. Physics, University of Virginia, USA
2005 Ph.D Physics, Arizona State University, USA
2005-2006 Postdoctoral Fellow, School of Informatics, Indiana University, US
2006-2008 Mathematical Institute Fellow, Imperial College London
2008-2013 Lecturer, University of Edinburgh
2013-2019 Reader, University of Edinburgh
2019- Professor University of Edinburgh
Undergraduate teaching
Quantification in Life Sciences (Course Organizer)
Structures and Functions of Proteins
Research summary
http://grimagroup.bio.ed.ac.uk/
My research is focused on the exact or approximate solution of the chemical master equation describing biochemical systems, with a particular focus on gene regulatory networks. I am also interested in the approximate solution of the reaction-diffusion master equation and its extension to take into account the complex nature of the cytoplasm e.g. phenomena such as macromolecular crowding. A main aim is to obtain closed-form solutions for the approximate distributions of molecule numbers (or of the moments) which can help us gain intuition about stochastic intracellular dynamics, in particular to understand how living cells have evolved to deal with inherent noise. More recently I have a burgeoning interest in developing efficient methods for the estimation of parameter values for gene regulatory networks from single cell and population snapshot data.
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Model reduction for the chemical master equation: An information-theoretic approach
(20 pages)
In:
The Journal of Chemical Physics, vol. 158
DOI: https://doi.org/10.1063/5.0131445
Research output: Contribution to Journal › Article (E-pub ahead of print) -
Steady-state distributions of nascent RNA for general initiation mechanisms
(14 pages)
In:
Physical Review Research, vol. 5
Research output: Contribution to Journal › Article (Published) -
Coupling gene expression dynamics to cell size dynamics and cell cycle events: Exact and approximate solutions of the extended telegraph model
(43 pages)
In:
iScience, vol. 26
DOI: https://doi.org/10.1016/j.isci.2022.105746
Research output: Contribution to Journal › Article (Published) -
Regulation of stem cell dynamics through volume exclusion
(22 pages)
In:
Proceedings of the royal society of london series a-Mathematical and physical sciences, vol. 478
DOI: https://doi.org/10.1098/rspa.2022.0376
Research output: Contribution to Journal › Article (Published) -
Quantifying how post-transcriptional noise and gene copy number variation bias transcriptional parameter inference from mRNA distributions
(49 pages)
In:
eLIFE, vol. 11
DOI: https://doi.org/10.7554/eLife.82493
Research output: Contribution to Journal › Article (Published) -
Concentration fluctuations in growing and dividing cells: Insights into the emergence of concentration homeostasis
(34 pages)
In:
PLoS Computational Biology, vol. 18
DOI: https://doi.org/10.1371/journal.pcbi.1010574
Research output: Contribution to Journal › Article (Published) -
Approximating solutions of the chemical master equation using neural networks
(22 pages)
In:
iScience, vol. 25
DOI: https://doi.org/10.1016/j.isci.2022.105010
Research output: Contribution to Journal › Article (Published) -
DelaySSAToolkit.jl: Stochastic simulation of reaction systems with time delays in Julia
(3 pages)
In:
Bioinformatics, vol. 38, pp. 4243-4245
DOI: https://doi.org/10.1093/bioinformatics/btac472
Research output: Contribution to Journal › Article (Published) -
Bayesian learning of effective chemical master equations in crowded intracellular conditions
(20 pages)
DOI: https://doi.org/10.1007/978-3-031-15034-0_12
Research output: Contribution to Conference › Conference contribution (E-pub ahead of print) -
Inference and Uncertainty Quantification of Stochastic Gene Expression via Synthetic Models
(10 pages)
In:
Journal of the Royal Society. Interface, vol. 19
DOI: https://doi.org/10.1098/rsif.2022.0153
Research output: Contribution to Journal › Article (Published) -
Modulation of nuclear and cytoplasmic mRNA fluctuations by time-dependent stimuli: Analytical distributions
(15 pages)
In:
Mathematical biosciences, vol. 347
DOI: https://doi.org/10.1016/j.mbs.2022.108828
Research output: Contribution to Journal › Article (E-pub ahead of print) -
Characterizing non-exponential growth and bimodal cell size distributions in fission yeast: An analytical approach
In:
PLoS Computational Biology, vol. 18
DOI: https://doi.org/10.1371/journal.pcbi.1009793
Research output: Contribution to Journal › Article (Published) -
Mean-field theory accurately captures the variation of copy number distributions across the mRNA life cycle
(17 pages)
In:
Physical Review E, vol. 105
DOI: https://doi.org/10.1103/PhysRevE.105.014410
Research output: Contribution to Journal › Article (Published) -
Cluster mean-field theory accurately predicts statistical properties of large-scale DNA methylation patterns
In:
Journal of the Royal Society. Interface, vol. 19
DOI: https://doi.org/10.1098/rsif.2021.0707
Research output: Contribution to Journal › Article (Published) -
Distinguishing between models of mammalian gene expression: Telegraph-like models versus mechanistic models
In:
Journal of the Royal Society. Interface, vol. 18
DOI: https://doi.org/10.1098/rsif.2021.0510
Research output: Contribution to Journal › Article (Published) -
MomentClosure.jl: Automated moment closure approximations in Julia
(2 pages)
In:
Bioinformatics, vol. 38, pp. 289-290
DOI: https://doi.org/10.1093/bioinformatics/btab469
Research output: Contribution to Journal › Article (Published) -
Neural network aided approximation and parameter inference of non-Markovian models of gene expression
(12 pages)
In:
Nature Communications, vol. 12
DOI: https://doi.org/10.1038/s41467-021-22919-1
Research output: Contribution to Journal › Article (Published) -
Frequency domain analysis of fluctuations of mRNA and protein copy numbers within a cell lineage: Theory and experimental validation
(23 pages)
In:
Physical Review X
DOI: https://doi.org/10.1103/PhysRevX.11.021032
Research output: Contribution to Journal › Article (Published) -
Cell size distribution of lineage data: Analytic results and parameter inference
(34 pages)
In:
iScience, vol. 24
DOI: https://doi.org/10.1016/j.isci.2021.102220
Research output: Contribution to Journal › Article (Published) -
Statistics of nascent and mature RNA fluctuations in a stochastic model of transcriptional initiation, elongation, pausing, and termination
(62 pages)
In:
Bulletin of Mathematical Biology, vol. 83
DOI: https://doi.org/10.1007/s11538-020-00827-7
Research output: Contribution to Journal › Article (Published)