in preparation

F. Hughes, A. Barr, P. Thomas (2021) “Stochastic inheritance models reveal biological oscillators driving the cell cycle”

D. Volteras, V. Shahrezaei, P. Thomas (2021) “Reducing the dimensionality of stochastic reaction networks using timescale separation”

F. Puccioni, P. Thomas (2021) “Analytical probability functionals for age-dependent stochastic agent-based models”

2021

P. Thomas, V. Shahrezaei (2021) “Coordination of gene expression noise with cell size: analytical results for agent-based models of growing cell populations” Royal Soc Interface 18, 20210274

Summary Abstract

J. Kuntz, P. Thomas, G.B. Stan, M. Barahona (2021) “Approximations of countably-infinite linear programs over bounded measure spaces” SIAM J Optimisation 31, 604–625.

Abstract

J. Kuntz, P. Thomas, G.B. Stan, M. Barahona (2021) “Stationary distributions of continuous-time Markov chains: a review of theory and truncation-based approximations” SIAM Review 63, 3–64.

Summary Abstract

2020

M. Tonn, P. Thomas, M. Barahona, & D.A. Oyarzún (2020). “Computation of single-cell metabolite distributions using mixture models” Front Cell Develop Biol, 8, 1596.

Abstract

P. Thomas (2020) “Stochastic modelling approaches for single-cell analyses” in Systems Medicine: Integrative Qualitative and Computational Approaches (ed. By O Wolkenhauer), Vol.3, pg. 45-55 Academic Press

Abstract

W. Tang, F. Bertaux, P. Thomas, C. Stefanelli, M. Saint, S. Marguerat, V. Shahrezaei (2020) “bayNorm: Bayesian gene expression recovery, imputation and normalization for single-cell RNA-sequencing data” Bioinformatics 36, 1174-1181

Abstract

2019

J. Kuntz, P. Thomas, G.B. Stan, M. Barahona (2019) “Bounding the stationary distributions of the chemical master equation via mathematical programming” J Chem Phys 151, 034109.

Abstract

M. Tonn, P. Thomas, M. Barahona, D. Oyarzún (2019) “Stochastic modelling reveals mechanisms of metabolic heterogeneity” Commun Biol 2, 108

Abstract

J. Kuntz, P. Thomas, G.B. Stan, M. Barahona (2019) “The exit time finite state projection scheme: bounding exit distributions and occupation measures of continuous-time Markov chains” SIAM Sci Comput 41, A748-A769

Abstract

P. Thomas (2019) “Intrinsic and extrinsic noise in gene expression in lineage trees” Nat Sci Rep 9, 474

Abstract

2018

B.M.C. Martins, A.K. Tooke, P. Thomas, J.C.W. Locke (2018) “Cell size control driven by the circadian clock and environment in cyanobacteria” PNAS 115, E11415-E11424

Summary Abstract

P. Thomas, G. Terradot, V. Danos, A.Y. Weisse (2018) “Sources, propagation and consequences of stochasticity in cellular growth” Nat Commun 9, 4528

Abstract

M. Voliotis, P. Thomas, C.G. Bowsher, R. Grima (2018) “Stochastic simulation of biomolecular networks in dynamic environments” in Quantitative Biology:Theory, Computational Methods, and Models (q-bio textbook, ed. by B. Munsky, W.S. Hlavacek, L.S. Tsimring ), MIT Press

Abstract

P. Thomas (2018) “Analysis of cell size homeostasis at the single cell and population level.” Front Phys 6, 64

Abstract

2017

P. Thomas (2017) “Making sense of snapshot data: ergodic principle for clonal cell populations” J Royal Soc Interface 14, 20170467

Abstract

M. Priestman, P. Thomas, B.D. Robertson, V. Shahrezaei (2017) “Mycobacteria modify their cell size control under sub-optimal carbon sources” Front Cell Dev Biol 5, 64

Abstract

A. Andreychenko, L. Bortolussi, R. Grima, P. Thomas, V. Wolf (2017) “Distribution approximations for the chemical master equation: comparison of the method of moments and the system size expansion” Modeling Cellular Systems, 39-66

Abstract

2016

F. Fröhlich, P. Thomas, A. Kazeroonian, F.J. Theis, R. Grima, J. Hasenauer (2016) “Inference for stochastic chemical kinetics using moment equations and system size expansion” PLoS Comput Biol 12, e1005030

Summary Abstract

M. Voliotis, P. Thomas, R. Grima, C.G. Bowsher (2016) “Stochastic simulation of biomolecular networks in dynamic environments” PLoS Comput Biol 12, e1004923

Summary Abstract

2015

P. Thomas (2015) “Systematic approximation methods for stochastic biochemical kinetics” PhD Thesis, University of Edinburgh

Abstract

P. Thomas, R. Grima (2015) “Approximate probability distributions of the master equation” Phys Rev E 92, 012120

Abstract

2014

P. Thomas, C. Fleck, R. Grima, N. Popovic (2014) “System size expansion using Feynman rules and diagrams” J Phys A: Math Theor 47, 455007 • Selected for J Phys A: Highlights 2014 and IOPselect

Abstract

P. Thomas, N. Popovic and R. Grima (2014) “Phenotypic switching in gene regulatory networks” PNAS 111:6994

Summary Abstract

2013

P. Thomas, A. V. Straube, J. Timmer, C. Fleck, R. Grima (2013) “Signatures of nonlinearity in single cell noise-induced oscillations” J Theor Biol 335:222

Abstract

P. Thomas, H. Matuschek, R. Grima (2013) “How reliable is the linear noise approximation of gene regulatory networks?” BMC Genomics 14(Suppl 4):S5

Abstract

2012

P. Thomas, R. Grima, A. V. Straube (2012) “Rigorous elimination of fast stochastic variables from the linear noise approximation using projection operators” Phys Rev E 86, 041110

Abstract

P. Thomas, H. Matuschek, R. Grima (2012) “Computation of biochemical pathway fluctuations beyond the linear noise approximation using iNA” In Proceedings IEEE Int Conf Bioinformatics Biomed, pp. 1-5

Abstract

P. Thomas, H. Matuschek, R. Grima (2012) “Intrinsic Noise Analyzer: A software package for the exploration of stochastic biochemical kinetics using the system size expansion” PloS One 7, e38518

Abstract

P. Thomas, A.V. Straube, R. Grima (2012) “The slow-scale linear noise approximation: an accurate, reduced stochastic description of biochemical networks under timescale separation conditions” BMC Syst Biol 6, 39 • Selected as editor’s pick 2012

Abstract

2011

P. Thomas, A.V. Straube, R. Grima (2011) “Communication: Limitations of the stochastic quasi-steady-state approximation in open biochemical reaction networks” J Chem Phys 135, 181103

Abstract

R. Grima, P. Thomas, A.V. Straube (2011) “How accurate are the nonlinear chemical Fokker-Planck and chemical Langevin equations?” J Chem Phys 135, 084103 • Selected as editor’s choice 2011

Abstract

2010

P. Thomas, A.V. Straube, R. Grima (2010) “Stochastic theory of large-scale enzyme-reaction networks: Finite copy number corrections to rate equation models” J Chem Phys 133, 195101

Abstract