PT
Philipp Thomas
Models, Biologicalsystems biologyq-bio.MNcond-mat.stat-mechq-bio.QMq-bio.PESoftwareGene Regulatory Networksmath.OCphysics.chem-ph
On Valency
published · living versionsW_gaqm9khp·v1 · currentpublished
Simulation-free approximate Bayesian computation for stochastic reaction networks
with Zekai Li, Mauricio Barahona
1 version
Preprints & journals
38 papers in the corpus · 1968–2026Integrin α11 is enriched in quiescence and promotes cell-cycle re-entry through destabilisation of the CDK inhibitor p2710.64898/2026.08.29.748043v1 · Kaur, E., Holt, J. A., Wilson, R. et al.2026 · 0 citationsbioRxiv
AgentBasedModeling.jl: A tool for stochastic simulation of structured population dynamics.42525710 · Piho, Paul, Thomas, Philipp2026 · 1 citationPLoS computational biology. 2026;22(7):e1014366
Cell size control in bacteria is modulated through extrinsic noise, single-cell- and population-growth2601.05193v1 · Arthur Genthon, Philipp Thomas2026 · 0 citationsarXiv
Environmental and molecular noise buffering by the cyanobacterial clock in individual cells.40234415 · Eremina, Aleksandra, Schwall, Christian, Saez, Teresa et al.2025 · 8 citationsNature communications. 2025;16(1):3566
Moment-based parameter inference with error guarantees for stochastic reaction networks.40183299 · Li, Zekai, Barahona, Mauricio, Thomas, Philipp2025 · 1 citationThe Journal of chemical physics. 2025;162(13)
Pro-survival roles for p21(Cip1/Waf1) in non-small cell lung cancer.39706988 · Cutty, S J, Hughes, F A, Ortega-Prieto, P et al.2025 · 6 citationsBritish journal of cancer. 2025;132(5):421-437
Survival Resonances during Fractional Killing of Cell Populations.39576926 · Puccioni, Francesco, Pausch, Johannes, Piho, Paul et al.2024 · 3 citationsPhysical review letters. 2024;133(19):198401
Global transcription regulation revealed from dynamical correlations in time-resolved single-cell RNA sequencing.39121860 · Volteras, Dimitris, Shahrezaei, Vahid, Thomas, Philipp2024 · 15 citationsCell systems. 2024;15(8):694-708.e12
Feedback between stochastic gene networks and population dynamics enables cellular decision-making.38787956 · Piho, Paul, Thomas, Philipp2024 · 7 citationsScience advances. 2024;10(21):eadl4895
Modelling capture efficiency of single-cell RNA-sequencing data improves inference of transcriptome-wide burst kinetics.37354494 · Tang, Wenhao, Jørgensen, Andreas Christ Sølvsten, Marguerat, Samuel et al.2023 · 43 citationsBioinformatics (Oxford, England). 2023;39(7)
Patterns of interdivision time correlations reveal hidden cell cycle factors.36377847 · Hughes, Fern A, Barr, Alexis R, Thomas, Philipp2023 · 6 citationseLife. 2022;11
Coordination of gene expression noise with cell size: analytical results for agent-based models of growing cell populations.34034535 · Thomas, Philipp, Shahrezaei, Vahid2021 · 47 citationsJournal of the Royal Society, Interface. 2021;18(178):20210274
Computation of Single-Cell Metabolite Distributions Using Mixture Models.33415109 · Tonn, Mona K, Thomas, Philipp, Barahona, Mauricio et al.2025 · 13 citationsFrontiers in cell and developmental biology. 2020;8:614832
bayNorm: Bayesian gene expression recovery, imputation and normalization for single-cell RNA-sequencing data.31584606 · Tang, Wenhao, Bertaux, François, Thomas, Philipp et al.2020 · 117 citationsBioinformatics (Oxford, England). 2020;36(4):1174-1181
Stationary distributions of continuous-time Markov chains: a review of theory and truncation-based approximations1909.05794v2 · Juan Kuntz, Philipp Thomas, Guy-Bart Stan et al.2019 · 42 citationsarXiv
Stochastic modelling reveals mechanisms of metabolic heterogeneity.30911683 · Tonn, Mona K, Thomas, Philipp, Barahona, Mauricio et al.2020 · 58 citationsCommunications biology. 2019;2:108
Intrinsic and extrinsic noise of gene expression in lineage trees.30679440 · Thomas, Philipp2020 · 70 citationsScientific reports. 2019;9(1):474
Cell size control driven by the circadian clock and environment in cyanobacteria.30409801 · Martins, Bruno M C, Tooke, Amy K, Thomas, Philipp et al.2019 · 87 citationsProceedings of the National Academy of Sciences of the United States of America. 2018;115(48):E11415-E11424
Sources, propagation and consequences of stochasticity in cellular growth.30375377 · Thomas, Philipp, Terradot, Guillaume, Danos, Vincent et al.2019 · 107 citationsNature communications. 2018;9(1):4528
Approximations of countably-infinite linear programs over bounded measure spaces1810.03658v3 · Juan Kuntz, Philipp Thomas, Guy-Bart Stan et al.2018 · 6 citationsarXiv
Analysis of cell size homeostasis at the single-cell and population level10.1101/338632v1 · Thomas, P.2018 · 42 citationsbioRxiv
Making sense of snapshot data: ergodic principle for clonal cell populations.29187636 · Thomas, Philipp2018 · 60 citationsJournal of the Royal Society, Interface. 2017;14(136)
Mycobacteria Modify Their Cell Size Control under Sub-Optimal Carbon Sources.28748182 · Priestman, Miles, Thomas, Philipp, Robertson, Brian D et al.2025 · 50 citationsFrontiers in cell and developmental biology. 2017;5:64
Single-cell histories in growing populations: relating physiological variability to population growth10.1101/100495v1 · Thomas, P.2017 · 17 citationsbioRxiv
Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion.27447730 · Fröhlich, Fabian, Thomas, Philipp, Kazeroonian, Atefeh et al.2017 · 79 citationsPLoS computational biology. 2016;12(7):e1005030
Stochastic Simulation of Biomolecular Networks in Dynamic Environments.27248512 · Voliotis, Margaritis, Thomas, Philipp, Grima, Ramon et al.2017 · 80 citationsPLoS computational biology. 2016;12(6):e1004923
Distribution approximations for the chemical master equation: comparison of the method of moments and the system size expansion1509.09104v1 · Alexander Andreychenko, Luca Bortolussi, Ramon Grima et al.2015 · 18 citationsarXiv
Approximate probability distributions of the master equation.26274137 · Thomas, Philipp, Grima, Ramon2016 · 32 citationsPhysical review. E, Statistical, nonlinear, and soft matter physics. 2015;92(1):012120
System size expansion using Feynman rules and diagrams1409.1439v1 · Philipp Thomas, Christian Fleck, Ramon Grima et al.2014 · 19 citationsarXiv
Phenotypic switching in gene regulatory networks.24782538 · Thomas, Philipp, Popović, Nikola, Grima, Ramon2014 · 171 citationsProceedings of the National Academy of Sciences of the United States of America. 2014;111(19):6994-9
Signatures of nonlinearity in single cell noise-induced oscillations.23831270 · Thomas, Philipp, Straube, Arthur V, Timmer, Jens et al.2014 · 51 citationsJournal of theoretical biology. 2013;335:222-34
How reliable is the linear noise approximation of gene regulatory networks?24266939 · Thomas, Philipp, Matuschek, Hannes, Grima, Ramon2014 · 47 citationsBMC genomics. 2013;14 Suppl 4:S5
Rigorous elimination of fast stochastic variables from the linear noise approximation using projection operators.23214532 · Thomas, Philipp, Grima, Ramon, Straube, Arthur V2013 · 52 citationsPhysical review. E, Statistical, nonlinear, and soft matter physics. 2012;86(4 Pt 1):041110
The slow-scale linear noise approximation: an accurate, reduced stochastic description of biochemical networks under timescale separation conditions.22583770 · Thomas, Philipp, Straube, Arthur V, Grima, Ramon2013 · 124 citationsBMC systems biology. 2012;6:39
Intrinsic noise analyzer: a software package for the exploration of stochastic biochemical kinetics using the system size expansion.22723865 · Thomas, Philipp, Matuschek, Hannes, Grima, Ramon2012 · 45 citationsPloS one. 2012;7(6):e38518
Stochastic theory of large-scale enzyme-reaction networks: finite copy number corrections to rate equation models.21090871 · Thomas, Philipp, Straube, Arthur V, Grima, Ramon2011 · 41 citationsThe Journal of chemical physics. 2010;133(19):195101
Synthesis of beta-lactones by the regioselective, cobalt and Lewis acid catalyzed carbonylation of simple and functionalized epoxides.11485465 · Lee, J T, Thomas, P J, Alper, H2001 · 154 citationsThe Journal of organic chemistry. 2001;66(16):5424-6
Use of a juvenile hormone analogue as insecticide for pests of stored grain.5673011 · Thomas, P J, Bhatnagar-Thomas, P L1968 · 33 citationsNature. 1968;219(5157):949
Career total: 117 works. 38 are in this corpus.
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