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For: Ale A, Kirk P, Stumpf MPH. A general moment expansion method for stochastic kinetic models. J Chem Phys 2013;138:174101. [DOI: 10.1063/1.4802475] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
1
Lunz D, Bonnans JF, Ruess J. Revisiting moment-closure methods with heterogeneous multiscale population models. Math Biosci 2022;350:108866. [PMID: 35753520 DOI: 10.1016/j.mbs.2022.108866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 04/10/2022] [Accepted: 06/08/2022] [Indexed: 11/29/2022]
2
Chen A, Qiu H, Tian T, Zhou T. Generalized fluctuation-dissipation theorem for non-Markovian reaction networks. Phys Rev E 2022;105:064409. [PMID: 35854490 DOI: 10.1103/physreve.105.064409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
3
Waizmann T, Bortolussi L, Vandin A, Tribastone M. Improved estimations of stochastic chemical kinetics by finite-state expansion. Proc Math Phys Eng Sci 2021. [DOI: 10.1098/rspa.2020.0964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
4
Sukys A, Grima R. MomentClosure.jl: automated moment closure approximations in Julia. Bioinformatics 2021;38:289-290. [PMID: 34170295 PMCID: PMC8696096 DOI: 10.1093/bioinformatics/btab469] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/15/2021] [Accepted: 06/22/2021] [Indexed: 02/03/2023]  Open
5
Kang YM, Liu RN. Moment dynamics for gene regulation with rational rate laws. Phys Rev E 2020;102:042407. [PMID: 33212610 DOI: 10.1103/physreve.102.042407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/09/2020] [Indexed: 06/11/2023]
6
Liu RN, Kang YM. Stochastic master equation for early protein aggregation in the transthyretin amyloid disease. Sci Rep 2020;10:12437. [PMID: 32709875 PMCID: PMC7381670 DOI: 10.1038/s41598-020-69319-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/10/2020] [Indexed: 11/09/2022]  Open
7
Rule ME, Schnoerr D, Hennig MH, Sanguinetti G. Neural field models for latent state inference: Application to large-scale neuronal recordings. PLoS Comput Biol 2019;15:e1007442. [PMID: 31682604 PMCID: PMC6855563 DOI: 10.1371/journal.pcbi.1007442] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 11/14/2019] [Accepted: 09/27/2019] [Indexed: 11/18/2022]  Open
8
Loskot P, Atitey K, Mihaylova L. Comprehensive Review of Models and Methods for Inferences in Bio-Chemical Reaction Networks. Front Genet 2019;10:549. [PMID: 31258548 PMCID: PMC6588029 DOI: 10.3389/fgene.2019.00549] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/24/2019] [Indexed: 01/30/2023]  Open
9
Vu TV, Hasegawa Y. An algebraic method to calculate parameter regions for constrained steady-state distribution in stochastic reaction networks. CHAOS (WOODBURY, N.Y.) 2019;29:023123. [PMID: 30823706 DOI: 10.1063/1.5047579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 01/25/2019] [Indexed: 06/09/2023]
10
Huang GR, Saakian DB, Hu CK. Accurate analytic solution of chemical master equations for gene regulation networks in a single cell. Phys Rev E 2018;97:012412. [PMID: 29448337 DOI: 10.1103/physreve.97.012412] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Indexed: 12/21/2022]
11
Solving Stochastic Reaction Networks with Maximum Entropy Lagrange Multipliers. ENTROPY 2018;20:e20090700. [PMID: 33265789 PMCID: PMC7513230 DOI: 10.3390/e20090700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/05/2018] [Accepted: 09/06/2018] [Indexed: 11/16/2022]
12
Rule M, Sanguinetti G. Autoregressive Point Processes as Latent State-Space Models: A Moment-Closure Approach to Fluctuations and Autocorrelations. Neural Comput 2018;30:2757-2780. [PMID: 30148704 DOI: 10.1162/neco_a_01121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
13
Backenkohler M, Bortolussi L, Wolf V. Moment-Based Parameter Estimation for Stochastic Reaction Networks in Equilibrium. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018;15:1180-1192. [PMID: 29990108 DOI: 10.1109/tcbb.2017.2775219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
14
Liang J, Din A, Zhou T. Linear approximations of global behaviors in nonlinear systems with moderate or strong noise. J Chem Phys 2018;148:104105. [PMID: 29544279 DOI: 10.1063/1.5012885] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
15
Vlysidis M, Kaznessis YN. A linearization method for probability moment equations. Comput Chem Eng 2018. [DOI: 10.1016/j.compchemeng.2018.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
16
Lakatos E, Stumpf MPH. Control mechanisms for stochastic biochemical systems via computation of reachable sets. ROYAL SOCIETY OPEN SCIENCE 2017;4:160790. [PMID: 28878957 PMCID: PMC5579072 DOI: 10.1098/rsos.160790] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/21/2017] [Indexed: 06/07/2023]
17
Zhang J, Nie Q, Zhou T. A moment-convergence method for stochastic analysis of biochemical reaction networks. J Chem Phys 2017;144:194109. [PMID: 27208938 DOI: 10.1063/1.4950767] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
18
Schilling C, Bogomolov S, Henzinger TA, Podelski A, Ruess J. Adaptive moment closure for parameter inference of biochemical reaction networks. Biosystems 2016;149:15-25. [DOI: 10.1016/j.biosystems.2016.07.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 06/30/2016] [Accepted: 07/12/2016] [Indexed: 01/27/2023]
19
Lück A, Wolf V. Generalized method of moments for estimating parameters of stochastic reaction networks. BMC SYSTEMS BIOLOGY 2016;10:98. [PMID: 27769280 PMCID: PMC5073941 DOI: 10.1186/s12918-016-0342-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 10/11/2016] [Indexed: 11/10/2022]
20
Fan S, Geissmann Q, Lakatos E, Lukauskas S, Ale A, Babtie AC, Kirk PDW, Stumpf MPH. MEANS: python package for Moment Expansion Approximation, iNference and Simulation. Bioinformatics 2016;32:2863-5. [PMID: 27153663 PMCID: PMC5018365 DOI: 10.1093/bioinformatics/btw229] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 03/23/2016] [Accepted: 04/21/2016] [Indexed: 11/14/2022]  Open
21
Lenive O, W Kirk PD, H Stumpf MP. Inferring extrinsic noise from single-cell gene expression data using approximate Bayesian computation. BMC SYSTEMS BIOLOGY 2016;10:81. [PMID: 27549182 PMCID: PMC4994381 DOI: 10.1186/s12918-016-0324-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 07/22/2016] [Indexed: 12/29/2022]
22
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 Comput Biol 2016;12:e1005030. [PMID: 27447730 PMCID: PMC4957800 DOI: 10.1371/journal.pcbi.1005030] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 06/23/2016] [Indexed: 11/18/2022]  Open
23
Smadbeck P, Kaznessis YN. On a theory of stability for nonlinear stochastic chemical reaction networks. J Chem Phys 2016;142:184101. [PMID: 25978877 DOI: 10.1063/1.4919834] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
24
Reverse Engineering Under Uncertainty. UNCERTAINTY IN BIOLOGY 2016. [DOI: 10.1007/978-3-319-21296-8_2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
25
Schnoerr D, Sanguinetti G, Grima R. Comparison of different moment-closure approximations for stochastic chemical kinetics. J Chem Phys 2015;143:185101. [DOI: 10.1063/1.4934990] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
26
Júlvez J. A straightforward method to compute average stochastic oscillations from data samples. BMC Bioinformatics 2015;16:333. [PMID: 26482438 PMCID: PMC4615616 DOI: 10.1186/s12859-015-0765-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 10/07/2015] [Indexed: 11/10/2022]  Open
27
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 2015;92:042124. [PMID: 26565185 DOI: 10.1103/physreve.92.042124] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Indexed: 06/05/2023]
28
Lakatos E, Ale A, Kirk PDW, Stumpf MPH. Multivariate moment closure techniques for stochastic kinetic models. J Chem Phys 2015;143:094107. [DOI: 10.1063/1.4929837] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
29
Thomas P, Grima R. Approximate probability distributions of the master equation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015;92:012120. [PMID: 26274137 DOI: 10.1103/physreve.92.012120] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Indexed: 06/04/2023]
30
Székely T, Burrage K. Stochastic simulation in systems biology. Comput Struct Biotechnol J 2014;12:14-25. [PMID: 25505503 PMCID: PMC4262058 DOI: 10.1016/j.csbj.2014.10.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 10/13/2014] [Indexed: 11/03/2022]  Open
31
Schnoerr D, Sanguinetti G, Grima R. Validity conditions for moment closure approximations in stochastic chemical kinetics. J Chem Phys 2014;141:084103. [DOI: 10.1063/1.4892838] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
32
Gupta A, Briat C, Khammash M. A scalable computational framework for establishing long-term behavior of stochastic reaction networks. PLoS Comput Biol 2014;10:e1003669. [PMID: 24968191 PMCID: PMC4072526 DOI: 10.1371/journal.pcbi.1003669] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 04/30/2014] [Indexed: 11/29/2022]  Open
33
Liepe J, Kirk P, Filippi S, Toni T, Barnes CP, Stumpf MP. A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation. Nat Protoc 2014;9:439-56. [PMID: 24457334 PMCID: PMC5081097 DOI: 10.1038/nprot.2014.025] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
34
Ruess J, Milias-Argeitis A, Lygeros J. Designing experiments to understand the variability in biochemical reaction networks. J R Soc Interface 2013;10:20130588. [PMID: 23985733 DOI: 10.1098/rsif.2013.0588] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
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