Moment-Based Methods for Parameter Inference and Experiment Design for Stochastic Biochemical Reaction Networks

Jakob Ruess; John Lygeros

doi:10.1145/2688906

Moment-Based Methods for Parameter Inference and Experiment Design for Stochastic Biochemical Reaction Networks

ACM Transactions on Modeling and Computer Simulation ◽

10.1145/2688906 ◽

2015 ◽

Vol 25 (2) ◽

pp. 1-25 ◽

Cited By ~ 19

Author(s):

Jakob Ruess ◽

John Lygeros

Keyword(s):

Experiment Design ◽

Biochemical Reaction ◽

Reaction Networks ◽

Biochemical Reaction Networks ◽

Parameter Inference

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Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks

Computational Methods in Systems Biology - Lecture Notes in Computer Science ◽

10.1007/978-3-319-23401-4_8 ◽

2015 ◽

pp. 77-89 ◽

Cited By ~ 3

Author(s):

Sergiy Bogomolov ◽

Thomas A. Henzinger ◽

Andreas Podelski ◽

Jakob Ruess ◽

Christian Schilling

Keyword(s):

Biochemical Reaction ◽

Moment Closure ◽

Reaction Networks ◽

Biochemical Reaction Networks ◽

Parameter Inference

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Adaptive moment closure for parameter inference of biochemical reaction networks

Biosystems ◽

10.1016/j.biosystems.2016.07.005 ◽

2016 ◽

Vol 149 ◽

pp. 15-25 ◽

Cited By ~ 6

Author(s):

Christian Schilling ◽

Sergiy Bogomolov ◽

Thomas A. Henzinger ◽

Andreas Podelski ◽

Jakob Ruess

Keyword(s):

Biochemical Reaction ◽

Moment Closure ◽

Reaction Networks ◽

Biochemical Reaction Networks ◽

Parameter Inference

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Likelihood-free nested sampling for parameter inference of biochemical reaction networks

PLoS Computational Biology ◽

10.1371/journal.pcbi.1008264 ◽

2020 ◽

Vol 16 (10) ◽

pp. e1008264

Author(s):

Jan Mikelson ◽

Mustafa Khammash

Keyword(s):

Biochemical Reaction ◽

Reaction Networks ◽

Biochemical Reaction Networks ◽

Parameter Inference ◽

Nested Sampling

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On the Use of the Moment Equations for Parameter Inference, Control and Experimental Design in Stochastic Biochemical Reaction Networks

Computational Methods in Systems Biology - Lecture Notes in Computer Science ◽

10.1007/978-3-642-40708-6_1 ◽

2013 ◽

pp. 1-4

Author(s):

Jakob Ruess ◽

John Lygeros

Keyword(s):

Experimental Design ◽

Biochemical Reaction ◽

Reaction Networks ◽

Moment Equations ◽

Biochemical Reaction Networks ◽

Parameter Inference ◽

Inference Control ◽

The Moment

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Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space

The Journal of Chemical Physics ◽

10.1063/1.4937937 ◽

2015 ◽

Vol 143 (24) ◽

pp. 244103 ◽

Cited By ~ 3

Author(s):

Jakob Ruess

Keyword(s):

State Space ◽

Stochastic Models ◽

Biochemical Reaction ◽

Reaction Networks ◽

Moment Equations ◽

Biochemical Reaction Networks ◽

Finite State ◽

Finite State Space

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A Dissipative Approach to the Identification of Biochemical Reaction Networks

IFAC Proceedings Volumes ◽

10.3182/20090706-3-fr-2004.00209 ◽

2009 ◽

Vol 42 (10) ◽

pp. 1259-1264

Author(s):

Dirk Fey ◽

Eric Bullinger

Keyword(s):

Biochemical Reaction ◽

Reaction Networks ◽

Biochemical Reaction Networks

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Model reduction and parameter estimation of non-linear dynamical biochemical reaction networks

IET Systems Biology ◽

10.1049/iet-syb.2015.0034 ◽

2016 ◽

Vol 10 (1) ◽

pp. 10-16 ◽

Cited By ~ 7

Author(s):

Xiaodian Sun ◽

Mario Medvedovic

Keyword(s):

Parameter Estimation ◽

Model Reduction ◽

Biochemical Reaction ◽

Reaction Networks ◽

Biochemical Reaction Networks ◽

Non Linear

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Robust ergodicity and tracking in antithetic integral control of stochastic biochemical reaction networks

2016 IEEE 55th Conference on Decision and Control (CDC) ◽

10.1109/cdc.2016.7798358 ◽

2016 ◽

Cited By ~ 2

Author(s):

Corentin Briat ◽

Mustafa Khammash

Keyword(s):

Biochemical Reaction ◽

Reaction Networks ◽

Biochemical Reaction Networks ◽

Integral Control

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Determining Elementary Modes of Functioning in Biochemical Reaction Networks at Steady State

Biomedical and Life Physics ◽

10.1007/978-3-322-85017-1_9 ◽

1996 ◽

pp. 101-114 ◽

Cited By ~ 5

Author(s):

S. Schuster ◽

C. Hilgetag ◽

R. Schuster

Keyword(s):

Steady State ◽

Biochemical Reaction ◽

Reaction Networks ◽

Biochemical Reaction Networks ◽

Elementary Modes

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Graph-Based Decomposition of Biochemical Reaction Networks into Monotone Subsystems

Lecture Notes in Computer Science - Algorithms in Bioinformatics ◽

10.1007/978-3-642-23038-7_13 ◽

2011 ◽

pp. 139-150 ◽

Cited By ~ 2

Author(s):

Hans-Michael Kaltenbach ◽

Simona Constantinescu ◽

Justin Feigelman ◽

Jörg Stelling

Keyword(s):

Biochemical Reaction ◽

Reaction Networks ◽

Biochemical Reaction Networks

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