Simulation and inference algorithms for stochastic biochemical reaction networks: from basic concepts to state-of-the-art

Simulation and inference algorithms for stochastic biochemical reaction networks: from basic concepts to state-of-the-art

Stochasticity is a key characteristic of intracellular processes such as gene regulation and chemical signalling. Therefore, characterizing stochastic effects in biochemical systems is essential to understand the complex dynamics of living things. Mathematical idealizations of biochemically reacting...

Full beskrivning

Bibliografiska uppgifter
Huvudupphovsmän:	Warne, D, Baker, R, Simpson, M
Materialtyp:	Journal article
Publicerad:	Royal Society 2019

Liknande verk

Rapid Bayesian inference for expensive stochastic models
av: Warne, DJ, et al.
Publicerad: (2021)

Multifidelity multilevel Monte Carlo to accelerate approximate Bayesian parameter inference for partially observed stochastic processes
av: Warne, D, et al.
Publicerad: (2022)

Fast simulation of stochastic biochemical reaction networks on cytomorphic chips
av: Woo, Sung Sik, Ph. D. Massachusetts Institute of Technology
Publicerad: (2017)

HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks
av: Luca Marchetti, et al.
Publicerad: (2017-01-01)

Statistical inference : basic concepts /
av: 409085 Ellis, Richard B.
Publicerad: (1975)

A practical guide to pseudo-marginal methods for computational inference in systems biology
av: Warne, DJ, et al.
Publicerad: (2020)

T-Growth Stochastic Model: Simulation and Inference via Metaheuristic Algorithms
av: Antonio Barrera, et al.
Publicerad: (2021-04-01)

Uniformization techniques for stochastic simulation of chemical reaction networks
av: Beentjes, CHL, et al.
Publicerad: (2019)

Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks
av: Elston Timothy C, et al.
Publicerad: (2004-03-01)

Fast stochastic simulation of biochemical reaction systems by alternative formulations of the Chemical Langevin Equation
av: Mélykúti, B, et al.
Publicerad: (2010)

Identifiability analysis for stochastic differential equation models in systems biology
av: Browning, AP, et al.
Publicerad: (2020)

Using experimental data and information criteria to guide model selection for reaction-diffusion problems in mathematical biology
av: Warne, D, et al.
Publicerad: (2019)

Simulating Emotions: An Active Inference Model of Emotional State Inference and Emotion Concept Learning
av: Ryan Smith, et al.
Publicerad: (2019-12-01)

Likelihood-free nested sampling for parameter inference of biochemical reaction networks.
av: Jan Mikelson, et al.
Publicerad: (2020-10-01)

Cox process representation and inference for stochastic reaction–diffusion processes
av: David Schnoerr, et al.
Publicerad: (2016-05-01)

Stochastic Methods for Inferring States of Cell Migration
av: R. J. Allen, et al.
Publicerad: (2020-07-01)

Simulation and inference for stochastic differential equations : with R examples /
av: 457221 Iacus, Stefano M.
Publicerad: (2008)

Efficient multifidelity likelihood-free Bayesian inference with adaptive computational resource allocation
av: Prescott, T, et al.
Publicerad: (2023)

Basic pathway decomposition of biochemical reaction networks within growing cells
av: Jay R. Walton, et al.
Publicerad: (2024-01-01)

Reduction of multiscale stochastic biochemical reaction networks using exact moment derivation.
av: Jae Kyoung Kim, et al.
Publicerad: (2017-06-01)

A Labview® program for illustrating the basic concepts of Bayesian inference
av: Giner Sanz, Juan Jose, et al.
Publicerad: (2020)

Efficient simulation techniques for biochemical reaction networks
av: Lester, C
Publicerad: (2017)

Inferring Biochemical Reactions and Metabolite Structures to Understand Metabolic Pathway Drift
av: Arnaud Belcour, et al.
Publicerad: (2020-02-01)

Probabilistic inference of biochemical reactions in microbial communities from metagenomic sequences.
av: Dazhi Jiao, et al.
Publicerad: (2013-01-01)

Machine Translation with Inferred Stochastic Finite-State Transducers
av: Francisco Casacuberta, et al.
Publicerad: (2021-03-01)

Acceleration of Discrete Stochastic Biochemical Simulation using GPGPU
av: Kei eSumiyoshi, et al.
Publicerad: (2015-02-01)

Markov chain Monte Carlo : stochastic simulation for Bayesian inference /
av: 360681 Gamerman, Dani, et al.
Publicerad: (2006)

Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level.
av: Anđela Davidović, et al.
Publicerad: (2022-03-01)

An Overview of Network-Based and -Free Approaches for Stochastic Simulation of Biochemical Systems
av: Abhishekh Gupta, et al.
Publicerad: (2018-01-01)

Stochastic modelling of reaction-diffusion processes: algorithms for bimolecular reactions.
av: Erban, R, et al.
Publicerad: (2009)

Stochastic modelling of reaction-diffusion processes: algorithms for bimolecular reactions
av: Erban, R, et al.
Publicerad: (2009)

An adaptive multi-level simulation algorithm for stochastic biological systems
av: Lester, C, et al.
Publicerad: (2015)

Stochastic simulation : algorithms and analysis /
av: 426970 Asmussen, Soren, et al.
Publicerad: (2007)

Fundamentals of speech synthesis and speech recognition : basic concepts, state-of-the-art and future challenges /
av: Keller, Eric
Publicerad: (1994)

Robustly simulating biochemical reaction kinetics using multi-level Monte Carlo approaches
av: Lester, C, et al.
Publicerad: (2018)

Reactive Transport: A Review of Basic Concepts with Emphasis on Biochemical Processes
av: Jesús Carrera, et al.
Publicerad: (2022-01-01)

Likelihood-free Bayesian inference for dynamic, stochastic simulators in the social sciences
av: Dyer, J
Publicerad: (2022)

Powers of the Stochastic Gompertz and Lognormal Diffusion Processes, Statistical Inference and Simulation
av: Eva María Ramos-Ábalos, et al.
Publicerad: (2020-04-01)

Stochastic simulation and statistical inference platform for visualization and estimation of transcriptional kinetics.
av: Gennady Gorin, et al.
Publicerad: (2020-01-01)

Multiscale simulation algorithm for stochastic cooling simulation
av: M. E. Dolinska, et al.
Publicerad: (2016-12-01)