(Q30741216)

4 October 2017

A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation (English)

1 reference

approximate Bayesian computation

4 October 2017

computational biology

0 references

1 reference

5

1 reference

4 October 2017

Paul Kirk

2

0 references

Sarah L. Filippi

series ordinal

3

object named as

Sarah Filippi

1 reference

4 October 2017

6

Michael P H Stumpf

1 reference

4 October 2017

Juliane Liepe

1

1 reference

PMCID

5081097

4 October 2017

Tina Toni

series ordinal

4

1 reference

4 October 2017

23 January 2014

1 reference

4 October 2017

1 reference

4 October 2017

9

1 reference

4 October 2017

2

1 reference

4 October 2017

439-456

1 reference

Approximate Bayesian computation (ABC) gives exact results under the assumption of model error

4 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Model selection in systems and synthetic biology

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

On optimality of kernels for approximate Bayesian computation using sequential Monte Carlo

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Maximizing the information content of experiments in systems biology

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Population dynamics of normal and leukaemia stem cells in the haematopoietic stem cell niche show distinct regimes where leukaemia will be controlled.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Approximate Bayesian computation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Bayesian parameter inference for stochastic biochemical network models using particle Markov chain Monte Carlo

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Elucidating the in vivo phosphorylation dynamics of the ERK MAP kinase using quantitative proteomics data and Bayesian model selection.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Graph spectral analysis of protein interaction network evolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Identifying sources of variation and the flow of information in biochemical networks

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

A Bayesian approach to targeted experiment design.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Calibrating spatio-temporal models of leukocyte dynamics against in vivo live-imaging data using approximate Bayesian computation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Designing attractive models via automated identification of chaotic and oscillatory dynamical regimes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Bayesian design of synthetic biological systems

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Lack of confidence in approximate Bayesian computation model choice

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Separating intrinsic from extrinsic fluctuations in dynamic biological systems

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

From qualitative data to quantitative models: analysis of the phage shock protein stress response in Escherichia coli

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Sensitivity, robustness, and identifiability in stochastic chemical kinetics models.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

GPU accelerated biochemical network simulation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0).

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

ABC as a flexible framework to estimate demography over space and time: some cons, many pros

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Sloppy models, parameter uncertainty, and the role of experimental design

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Approximate Bayesian Computation (ABC) in practice.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

GPU computing for systems biology

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Simulation-based model selection for dynamical systems in systems and population biology

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

ABC: a useful Bayesian tool for the analysis of population data.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Bayesian inference of biochemical kinetic parameters using the linear noise approximation.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Bayesian computation and model selection without likelihoods

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Parameter inference for biochemical systems that undergo a Hopf bifurcation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Hybrid optimization method with general switching strategy for parameter estimation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Universally sloppy parameter sensitivities in systems biology models

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Sequential Monte Carlo without likelihoods

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Markov chain Monte Carlo without likelihoods

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Approximate Bayesian computation in population genetics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Population growth of human Y chromosomes: a study of Y chromosome microsatellites

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Inferring coalescence times from DNA sequence data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Inferring signaling pathway topologies from multiple perturbation measurements of specific biochemical species.

20 June 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2014.025

Mathematics. Bayes' theorem in the 21st century.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2014.025

Bayesian ranking of biochemical system models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2014.025

An invariant form for the prior probability in estimation problems

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2014.025

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2014.025

Practical limits for reverse engineering of dynamical systems: a statistical analysis of sensitivity and parameter inferability in systems biology models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2014.025

Bayesian inference for stochastic kinetic models using a diffusion approximation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2014.025

Adaptive approximate Bayesian computation

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2014.025

Constructing summary statistics for approximate Bayesian computation: semi-automatic approximate Bayesian computation

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2014.025

A general moment expansion method for stochastic kinetic models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2014.025

BioBayes: a software package for Bayesian inference in systems biology.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2014.025

Mapping global sensitivity of cellular network dynamics: sensitivity heat maps and a global summation law.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2014.025

The ABC of reverse engineering biological signalling systems.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2014.025

A general method for numerically simulating the stochastic time evolution of coupled chemical reactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2014.025

Optimizing threshold-schedules for sequential approximate Bayesian computation: applications to molecular systems.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

On optimal selection of summary statistics for approximate Bayesian computation.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Approximately sufficient statistics and bayesian computation.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Bayesian sequential inference for stochastic kinetic biochemical network models.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5081097

Handbook of Statistical Systems Biology

25 November 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2014.025

The Selection of Prior Distributions by Formal Rules

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2014.025

Considerate approaches to constructing summary statistics for ABC model selection

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2014.025

Approximate Bayesian computation using indirect inference

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2014.025

ABC methods for model choice in Gibbs random fields

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2014.025

31 March 2020

Identifiers

DOI

10.1038/NPROT.2014.025

1 reference

PMCID

5081097

Dimensions Publication ID

4 October 2017

0 references

1 reference

4 October 2017

1 reference

PMCID

5081097