Literature DB >> 23578462

Model selection in systems and synthetic biology.

Paul Kirk1, Thomas Thorne, Michael P H Stumpf.   

Abstract

Developing mechanistic models has become an integral aspect of systems biology, as has the need to differentiate between alternative models. Parameterizing mathematical models has been widely perceived as a formidable challenge, which has spurred the development of statistical and optimisation routines for parameter inference. But now focus is increasingly shifting to problems that require us to choose from among a set of different models to determine which one offers the best description of a given biological system. We will here provide an overview of recent developments in the area of model selection. We will focus on approaches that are both practical as well as build on solid statistical principles and outline the conceptual foundations and the scope for application of such methods in systems biology.
Copyright © 2013 Elsevier Ltd. All rights reserved.

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Year:  2013        PMID: 23578462     DOI: 10.1016/j.copbio.2013.03.012

Source DB:  PubMed          Journal:  Curr Opin Biotechnol        ISSN: 0958-1669            Impact factor:   9.740


  42 in total

1.  Topological sensitivity analysis for systems biology.

Authors:  Ann C Babtie; Paul Kirk; Michael P H Stumpf
Journal:  Proc Natl Acad Sci U S A       Date:  2014-12-15       Impact factor: 11.205

2.  Parameter-free methods distinguish Wnt pathway models and guide design of experiments.

Authors:  Adam L MacLean; Zvi Rosen; Helen M Byrne; Heather A Harrington
Journal:  Proc Natl Acad Sci U S A       Date:  2015-02-17       Impact factor: 11.205

3.  Cutting the wires: modularization of cellular networks for experimental design.

Authors:  Moritz Lang; Sean Summers; Jörg Stelling
Journal:  Biophys J       Date:  2014-01-07       Impact factor: 4.033

4.  Modeling heterogeneous tumor growth dynamics and cell-cell interactions at single-cell and cell-population resolution.

Authors:  Leonard A Harris; Samantha Beik; Patricia M M Ozawa; Lizandra Jimenez; Alissa M Weaver
Journal:  Curr Opin Syst Biol       Date:  2019-09-16

Review 5.  How to deal with parameters for whole-cell modelling.

Authors:  Ann C Babtie; Michael P H Stumpf
Journal:  J R Soc Interface       Date:  2017-08-02       Impact factor: 4.118

6.  Modeling the effects of EMT-immune dynamics on carcinoma disease progression.

Authors:  Daniel R Bergman; Matthew K Karikomi; Min Yu; Qing Nie; Adam L MacLean
Journal:  Commun Biol       Date:  2021-08-18

7.  A Systematic Ensemble Approach to Thermodynamic Modeling of Gene Expression from Sequence Data.

Authors:  Md Abul Hassan Samee; Bomyi Lim; Núria Samper; Hang Lu; Christine A Rushlow; Gerardo Jiménez; Stanislav Y Shvartsman; Saurabh Sinha
Journal:  Cell Syst       Date:  2015-12-23       Impact factor: 10.304

8.  In silico model-based inference: an emerging approach for inverse problems in engineering better medicines.

Authors:  David J Klinke; Marc R Birtwistle
Journal:  Curr Opin Chem Eng       Date:  2015-11-01       Impact factor: 5.163

9.  A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation.

Authors:  Juliane Liepe; Paul Kirk; Sarah Filippi; Tina Toni; Chris P Barnes; Michael P H Stumpf
Journal:  Nat Protoc       Date:  2014-01-23       Impact factor: 13.491

10.  Nested sampling for parameter inference in systems biology: application to an exemplar circadian model.

Authors:  Stuart Aitken; Ozgur E Akman
Journal:  BMC Syst Biol       Date:  2013-07-30
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