scholarly journals Model Selection in Systems Biology Depends on Experimental Design

2014 ◽  
Vol 10 (6) ◽  
pp. e1003650 ◽  
Author(s):  
Daniel Silk ◽  
Paul D. W. Kirk ◽  
Chris P. Barnes ◽  
Tina Toni ◽  
Michael P. H. Stumpf
2013 ◽  
Vol 29 (20) ◽  
pp. 2625-2632 ◽  
Author(s):  
Alberto Giovanni Busetto ◽  
Alain Hauser ◽  
Gabriel Krummenacher ◽  
Mikael Sunnåker ◽  
Sotiris Dimopoulos ◽  
...  

2019 ◽  
Vol 42 ◽  
Author(s):  
J. Alfredo Blakeley-Ruiz ◽  
Carlee S. McClintock ◽  
Ralph Lydic ◽  
Helen A. Baghdoyan ◽  
James J. Choo ◽  
...  

Abstract The Hooks et al. review of microbiota-gut-brain (MGB) literature provides a constructive criticism of the general approaches encompassing MGB research. This commentary extends their review by: (a) highlighting capabilities of advanced systems-biology “-omics” techniques for microbiome research and (b) recommending that combining these high-resolution techniques with intervention-based experimental design may be the path forward for future MGB research.


2011 ◽  
pp. 99-125 ◽  
Author(s):  
Roberto Trotta ◽  
Martin Kunz ◽  
Pia Mukherjee ◽  
David Parkinson

Processes ◽  
2020 ◽  
Vol 8 (2) ◽  
pp. 190
Author(s):  
Moritz Schulze ◽  
René Schenkendorf

Considering the competitive and strongly regulated pharmaceutical industry, mathematical modeling and process systems engineering might be useful tools for implementing quality by design (QbD) and quality by control (QbC) strategies for low-cost but high-quality drugs. However, a crucial task in modeling (bio)pharmaceutical manufacturing processes is the reliable identification of model candidates from a set of various model hypotheses. To identify the best experimental design suitable for a reliable model selection and system identification is challenging for nonlinear (bio)pharmaceutical process models in general. This paper is the first to exploit differential flatness for model selection problems under uncertainty, and thus translates the model selection problem to advanced concepts of systems theory and controllability aspects, respectively. Here, the optimal controls for improved model selection trajectories are expressed analytically with low computational costs. We further demonstrate the impact of parameter uncertainties on the differential flatness-based method and provide an effective robustification strategy with the point estimate method for uncertainty quantification. In a simulation study, we consider a biocatalytic reaction step simulating the carboligation of aldehydes, where we successfully derive optimal controls for improved model selection trajectories under uncertainty.


SIMULATION ◽  
2003 ◽  
Vol 79 (12) ◽  
pp. 717-725 ◽  
Author(s):  
D. Faller ◽  
U. Klingmüller ◽  
J. Timmer

2007 ◽  
Vol 40 (4) ◽  
pp. 73-78
Author(s):  
Eva Balsa-Canto ◽  
Antonio A. Alonso ◽  
Julio R. Banga

2021 ◽  
Author(s):  
Moataz Dowaidar

The value of systems biology in cardiology is becoming more recognized. There has been a tremendous rise in the number of articles in the last two decades, as publicly available datasets have been provided online and high-throughput tissue analysis has become more prevalent. In animal models, however, the future of cardiovascular medicine is less likely to be reanalyzing data and more likely to be investigating the function of GWAS-identified SNPs or network change using informatics and gene-editing technologies. These techniques, when combined with other omics interrogations and rigorous experimental design, have the potential to improve our understanding of gene-to-disease pathways.Systems biology is a method for studying large amounts of multidimensional data generated by omics technologies and, more broadly, the transition to big data in health care.Cross-validation of the various technological platforms is critical because omics studies are prone to bias and overinterpretation.Investigators must carefully determine which publicly accessible datasets, if any, to employ while conducting a systems analysis. Despite the fact that network theory and machine learning may yield amazing outcomes, these methods are not yet standardized. The studies mentioned here are excellent examples, in part because they use empirical models to support emergent systems biology results. In the few successful cases, careful experimental design, including interventional research and clinical trials, is required, in addition to the insights supplied by bioinformatics analysis of omics approaches. While it may be tempting to use emergent qualities to capture these new discoveries in more fundamental concepts, we agree with the English philosopher William of Ockham when he says, "It is futile to do with more things what can be done with fewer."


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