scholarly journals Parallel Tempering with Lasso for model reduction in systems biology

2020 ◽  
Vol 16 (3) ◽  
pp. e1007669 ◽  
Author(s):  
Sanjana Gupta ◽  
Robin E. C. Lee ◽  
James R. Faeder
Keyword(s):  
Systems Biology ◽  
Model Reduction ◽  
Parallel Tempering

scholarly journals Parallel Tempering with Lasso for Model Reduction in Systems Biology

2019 ◽  
Author(s):  
Sanjana Gupta ◽  
Robin E.C. Lee ◽  
James R. Faeder
Keyword(s):  
Systems Biology ◽  
Model Reduction ◽  
Feedback Loops ◽  
Signaling Network ◽  
Parallel Tempering ◽  
Emergent Properties ◽  
Signaling Systems ◽  
Cellular Behaviors ◽  
Complex Signaling ◽  
The Bayesian Approach

AbstractSystems Biology models reveal relationships between signaling inputs and observable molecular or cellular behaviors. The complexity of these models, however, often obscures key elements that regulate emergent properties. We use a Bayesian model reduction approach that combines Parallel Tempering with Lasso regularization to identify minimal subsets of reactions in a signaling network that are sufficient to reproduce experimentally observed data. The Bayesian approach finds distinct reduced models that fit data equivalently. A variant of this approach based on Group Lasso is applied to the NF-κB signaling network to test the necessity of feedback loops for responses to pulsatile and continuous pathway stimulation. Taken together, our results demonstrate that Bayesian parameter estimation combined with regularization can isolate and reveal core motifs sufficient to explain data from complex signaling systems.

scholarly journals Experimental design and model reduction in systems biology

2018 ◽  
Vol 6 (4) ◽  
pp. 287-306 ◽  
Author(s):  
Jenny E. Jeong ◽  
Qinwei Zhuang ◽  
Mark K. Transtrum ◽  
Enlu Zhou ◽  
Peng Qiu
Keyword(s):  
Systems Biology ◽  
Experimental Design ◽  
Model Reduction

Combining integrated systems-biology approaches with intervention-based experimental design provides a higher-resolution path forward for microbiome research

2019 ◽  
Vol 42 ◽  
Author(s):  
J. Alfredo Blakeley-Ruiz ◽  
Carlee S. McClintock ◽  
Ralph Lydic ◽  
Helen A. Baghdoyan ◽  
James J. Choo ◽  
...  
Keyword(s):  
Systems Biology ◽  
High Resolution ◽  
Experimental Design ◽  
Integrated Systems ◽  
Microbiome Research ◽  
Constructive Criticism

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.

Systems Biology

2009 ◽  
Author(s):  
Bernhard O. Palsson ◽  
Marc Abrams
Keyword(s):  
Systems Biology

Using integrative lipid systems biology to understand the role of Liver X receptors (LXRs) in male reproduction

2018 ◽  
Author(s):  
Sheba Jarvis ◽  
Lee Gethings ◽  
Raffaella Gadeleta ◽  
Emmanuelle Claude ◽  
Robert Winston ◽  
...  
Keyword(s):  
Systems Biology ◽  
Male Reproduction ◽  
Liver X Receptors ◽  
X Receptors
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