Modeling multiple experiments using regularized optimization: A case study on bacterial glucose utilization dynamics

Hartmann, András; Lemos, João M.; Vinga, Susana

doi:10.1016/j.compbiomed.2014.08.027

Cited by 4 publications

(1 citation statement)

References 21 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…9 As an alternative, one could try to identify some fitting function without being constrained by mechanistic considerations. 41 One could furthermore use the data directly as (''off-line'') inputs instead of representing them functionally in the model. 42 Finally, one could imagine that insufficient amounts of FBP accumulate during the first two minutes, thereby limiting the material flux into the pool of PEP and 3PGA.…”

Section: 41mentioning

confidence: 99%

New insights into the complex regulation of the glycolytic pathway in Lactococcus lactis. I. Construction and diagnosis of a comprehensive dynamic model

2016

View full text Add to dashboard Cite

This article and the companion paper use computational systems modeling to decipher the complex coordination of regulatory signals controlling the glycolytic pathway in the dairy bacterium Lactococcus lactis. In this first article, the development of a comprehensive kinetic dynamic model is described. The model is based on in vivo NMR data that consist of concentration trends in key glycolytic metabolites and cofactors. The model structure and parameter values are identified with a customized optimization strategy that uses as its core the method of dynamic flux estimation. For the first time, a dynamic model with a single parameter set fits all available glycolytic time course data under anaerobic operation. The model captures observations that had not been addressed so far and suggests the existence of regulatory effects that had been observed in other species, but not in L. lactis. The companion paper uses this model to analyze details of the dynamic control of glycolysis under aerobic and anaerobic conditions.

show abstract

Section: 41mentioning

confidence: 99%

New insights into the complex regulation of the glycolytic pathway in Lactococcus lactis. I. Construction and diagnosis of a comprehensive dynamic model

2016

View full text Add to dashboard Cite

show abstract

BacHBerry: BACterial Hosts for production of Bioactive phenolics from bERRY fruits

et al. 2017

Self Cite

View full text Add to dashboard Cite

BACterial Hosts for production of Bioactive phenolics from bERRY fruits (BacHBerry) was a 3-year project funded by the Seventh Framework Programme (FP7) of the European Union that ran between November 2013 and October 2016. The overall aim of the project was to establish a sustainable and economically-feasible strategy for the production This article is written by the BacHBerry consortium (www. bachberry.eu) and represents the collective effort of all participating institutions. The authors are therefore listed in alphabetical order.Electronic supplementary material The online version of this article

show abstract

Identification of switched ARX models via convex optimization and expectation maximization

Hartmann

Lemos

Costa

et al. 2015

Journal of Process Control

View full text Add to dashboard Cite

Modeling multiple experiments using regularized optimization: A case study on bacterial glucose utilization dynamics

Cited by 4 publications

References 21 publications

New insights into the complex regulation of the glycolytic pathway in Lactococcus lactis. I. Construction and diagnosis of a comprehensive dynamic model

New insights into the complex regulation of the glycolytic pathway in Lactococcus lactis. I. Construction and diagnosis of a comprehensive dynamic model

BacHBerry: BACterial Hosts for production of Bioactive phenolics from bERRY fruits

Identification of switched ARX models via convex optimization and expectation maximization

Contact Info

Product

Resources

About