Prediction of Escherichia coli single gene deletion mutants by projection to latent pathways
In metabolic engineering or synthetic biology robust models with high predictive power are required. Constraints-based modelling methods such as metabolic flux analysis (MFA), flux balance analysis (FBA), elementary flux modes (EFMs) or extreme pathways (EP) have been widely used. The success of these methods is however conditioned by the many times insufficient mechanistic knowledge base. In this study, we built upon a previously developed hybrid constraints-based modelling method to develop E. coli models with improved predictive power. In particular, we apply a projection to latent pathways (PLP) method that merges together mechanistic and statistical constraints. It may be considered as a middle-out modelling approach that combines reliable knowledge and reverse engineering to extract unknown mechanisms from “omics” data sets. The method is applied to predict the central carbon fluxes of several E. coli strains (both wild-type and single gene KO mutants). We show that the central carbon fluxes of several single gene KO E. coli mutants could be predicted with high accuracy from the combined information of gene deletion and environmental conditions.
Date: 2012-May-25 Time: 14:30:00 Room: 020
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Workshop “Metabolism and mathematical models: Two for a tango” – 2nd Edition
Title: Workshop Metabolism and mathematical models: Two for a tango – 2nd Edition
Dates: October 25-26, 2022
Location: This workshop will be held in a virtual way
The topic of this workshop is metabolism in general, with a special focus, although not exclusive, on parasitology. Besides an exploration of the biological, biochemical and biomedical aspects, the workshop will also aim at presenting some of the mathematical modelling, algorithmic theory and software development that have become crucial to explore such aspects.
This workshop is being organised in the context of two projects, both with the Inria European Team Erable. One of the projects involves a partnership with the University of São Paulo (USP), in São Paulo, Brazil, more specifically the Institute of Mathematics and Statistics (IME) and the Institute of Biomedical Sciences – Inria Associated Team Capoeira – and the other involves the Inesc-ID/IST in Portugal, ETH in Zürich and EMBL in Heidelberg – H2020 Twinning Project Olissipo.
The workshop is open to all members of these two projects but also, importantly, to the community in general.
The program and more details are available here.