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MERRIN: MEtabolic Regulation Rule INference from time series data

Abstract : Motivation: Many techniques have been developed to infer Boolean regulations from a prior knowledge network and experimental data. Existing methods are able to reverse-engineer Boolean regulations for transcriptional and signaling networks, but they fail to infer regulations that control metabolic networks. Results: We present a novel approach to infer Boolean rules for metabolic regulation from time series data and a prior knowledge network. Our method is based on a combination of answer set programming and linear programming. By solving both combinatorial and linear arithmetic constraints we generate candidate Boolean regulations that can reproduce the given data when coupled to the metabolic network. We evaluate our approach on a core regulated metabolic network and show how the quality of the predictions depends on the available kinetic, fluxomics or transcriptomics time series data.
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https://hal.archives-ouvertes.fr/hal-03701755
Contributor : Kerian Thuillier Connect in order to contact the contributor
Submitted on : Wednesday, June 22, 2022 - 5:06:18 PM
Last modification on : Friday, July 1, 2022 - 3:04:10 AM

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  • HAL Id : hal-03701755, version 1

Citation

Kerian Thuillier, Caroline Baroukh, Alexander Bockmayr, Ludovic Cottret, Loïc Paulevé, et al.. MERRIN: MEtabolic Regulation Rule INference from time series data. European Conference on Computational Biology - ECCB, Sep 2022, Barcelone, Spain. ⟨hal-03701755⟩

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