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Article Dans Une Revue IFAC-PapersOnLine Année : 2016

A constrained NMF approach to analyze quantitative metagenomic data

Résumé

In this paper, we propose a new method for inferring the metabolic potential of microbial ecosystems based on gene frequencies generated from shotgun metagenomic data. Our approach is based on Non-Negative Matrix Factorization with constraints accounting for prior biological knowledge of bacterial metabolism. The problem is solved using efficient accelerated projected gradient methods. The approach is illustrated on a toy model and on real data on fiber metabolism by the gut microbiota in humans. We show how this approach leads to the inference of biologically relevant gene clusters.

Dates et versions

hal-01455859 , version 1 (03-02-2017)

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Citer

Sébastien Raguideau, Béatrice Laroche, Marion Leclerc, Sandra Plancade. A constrained NMF approach to analyze quantitative metagenomic data. IFAC-PapersOnLine, 2016, 49 (26), pp.71-76. ⟨10.1016/j.ifacol.2016.12.105⟩. ⟨hal-01455859⟩
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