Maria Pires Pacheco

TL;DR: This work presents fastcore, a generic algorithm for reconstructing context-specific metabolic network models from global genome-wide metabolicnetwork models such as Recon X, and shows that a minimal consistent reconstruction can be defined via a set of sparse modes of the global network.

TL;DR: In this article , formate, a metabolite produced by the colorectal cancer associated bacterium Fusobacterium nucleatum, was shown to promote CRC development, and the authors identified formate as a gut derived oncometabolite that is relevant for CRC progression.

TL;DR: Focusing on the metabolic genes under high regulatory load from multiple enhancers or super-enhancers, these genes are found to show the most cell type-restricted and abundant expression profiles within their respective pathways.

TL;DR: This review describes and analyses common validation methods used for testing model building algorithms and deduce properties of these algorithms that can be compared with future developments.

TL;DR: This contribution proposes to improve the predictive power of metabolic models by switching from gene-protein-re reaction associations to transcript-isoform-reaction associations, thus taking advantage of the improvement of precision in gene expression measurements.