Osbaldo Resendis-Antonio

TL;DR: A community effort to develop a test suite named MEMOTE (for metabolic model tests) to assess GEM quality, and advocate adoption of the latest version of the Systems Biology Markup Language level 3 flux balance constraints (SBML3FBC) package as the primary description and exchange format.

TL;DR: This review transmits the main ideas or concepts behind regulation by transcription factors and gives just enough examples to sustain these main ideas, thus avoiding a classical ennumeration of facts.

TL;DR: In this article, a customizable metabolic model of the human gut microbiome is presented, based on a heuristic optimization approach based on L2 regularization, which is able to obtain a unique set of realistic growth rates that corresponded well with observed replication rates.

TL;DR: These modules were identified by a clustering approach, using the shortest path to trace regulatory relationships across genes in the network, and the type and distribution of motifs between and within modules supported the notion of a hierarchical network with defined functional modules.

TL;DR: Some evidence is presented supporting that FBA of the reconstructed metabolic network for R. etli provides results that are in agreement with physiological observations, and the reconstructed genome-scale metabolic network provides an important framework which allows us to compare model predictions with experimental measurements and eventually generate hypotheses on ways to improve nitrogen fixation.