Browsing by Autor "William Gebbie"

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    Ten Quick Tips for Accurate Reconstruction of Prokaryotic and Eukaryotic Genome-Scale Metabolic Models
    (2023) Gabriela Canto-Encalada; Jenna L. Armstrong; Carlos Focil-Espinosa; Ademikanra Adekunle-Fiyin; Ila Peeler; William Gebbie; J. Nuñez‐Garcia; Alexis Saldivar; Diego Martínez; Cristal Zúñiga
    Constraint-based metabolic modeling approaches have enhanced our knowledge and understanding of the metabolism of prokaryotes and eukaryotes. This approach highly depends on the reconstruction process of genome-scale metabolic models (Mmodels). M-models can guide effective experimental design and yield new insights into the function and control of biological systems. Despite the recent advances in the automated generation of draft metabolic network reconstructions, the manual curation of these networks remains a labor-intensive and challenging task. Thus, these ten quick tips for the manual curation process are essential for optimizing high-quality metabolic model generation in less time. This collection of tips describes in great detail the resources and methods to ensure successful reconstruction. Furthermore, it increases the scope of other protocols of metabolic modeling by including resources to reconstruct eukaryotic organisms. Thus, all tips are applicable to a wide range of eukaryotic organisms. We believe this manuscript will interest a broad audience and researchers from different disciplines, spanning from microbiology and systems biology to biotechnology.