Browsing by Author "Garrido Cortes, Daniel"
Now showing 1 - 10 of 10
Results Per Page
Sort Options
- ItemAssessment of Changes in the Oral Microbiome That Occur in Dogs with Periodontal Disease(2021) Rodrigo Santibáñez; Camila Rodríguez-Salas; Carla Flores-Yáñez; Garrido Cortes, Daniel; Pamela Thomson
- ItemAtlas: automatic modeling of regulation of bacterial gene expression and metabolism using rule-based languages(2020) Rodrigo Santibáñez; Garrido Cortes, Daniel; Alberto J M Martin; Pier Luigi Martelli
- ItemComparative Genomic Analysis of Novel Bifidobacterium longum subsp. longum Strains Reveals Functional Divergence in the Human Gut Microbiota(2021) Romina Díaz; Alexis Torres-Miranda; Guillermo Orellana; Garrido Cortes, Daniel
- ItemComparative Genomics of Clostridium baratii Reveals Strain-Level Diversity in Toxin Abundance(2022) Claudia Silva-Andrade; Alberto J.M. Martin; Garrido Cortes, Daniel
- ItemDeveloping a Fluorescent Inducible System for Free Fucose Quantification in Escherichia coli(2023) Samantha Nuñez; Maria Barra; Garrido Cortes, Daniel
- ItemEngineered Bacteria for Short-Chain-Fatty-Acid-Repressed Expression of Biotherapeutic Molecules(2023) Kineret Serebrinsky-Duek; Maria Barra; Tal Danino; Garrido Cortes, Daniel; Jasna Kovac
- ItemMetabolic Modeling and Bidirectional Culturing of Two Gut Microbes Reveal Cross-Feeding Interactions and Protective Effects on Intestinal Cells(2022) Belén Hirmas; Naschla Gasaly; Guillermo Orellana; Marco Vega-Sagardía; Pedro Saa; Martín Gotteland; Garrido Cortes, Daniel; Sergio Baranzini
- ItemMETACONE: A scalable framework for exploring the conversion cone of metabolic networks(2026) Altamirano Muñoz, Alvaro Sebastian; Tapia García, Ignacio Tomas; Acuña, Vicente ; Garrido Cortes, Daniel; Saa Higuera, PedroElementary Conversion Modes (ECMs) – a subset of Elementary Flux Modes (EFMs) – capture the entire production/consumption potential of a metabolic network, providing a more practical view of its interactions with the environment. Despite its reduced size, the set of ECMs is too large for exhaustive enumeration in models reaching genome scale. To address this limitation, we have developed METACONE (METAbolic Conversion cOne for Network Exploration), a scalable algorithm for the computation of a representative linear basis of the conversion cone, the subspace in which all ECMs lie. Two METACONE variants are proposed based on the solution of a series of linear programs following different heuristics. We evaluated the performance of the variants on metabolic models of different sizes, demonstrating their scalability. We further analyzed the resulting basis to explore metabolic capabilities under different environmental conditions in Escherichia coli, identifying metabolic patterns consistent with reported data. Finally, we applied the algorithm to explore metabolic interactions in a microbial consortium of Phocaeicola dorei and Lachnoclostridium symbiosum, recapitulating known cross-feeding interactions and suggesting new possibilities. We envision METACONE as a valuable tool for understanding microbial metabolism in increasingly complex consortia while addressing current scalability challenges.
- ItemProteomic analyses of Bacteroides ovatus and Bifidobacterium longum in xylan bidirectional culture shows sugar cross-feeding interactions(2023) Marco Vega-Sagardía; Josué Delgado; Santiago Ruiz-Moyano; Garrido Cortes, Daniel
- ItemScreening Microbial Interactions During Inulin Utilization Reveals Strong Competition and Proteomic Changes in Lacticaseibacillus paracasei M38(2023) Marco Vega-Sagardía; Eva Cebrián Cabezón; Josué Delgado; Santiago Ruiz-Moyano; Garrido Cortes, Daniel