Mechanistic models of microbial community metabolism

Mol Omics. 2021 Jun 14;17(3):365-375. doi: 10.1039/d0mo00154f. ABSTRACT Microbial communities affect many facets of human health and well-being. Naturally occurring bacteria, whether in nature or the human body, rarely exist in isolation. A deeper understanding of the metabolic functions of these communities is now possible with emerging computational models. In this review, we summarize frameworks […]

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Collaborating with our community to increase code sharing

PLoS Comput Biol. 2021 Mar 30;17(3):e1008867. doi: 10.1371/journal.pcbi.1008867. eCollection 2021 Mar. NO ABSTRACT PMID:33784294 | PMC:PMC8009435 | DOI:10.1371/journal.pcbi.1008867

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Identifying functional metabolic shifts in heart failure with the integration of omics data and a heart-specific, genome-scale model

Cell Rep. 2021 Mar 9;34(10):108836. doi: 10.1016/j.celrep.2021.108836. ABSTRACT In diseased states, the heart can shift to use different carbon substrates, measured through changes in uptake of metabolites by imaging methods or blood metabolomics. However, it is not known whether these measured changes are a result of transcriptional changes or external factors. Here, we explore transcriptional […]

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Predicting changes in renal metabolism after compound exposure with a genome-scale metabolic model

Toxicol Appl Pharmacol. 2021 Feb 1;412:115390. doi: 10.1016/j.taap.2020.115390. Epub 2020 Dec 31. ABSTRACT The kidneys are metabolically active organs with importance in several physiological tasks such as the secretion of soluble wastes into the urine and synthesizing glucose and oxidizing fatty acids for energy in fasting (non-fed) conditions. Once damaged, the metabolic capability of the […]

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Clostridioides difficile: Sometimes It Pays To Be Difficult

Cell Host Microbe. 2020 Sep 9;28(3):358-359. doi: 10.1016/j.chom.2020.08.010. ABSTRACT In this issue of Cell Host & Microbe, publications from Bushman et al. (2020) and Knippel et al. (2020) outline elements of host epithelial damage or inflammation that Clostridioides difficile subverts, enabling continued growth. These mechanisms provide insight into how this important pathogen influences the gut […]

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Community standards to facilitate development and address challenges in metabolic modeling

Mol Syst Biol. 2020 Aug;16(8):e9235. doi: 10.15252/msb.20199235. ABSTRACT Standardization of data and models facilitates effective communication, especially in computational systems biology. However, both the development and consistent use of standards and resources remain challenging. As a result, the amount, quality, and format of the information contained within systems biology models are not consistent and therefore […]

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Minimum Bactericidal Concentration of Ciprofloxacin to Pseudomonas aeruginosa Determined Rapidly Based on Pyocyanin Secretion

Sens Actuators B Chem. 2020 Jun 1;312:127936. doi: 10.1016/j.snb.2020.127936. Epub 2020 Mar 4. ABSTRACT Infections due to Pseudomonas aeruginosa (P. aeruginosa) often exhibit broad-spectrum resistance and persistence to common antibiotics. Persistence is especially problematic with immune-compromised subjects who are unable to eliminate the inhibited bacteria. Hence, antibiotics must be used at the appropriate minimum bactericidal […]

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Improving reproducibility in computational biology research

PLoS Comput Biol. 2020 May 19;16(5):e1007881. doi: 10.1371/journal.pcbi.1007881. eCollection 2020 May. NO ABSTRACT PMID:32427998 | PMC:PMC7236972 | DOI:10.1371/journal.pcbi.1007881

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Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions

PLoS Comput Biol. 2020 Apr 29;16(4):e1007847. doi: 10.1371/journal.pcbi.1007847. eCollection 2020 Apr. ABSTRACT Uncertainty in the structure and parameters of networks is ubiquitous across computational biology. In constraint-based reconstruction and analysis of metabolic networks, this uncertainty is present both during the reconstruction of networks and in simulations performed with them. Here, we present Medusa, a Python […]

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Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments

PLoS Comput Biol. 2020 Apr 16;16(4):e1007099. doi: 10.1371/journal.pcbi.1007099. eCollection 2020 Apr. ABSTRACT The metabolic responses of bacteria to dynamic extracellular conditions drives not only the behavior of single species, but also entire communities of microbes. Over the last decade, genome-scale metabolic network reconstructions have assisted in our appreciation of important metabolic determinants of bacterial physiology. […]

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