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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Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

Nat Biotechnol. 2020 Apr;38(4):504. doi: 10.1038/s41587-020-0477-4. ABSTRACT An amendment to this paper has been published and can be accessed via a link at the top of the paper. PMID:32265554 | PMC:PMC7138757 | DOI:10.1038/s41587-020-0477-4

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MEMOTE for standardized genome-scale metabolic model testing

Nat Biotechnol. 2020 Mar;38(3):272-276. doi: 10.1038/s41587-020-0446-y. NO ABSTRACT PMID:32123384 | PMC:PMC7082222 | DOI:10.1038/s41587-020-0446-y

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Core Competencies for Undergraduates in Bioengineering and Biomedical Engineering: Findings, Consequences, and Recommendations

Ann Biomed Eng. 2020 Mar;48(3):905-912. doi: 10.1007/s10439-020-02468-2. Epub 2020 Feb 5. ABSTRACT This paper provides a synopsis of discussions related to biomedical engineering core curricula that occurred at the Fourth BME Education Summit held at Case Western Reserve University in Cleveland, Ohio in May 2019. This summit was organized by the Council of Chairs of […]

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Guiding the Refinement of Biochemical Knowledgebases with Ensembles of Metabolic Networks and Machine Learning

Cell Syst. 2020 Jan 22;10(1):109-119.e3. doi: 10.1016/j.cels.2019.11.006. Epub 2020 Jan 8. ABSTRACT Mechanistic models explicitly represent hypothesized biological knowledge. As such, they offer more generalizability than data-driven models. However, identifying model curation efforts that improve performance for mechanistic models is nontrivial. Here, we develop a solution to this problem for genome-scale metabolic models. We generate […]

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Genome-Scale Model-Based Identification of Metabolite Indicators for Early Detection of Kidney Toxicity

Toxicol Sci. 2020 Feb 1;173(2):293-312. doi: 10.1093/toxsci/kfz228. ABSTRACT Identifying early indicators of toxicant-induced organ damage is critical to provide effective treatment. To discover such indicators and the underlying mechanisms of toxicity, we used gentamicin as an exemplar kidney toxicant and performed systematic perturbation studies in Sprague Dawley rats. We obtained high-throughput data 7 and 13 […]

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Genome-Scale Characterization of Toxicity-Induced Metabolic Alterations in Primary Hepatocytes

Toxicol Sci. 2019 Dec 1;172(2):279-291. doi: 10.1093/toxsci/kfz197. ABSTRACT Context-specific GEnome-scale metabolic Network REconstructions (GENREs) provide a means to understand cellular metabolism at a deeper level of physiological detail. Here, we use transcriptomics data from chemically-exposed rat hepatocytes to constrain a GENRE of rat hepatocyte metabolism and predict biomarkers of liver toxicity using the Transcriptionally Inferred […]

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Evaluating the efficacy of an algae-based treatment to mitigate elicitation of antibiotic resistance

Chemosphere. 2019 Dec;237:124421. doi: 10.1016/j.chemosphere.2019.124421. Epub 2019 Jul 20. ABSTRACT Antibiotics in the effluents of municipal wastewater treatment plants (WWTP) may create selective pressures to induce antibiotic resistance in bacteria downstream. This study evaluates ciprofloxacin (CIP) removal by a freshwater alga, Scenedesmus dimorphus, to assess the efficacy of algae-based tertiary treatment in reducing effluent-induced CIP […]

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Wisdom of crowds in computational biology

PLoS Comput Biol. 2019 May 23;15(5):e1007032. doi: 10.1371/journal.pcbi.1007032. eCollection 2019 May. NO ABSTRACT PMID:31120879 | PMC:PMC6532836 | DOI:10.1371/journal.pcbi.1007032

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