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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In Vivo Gene Essentiality and Metabolism in Bordetella pertussis

mSphere. 2019 May 22;4(3):e00694-18. doi: 10.1128/mSphere.00694-18. ABSTRACT Bordetella pertussis is the causative agent of whooping cough, a serious respiratory illness affecting children and adults, associated with prolonged cough and potential mortality. Whooping cough has reemerged in recent years, emphasizing a need for increased knowledge of basic mechanisms of B. pertussis growth and pathogenicity. While previous […]

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Leveraging the effects of chloroquine on resistant malaria parasites for combination therapies

BMC Bioinformatics. 2019 Apr 15;20(1):186. doi: 10.1186/s12859-019-2756-y. ABSTRACT BACKGROUND: Malaria is a major global health problem, with the Plasmodium falciparum protozoan parasite causing the most severe form of the disease. Prevalence of drug-resistant P. falciparum highlights the need to understand the biology of resistance and to identify novel combination therapies that are effective against resistant […]

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