Reconciling high-throughput gene essentiality data with metabolic network reconstructions
PLoS Comput Biol. 2019 Apr 11;15(4):e1006507. doi: 10.1371/journal.pcbi.1006507. eCollection 2019 Apr. ABSTRACT The identification of genes essential for bacterial growth and survival represents a promising strategy for the discovery of antimicrobial targets. Essential genes can be identified on a genome-scale using transposon mutagenesis approaches; however, variability between screens and challenges with interpretation of essentiality data […]
Read MoreMechanistic identification of biofluid metabolite changes as markers of acetaminophen-induced liver toxicity in rats
Toxicol Appl Pharmacol. 2019 Jun 1;372:19-32. doi: 10.1016/j.taap.2019.04.001. Epub 2019 Apr 8. ABSTRACT Acetaminophen (APAP) is the most commonly used analgesic and antipyretic drug in the world. Yet, it poses a major risk of liver injury when taken in excess of the therapeutic dose. Current clinical markers do not detect the early onset of liver […]
Read MoreIntegrated Experimental and Computational Analyses Reveal Differential Metabolic Functionality in Antibiotic-Resistant Pseudomonas aeruginosa
Cell Syst. 2019 Jan 23;8(1):3-14.e3. doi: 10.1016/j.cels.2018.12.002. Epub 2019 Jan 2. ABSTRACT Metabolic adaptations accompanying the development of antibiotic resistance in bacteria remain poorly understood. To study this relationship, we profiled the growth of lab-evolved antibiotic-resistant lineages of the opportunistic pathogen Pseudomonas aeruginosa across 190 unique carbon sources. Our data revealed that the evolution of […]
Read MoreA simplified metabolic network reconstruction to promote understanding and development of flux balance analysis tools
Comput Biol Med. 2019 Feb;105:64-71. doi: 10.1016/j.compbiomed.2018.12.010. Epub 2018 Dec 17. ABSTRACT GEnome-scale Network REconstructions (GENREs) mathematically describe metabolic reactions of an organism or a specific cell type. GENREs can be used with a number of constraint-based reconstruction and analysis (COBRA) methods to make computational predictions on how a system changes in different environments. We […]
Read MoreOne thousand simple rules
PLoS Comput Biol. 2018 Dec 20;14(12):e1006670. doi: 10.1371/journal.pcbi.1006670. eCollection 2018 Dec. NO ABSTRACT PMID:30571692 | PMC:PMC6301566 | DOI:10.1371/journal.pcbi.1006670
Read MoreInferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota
Cell Syst. 2018 Sep 26;7(3):245-257.e7. doi: 10.1016/j.cels.2018.08.003. Epub 2018 Sep 5. ABSTRACT The diversity and number of species present within microbial communities create the potential for a multitude of interspecies metabolic interactions. Here, we develop, apply, and experimentally test a framework for inferring metabolic mechanisms associated with interspecies interactions. We perform pairwise growth and metabolome […]
Read MoreInfluential Parameters for the Analysis of Intracellular Parasite Metabolomics
mSphere. 2018 Apr 18;3(2):e00097-18. doi: 10.1128/mSphere.00097-18. Print 2018 Apr 25. ABSTRACT Metabolomics is increasingly popular for the study of pathogens. For the malaria parasite Plasmodium falciparum, both targeted and untargeted metabolomics have improved our understanding of pathogenesis, host-parasite interactions, and antimalarial drug treatment and resistance. However, purification and analysis procedures for performing metabolomics on intracellular […]
Read MoreTen simple rules for biologists learning to program
PLoS Comput Biol. 2018 Jan 4;14(1):e1005871. doi: 10.1371/journal.pcbi.1005871. eCollection 2018 Jan. NO ABSTRACT PMID:29300745 | PMC:PMC5754048 | DOI:10.1371/journal.pcbi.1005871
Read MoreBiomedical applications of genome-scale metabolic network reconstructions of human pathogens
Curr Opin Biotechnol. 2018 Jun;51:70-79. doi: 10.1016/j.copbio.2017.11.014. Epub 2017 Dec 7. ABSTRACT The growing global threat of antibiotic resistant human pathogens has coincided with improved methods for developing and using genome-scale metabolic network reconstructions. Consequently, there has been an increase in the number of high-quality reconstructions of relevant human and zoonotic pathogens. Novel biomedical applications […]
Read MoreHow can computation advance microbiome research?
PLoS Comput Biol. 2017 Sep 21;13(9):e1005547. doi: 10.1371/journal.pcbi.1005547. eCollection 2017 Sep. NO ABSTRACT PMID:28934204 | PMC:PMC5608165 | DOI:10.1371/journal.pcbi.1005547
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