Integrated 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
Read MoreHistory of antibiotic adaptation influences microbial evolutionary dynamics during subsequent treatment
PLoS Biol. 2017 Aug 8;15(8):e2001586. doi: 10.1371/journal.pbio.2001586. eCollection 2017 Aug. ABSTRACT Antibiotic regimens often include the sequential changing of drugs to limit the development and evolution of resistance of bacterial pathogens. It remains unclear how history of adaptation to one antibiotic can influence the resistance profiles when bacteria subsequently adapt to a different antibiotic. Here, […]
Read MoreNovel co-culture plate enables growth dynamic-based assessment of contact-independent microbial interactions
PLoS One. 2017 Aug 2;12(8):e0182163. doi: 10.1371/journal.pone.0182163. eCollection 2017. ABSTRACT Interactions between microbes are central to the dynamics of microbial communities. Understanding these interactions is essential for the characterization of communities, yet challenging to accomplish in practice. There are limited available tools for characterizing diffusion-mediated, contact-independent microbial interactions. A practical and widely implemented technique in […]
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