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Category Archives: Published Works

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September 10 2018
  • Published Works

Inferring 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 […]

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April 20 2018
  • Published Works

Influential 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 […]

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January 5 2018
  • Published Works

Ten 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

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December 11 2017
  • Published Works

Biomedical 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 […]

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September 22 2017
  • Published Works

How 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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August 10 2017
  • Published Works

History 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, […]

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August 3 2017
  • Published Works

Novel 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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July 21 2017
  • Published Works

Novel Plasmodium falciparum metabolic network reconstruction identifies shifts associated with clinical antimalarial resistance

BMC Genomics. 2017 Jul 19;18(1):543. doi: 10.1186/s12864-017-3905-1. ABSTRACT BACKGROUND: Malaria remains a major public health burden and resistance has emerged to every antimalarial on the market, including the frontline drug, artemisinin. Our limited understanding of Plasmodium biology hinders the elucidation of resistance mechanisms. In this regard, systems biology approaches can facilitate the integration of existing […]

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June 8 2017
  • Published Works

An engineering design approach to systems biology

Integr Biol (Camb). 2017 Jul 17;9(7):574-583. doi: 10.1039/c7ib00014f. ABSTRACT Measuring and modeling the integrated behavior of biomolecular-cellular networks is central to systems biology. Over several decades, systems biology has been shaped by quantitative biologists, physicists, mathematicians, and engineers in different ways. However, the basic and applied versions of systems biology are not typically distinguished, which […]

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May 19 2017
  • Published Works

Increased Urinary Trimethylamine N-Oxide Following Cryptosporidium Infection and Protein Malnutrition Independent of Microbiome Effects

J Infect Dis. 2017 Jul 1;216(1):64-71. doi: 10.1093/infdis/jix234. ABSTRACT Cryptosporidium infections have been associated with growth stunting, even in the absence of diarrhea. Having previously detailed the effects of protein deficiency on both microbiome and metabolome in this model, we now describe the specific gut microbial and biochemical effects of Cryptosporidium infection. Protein-deficient mice were […]

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Computational Systems Biology Laboratory; The research group of Dr. Jason Papin in the Department of Biomedical Engineering at the University of Virginia.

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The research group of Dr. Jason Papin in the Department of Biomedical Engineering at the University of Virginia

  • Email: papinlab@virginia.edu
  • Phone (434) 924-8195

  • Home
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  • Meet Our Team
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