Assistant Research Scientist
Department of Internal Medicine Division of Pulmonary
and Critical Care Medicine
University of Michigan, Ann Arbor MI
jre[at]umich.edu

My investigative career has focused on the communication between host and microbe, including the microbiome.  Some of my initial publications utilized mass spectrometry to identify the ability of pathogenic fungi, Cryptococcus neoformans and Candida albicans, to produce immunomodulatory prostaglandins.  These investigations demonstrated that through small molecules, microbes were capable of communicating directly with mammalian host cells in the same language that the host cells use to communicate with each other.  This research led me to study computational and bioinformatic methods to investigate microbial communities and their interactions with the host. Over the last decade I have developed substantial expertise in the analysis and integration of different kinds of large scale data sets ranging from metabolomics, to bacterial 16S profiling and transcriptomics. In addition of computational biology, I have broad expertise ranging from biochemistry and immunology to microbial ecology.  I have worked extensively with Dr. Huffnagle in analysis of the microbiome of the lungs and in establishing high throughput pyrosequencing as a platform in our lab at the University of Michigan, as well as establishing the informatics support for these analyses and the host-microbiome interaction analyses.  I have written the code for several of the applications that we use for data analysis.