Assistant Professor of Pathology and Laboratory Medicine (Research)
Bio Med Pathology & Laboratory Medicine
My research focuses on the role of both the microbiome and epigenetics in human health. My contributions to these fields is through the bioinformatic analysis of the next-generation sequencing and high-density microarrays which provide hundreds of thousands to millions of data points per sample.
BiographyMy research interests concern the role of the human microbiome and epigenetics in human and environmental health. The human microbiome affects a surprisingly broad spectrum of disease states including inflammatory bowel disease and ulcerative colitis, periodontal disease, infections, and malnutrition to name a few. Epigenetic changes caused by early and in-utero exposure to toxicants can impact adult health through DNA methylation. Both research areas use emerging technologies such as next-generation sequencing and microarrays that generate extremely large datasets. My expertise is in the data analysis using bioinformatic tools designed for these new methods.
AffiliationsMember American Society for Microbiology
Funded ResearchNSF Biological Databases and Infrastructure. Expanding visualization and analysis tools for comparative microbial ecology (10/01/2011 - 09/30/2013)
- Young VB, Raffals LH, Huse SM, Vital M, Dai D, Schloss PD, Brulc JM, Antonopoulous DA, Arrieta RL, Kwon JH, Reddy KG, Hubert NA, Grimm SL, Vineis JH, Dalal S, Morrison HG, Eren AM, Meyer F, Schmidt TM, Tiedje JM, Chang EB and Sogin, ML (2013) Multiphasic Analysis of the Temporal Development of the Distal Gut Microbiota in Patients Following Ileal Pouch Anal Anastomosis. Microbiome 1(1):9 http://www.microbiomejournal.com/content/1/1/9 (2013)
- Human Microbiome Project Consortium (2012) Structure, function and diversity of the healthy human microbiome. Nature 486:207-214. PMC3564958 (2012)
- Human Microbiome Project Consortium (2012) A Framework for human microbiome research. Nature 486:215-221. (2012)
- Huse S, Ye Y, Zhou Y, and Fodor, AA (2012) A Core human microbiome as viewed through 16S rRNA sequence clusters. PLoS ONE 7(6): e34242. PMC3374614 (2012)
- Huse SM, Mark Welch D, Morrison HG, and Sogin ML (2010) Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environmental Microbiology 12:1889-1898. PMC2909393 Top Cited (2010)
- Huse SM, Dethlefsen L, Huber JA, Mark Welch DB, Relman DA, and Sogin ML (2008) Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing. PLoS Genetics 4: e1000255. PMC2577301 (2008)
- Huse S, Huber J, Morrison H, Sogin M, and Mark Welch D (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biology 8: R143. PMC2323236 Highly Accessed (2007)
- Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR Arrieta J, and Herndl G (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". Proceedings of the National Academy of Sciences 103: 12115-12120. PMC1524930 (2006)