Paul M. Ruegger

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BACKGROUND Consistent compositional shifts in the gut microbiota are observed in IBD and other chronic intestinal disorders and may contribute to pathogenesis. The identities of microbial biomolecular mechanisms and metabolic products responsible for disease phenotypes remain to be determined, as do the means by which such microbial functions may be(More)
BACKGROUND Replant disease often occurs when certain crops are "replanted" in a soil that had previously supported the same or similar plant species. This disease typically leads to reductions in plant growth, crop yields, and production duration, and its etiology remains ill-defined. The objective of this study was to identify microorganisms associated(More)
—Polony technology is a low-cost, high-throughput platform employed in several applications such as DNA sequenc-ing, haplotyping and alternative pre-mRNA splicing analysis. Owing to their random placement, however, overlapping polonies occur often and may result in inaccurate or unusable data. Accurately identifying polony positions and sizes is essential(More)
Intestinal microbiota play a significant role in nutrient metabolism, modulation of the immune system, obesity, and possibly in carcinogenesis, although the underlying mechanisms resulting in disease or impacts on longevity caused by different intestinal microbiota are mostly unknown. Herein we use isogenic Atm-deficient and wild type mice as models to(More)
Developing computational methodology for processing, integrating and interpreting high-throughput genomic data (especially next-generation sequencing data like ChIP-Seq and RNA-Seq), and its applications in biomedical and cancer research. The 2 nd Ph.D. intern since NIBR established in Emeryville, CA. Large-scale RNA-Seq analysis over 4 TB data of over 100(More)
BACKGROUND Population levels of microbial phylotypes can be examined using a hybridization-based method that utilizes a small set of computationally-designed DNA probes targeted to a gene common to all. Our previous algorithm attempts to select a set of probes such that each training sequence manifests a unique theoretical hybridization pattern (a binary(More)
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