Supplements

“Multi-omics modeling of bacterial metabolism and effects on immune physiology”

Dr. Anne Hoen, Associate Professor, Epidemiology
Dr. Benjamin Ross, Assistant Professor, Micro Immunology
Dr. Li Song, Assistant Professor, Biomedical Data Science
Dr. Mark Sundrud, Professor of Medicine; Professor of Immunology and Microbiology

We propose to use a novel multi-omic approach to investigate the impact of key microbiota-derived metabolites on host gene expression, leveraging our diverse expertise. We will employ sophisticated sampling modalities in conventionally-colonized, germfree, and gnotobiotic mice colonized with a defined synthetic microbiota to generate complex metabolomic, metagenomic, and transcriptomic datasets. We will then develop new biostatistical methods to integrate these datasets in order to reveal how key metabolites, including those derived from microbial metabolism of bile acids and tryptophan, orchestrate transcriptomic and immunologic responses in host tissues like the intestinal lamina propria. Together, this project will provide comprehensive datasets and new models which will facilitate a greater understanding of host-microbe-metabolite interactions in the gut.

“Defining the pathogenic role of myeloid cell populations in glomerulonephritis using Spatial Transcriptomics and DNA Methylation”

Dr. Sladjana Skopelja-Gardner, Assistant Professor, Medicine
Dr. Lucas Salas Diaz, Assistant Professor, Epidemiology
Dr. Christopher Burns, Assistant Professor, Medicine

Understanding how myeloid cells mediate glomerulonephritis is essential to elucidating the mechanisms of lupus nephritis, the main cause of morbidity and mortality in lupus patients. This application directly addresses the focus of the NIGMS COBRE Supplement to develop team science projects to address complex clinical and translational research questions. In addition to identifying potential targetable pathways to prevent lupus nephritis flares, these studies will develop a non-invasive approach to define myeloid cell contributions to kidney disease through novel urine DNA methylation approaches, thus addressing the NIH’s mission to enhance health and reduce the burden of illness.

Cloud Computing Supplement

Core personnel associated with the Center for Quantitative Biology (CQB) applied for an Administrative Supplement available to current awardees of the Institutional Development Award (IDeA) program. The goal is to  explore and test potential opportunities for leveraging cloud solutions to enhance existing NIH activities.

“NOSI Cloud Computing Supplement”

Dr. Shannon Soucy, Senior Research Scientist, Biomedical Data Science
Mr. Timothy Sullivan, Research Scientist/Analyst/Engineer, Biomedical Data Science

The increasing size and complexity of genomic datasets, and the ensuing analyses, requires optimization of the research data ecosystem; it is imperative that Cloud computing and storage be part of this solution. The CQB Data Analytics Core has significant experience and expertise in genomic data science and the development of new workflows. In this proposal, we will leverage our expertise to evaluate and optimize cloud compute systems for genomic data science. We will disseminate our findings through training documentation; new advances will be passed onto users through decreased cost and shorter turnaround times.