Molecular Informatics Core (MIC)
The field of biomedical data science is constantly changing and it can be difficult for researchers to keep track of the new technologies and instruments available. At the Molecular Informatics Core, we strive to help our customers not only with their current research projects but also to keep you apprised of future opportunities. We are currently working on several exciting projects at the MIC.
In the past few years, the Terra cloud-based ecosystem developed by the Broad Institute has become a vital tool for large-scale or complex data analysis. Terra is bult on Google Cloud and is designed to simplify the process of allocating cloud resources and implementing workflows. Users can run any standard bioinformatics workflows through Terra, but it’s selling point is easy access to many large biomedical datasets such as the Cancer Genome Atlas, the 1000 Genomes Project, and others. The MIC is increasingly working with Terra-based resources to enhance the ability of our researchers to conduct cutting edge research.
One project we’re working on with Drs. Jamie Ross and Giuseppe Coppotelli and graduate student Hannah Tobias-Wallingford at URI involves studying mitochondrial variants linked to age-related diseases. As part of this project, the MIC is developing a Snakemake implementation of a Broad Institute mitochondrial variant analysis pipeline (originally implemented on Terra) that is generalizable to any organism. This will allow us to use this pipeline in other mitochondrial animal models that other researchers are interested in.
The All of Us platform (Participant Page, Researcher Hub) is a Terra-based platform designed for large-scale cohort analyses that more accurately represent the genetic diversity of the United States population. While many types of analyses are possible on AoU, the MIC is currently focusing on genome-wide association studies that link genetic variants to diseases. The first project we worked on with AoU was with Drs. Gabrielle Papalle and Jillian Wise and student Kaitlyn Ford at Salve Regina University, and MIC intern Vrunda Patel and involved analysis of StarD6 variants linked to Alzheimer’s Disease. A second project with Drs. Nisanne Ghonem and Xuerong Wen and graduate student Colleen Hayes at URI involves analysis of UDP-glucuronosyltransferase variants linked to cholestatic liver disease.
The MIC has also been working closely with Dr. Ang Cai in the RI-INBRE CRCF, Dr. Chang Liu and Ni Deng in the College of Pharmacy to develop standardized workflows for proteomics projects. These workflows will cover experimental design, data acquisition, and data analysis.
Finally, we are working with the CRCF to purchase a 10X Genomics Chromium X single cell omics system and a 10X Genomics Visium CytAssist for the CRCF. This will allow our cores to offer services in single cell omics and discovery level spatial omics. These technologies will significantly upgrade the ability of RI-INBRE and affiliated researchers to conduct cutting edge omics-based analyses. As these instruments become available, we will keep the community updated on training opportunities.