Research Cores & Services
Administrative Core (AC)
The MKTC Administrative Core is dedicated to maintaining a vibrant educational environment for kidney research, with a focus on T1 translational research.
Fostering an Educational Environment for Translational Research
We aim to entice trainees and faculty into kidney research and support researchers in their ongoing kidney research by providing educational programs such as:
Annual educational retreat
Our annual educational retreat is where research progress is reviewed and feedback on Center services is obtained.
Summer Students Research Program
Participate in our student programs to explore kidney research.
Learn moreApplied Systems Biology Core (ASBC)
The ASBC provides expert consulting services for integrative data mining of genome-wide renal data sets. The ASBC team has developed a unique set of tools and skills to serve as the bridge connecting the deep biological and clinical knowledge of the domain experts in our research labs with the relevant segments in large-scale molecular and clinical renal disease data sets.
The ASBC supports a wide range of research efforts by kidney researchers ranging from NIH training and career development grant awardees, independent investigators and NIH-funded multi-center research networks.
Interactive shared data mining services
Initial study design consultation
Identify public data responsive to user needs
Transcriptomics: RNAseq, single cell/nucleus RNA sequencing analysis
Streamlined self-organizing map (SOM) to identify functional subgroups
Weighted Correlation Network Analysis (WGCNA) analysis
.svg){kind=icon}
Metabolomics: platform specific data processing, data normalization, identification of differentially expressed metabolites
Spatial Metabolomics in partnership with the Center for Precision Medicine at the University of Texas Health Science Center at San Antonio.
Pathway mapping and enrichment analysis
.svg){kind=icon}
Multi-scalar data integration of: clinical phenotype, morphology, genetic, epigenomic, transcriptomic, proteomic, metabolomic datasets
Quantitative morphometric analyses of kidney biopsy samples
Model systems studies
Structured RNA-DNA sequence data integration
Training on common bioinformatic tools (Nephroseq, Cellxgene, etc.)
Data Analytic services Core (DASC)
The Data Analytic Services Core (DASC) curates and collates different types of data from various kidney disease cohorts and disease model systems. These data are then maintained, updated and made available to the research community. DASC-hosted data mining and sharing platforms have been developed to enable integration of multi-scale data sets to be mined, analyzed, and shared by research base investigators. The data mining and analytic interfaces to interrogate genetic, molecular, histological, or clinical features of interest have been specifically developed towards the needs of the kidney researcher.
Data Mining Tools for the Kidney Research Community
The DASC provides access, training and support for data exploration with the following user-friendly analysis tools:
Resource Development Core (RDC)
The Resource Development Core (RDC) supports the Applied Systems Biology Core (ASBC), the Data Analytic Services Core (DASC) and the kidney research community at large by developing a unified platform and methods that integrate multidimensional data, cohort selection and clinical trial design.
Building pipelines to advance research and Improve patient care
The University of Michigan Precision Health Initiative (PHI), which incorporates all data from Michigan Medicine patients in addition to biological samples, represents a unique resource that the RDC will expand upon to develop the following pipelines.
The pipelines and workflows to be developed by the RDC will provide investigators across the spectrum of research stages – from bench (biomarker discovery) to bedside (clinical trial design) – the ability to integrate multidimensional data – in addressing the major challenges the management of patients with kidney disease.
.svg){kind=icon}
Biomarker candidate selection, assay, validation, and incorporation into study design
Establish a database and pipeline to provide investigators the most promising biomarkers, relevant assays based on the outcomes investigated, in addition to guidance surrounding validation and quality control.
.svg){kind=icon}
Cohort development
Leverage the infrastructure of the PHI to build algorithms to identify and curate with high confidence kidney-specific diagnoses, relevant clinical characteristics, laboratory testing, as well as outcomes through integrating multiple data sources including billing codes and natural language processing. The end-result will provide investigators the ability to easily identify relevant cohorts and rapidly retrieve data in a format that is ready to analyze through a graphical user interface.
Kidney outcomes
Build a pipeline to incorporate United States Renal Data System (USRDS) data into the PHI platform, enriching the Michigan Medicine dataset and providing confirmatory data for cohort- specific analyses.
Novel metabolomic technologies and multi-omic integration
In addition to developing a spatial metabolomic platform, we improve tools for annotation of untargeted metabolomics data and identification of new compounds and provide novel integrative analysis of metabolomics-proteomics-transcriptomics- epigenomics data.
Clinical trial design
Develop a workflow for kidney-specific clinical trial design and implementation, as well as provide associated workshops through the highly successful Clinical Trials Academy.