Bioinformatics

The Bioinformatics component of the Biostatistics and Bioinformatics Shared Resource Facility (BB SRF) aims to build and maintain robust and state-of-the-art analysis pipelines for analyzing, interpreting, and visualization of large-scale genomic, epigenomic, transcriptomic and metabolomic data generated by the Markey Cancer Center's (MCC) cancer research experiments. While these pipelines can be used for general purpose bioinformatics applications, they are specifically tailored to reveal complex molecular characteristics of cancer. We work closely with and provide custom bioinformatics solutions for MCC investigators. The focus of the Bioinformatics component is on study design, power/sample size, data processing and downstream statistical analysis of high throughput platforms. 

Highlights of Services and Key Technical Expertise. New services will be added depending on demand.

• Next Generation Sequencing Data Analysis. The Bioinformatics component has developed comprehensive pipelines to process and analyze data from:
  • Whole-genome or whole-exome sequencing.
  • RNAseq.
  • scRNAseq.
  • snATACseq.
  • ChIPseq.
  • ATACseq.
  • Whole-genome bisulfite sequencing.
  • Metagenomic sequencing.
  • Visium spatial gene expression profiling.
• Metabolomics Data Analysis. The Bioinformatics component provides bioinformatics support for raw and intermediate data analysis of metabolomics datasets, especially stable isotope-resolved metabolomics datasets. Results of these analyses can feed into other biostatistical analyses provided by the component. Custom downstream metabolic modeling and relative flux analyses can be provided on a limited basis.
• Integrative Analysis of Multiple Omics Datasets. The Bioinformatics component provides bioinformatics support to analyze the interaction or correlation across multiple genomic data. Some examples include the integrative analysis of DNA-methylation data and RNA-seq data to look at the regulation of global gene expression, and the integrative analysis of RNA-seq and ATAC-seq to identify potential therapeutic targets. The component also provides support for soft multi-omics integration using CategoryCompare, which provides integration at the level of annotations across omics datasets. Please contact us for more details.
• Genomic Data Mining. The component uses genomic data repositories such as GEO and TCGA to correlate genomic data from specific gene(s) of interest with clinical outcomes.
• NanoString digital spatial profiling. The component provides bioinformatics support for quality control, data normalization, and downstream statistical analysis for the NanoString digital spatial profiling system.
• Grant-writing Support. The component will help investigators with genomic study design, sample size/power calculation, data analysis plans, and writing bioinformatics sections.
• Training and Consultation. It is important to establish a rapport and dialogue between biomedical researchers, bioinformaticians and computational biologists. The Bioinformatics component works with investigators to establish new data analysis pipelines. The component's personnel host training/consultation/courses/lectures on bioinformatics study designs, tools, resources and databases. New services will be advertised as they become available.

Storage and Computational Resources

The BB SRF is adequately equipped with state-of-the art computing resources to support all levels of research, particularly clinical and bioinformatics studies. Computing resources for the BB SRF and other MCC facilities are centrally coordinated by the MCC Cancer Research Informatics Shared Resource Facility (CRI SRF). The CRI SRF also takes the lead in coordinating resources from the university’s Center for Computational Sciences to support big data initiatives. The BB SRF leverages MCC resources and University of Kentucky campus-wide resources to ensure optimal and secure infrastructure for computational and analytical activities.

BB SRF personnel have priority access to four nodes (128 cores and 512 GB RAM per node) in addition to access to all other nodes of Morgan Computing Cluster. BB SRF personnel also have priority access to one node of Kentucky Research Infrastructure Cloud (KyRIC) OpenStack (40 cores and 3 TB RAM). Both systems are operated by UK Center for Computational Sciences.

Personnel

Dr. Chi Wang, Assistant Director of Bioinformatics (chi.wang@uky.edu)
Dr. Jinpeng Liu, Assistant Professor
Dr. Hunter Moseley, Professor  (hunter.moseley@uky.edu)