Biomedical Data Science Core (BDSC)

The “Biomedical Data Science Core” (BDSC) provides consultations and fee-for-service support in big data analyses using state-of-the-art methods of data science in biomedical and health research related to digestive disease and liver research.  The BDSC provides a critical foundation for advancing the frontiers of biomedical research, providing cutting-edge analytical tools to help Penn researchers mine their rich and complex data. To facilitate human subject research in digestive disease, the BDSC also provides support for human translational research.

Grant Citation

Please cite the Center for Molecular Studies in Digestive and Liver Diseases (P30DK050306) in all publications related to core usage.

Director

Hongzhe Li, Ph.D. - hongzhe@pennmedicine.upenn.edu

Co-Director

James D. Lewis, MD, MSCE - lewisjd@pennmedicine.upenn.edu

Core Personnel

Program Manager

Lisa Nessel, MSS, MLSP - nessel@pennmedicine.upenn.edu

Bioinformationalist

Yue Ren - yueren@pennmedicine.upenn.edu

Contact Dr. Hongzhe Li (hongzhe@pennmedicine.upenn.edu) with request for the following services.

A) Basic Analyses (1 free meeting with Dr. Hongzhe Li, Cost: $100 per hour for staff analysis supervised by Dr. Li): The Core will provide the following basic biostatistics and bioinformatics analysis for omics data with analyses performed by MS level statisticians/bioinformaticians under the supervision of the Core PI.

  • Basic statistical tests/regression analysis etc.
  • Data processing, quality control, batch-effects adjustments for high-throughput genomics, metagenomics, epigenomics and metabolomics.
  • Exploratory analysis to identify clusters and patterns in the data sets using methods such a PCA, MDS, eSNE, etc.
  • Differential expression and differential abundance analysis based on omics data, including differential gene expression analysis based on RNA-seq data and differential abundance analysis based on shotgun metagenomics data.
  • Machine learning methods such as random forests to build predictive models for various clinical outcomes using high dimensional omics data.
  • Support fully-collaborative grant-funded investigations. This includes preliminary data development, hypothesis formulation, grant narrative development, data analysis and biological inference, custom software development, and co-authored dissemination of findings.

B) Customized Advanced Analyses(Cost: Discuss with Dr. Hongzhe Li): The Core can also provide more advanced statistical models which may involve developing new statistical methods for more complex problems or for new data types. The Core PI will work closely with the Center investigators and MS statisticians to develop and evaluate these methods. Some examples include:

  • Integrative analysis and causal inference of multiple omics data sets in order to gain mechanistic insights into diseases and biological processes.
  • Integrative network and pathways analysis for omics data.
  • Analysis of single cell genomics data, including scRNA-seq data using the state-of-art methods.

Contact Dr. James Lewis (lewisjd@pennmedicine.upenn.edu) for the following services.

1) Consultative services to support the design and analysis of clinical and translational research:
Study design, provision of SOPs, training of research staff, and/or providing trained research staff to implement human subject research protocols. The core can provide assistance with grant preparation through consultation on study design, statistical analysis design, power calculations, and assisting in drafting text for analyses and translational study designs.

2) Consultative support for use of clinical and translational research databases:
Access to existing clinical and translational research databases through consultation and development of standard operating procedure documentation. Databases include commercial and government run health plan insurance claims data, Epic and other linked electronic health record data, and patient registries with linked biospecimens and derived data. Support is provided to assist investigators in the implementation of their research through the provision of standardized programming and metadata.

To help with the sustainability of these core services, following one free consultation with Dr. James Lewis, subsequent work on project would be at a cost of approximately $40/hour for research coordinator time, $75/hour for senior coordinator time, $125/hour for senior project manager time, and $150/hour for core director time.