Provide analytical consulting services and direct support in study design, data analysis, data integration across data modalities, including guiding best practices for incorporating AI in computational research workflows to advance precision medicine in rheumatic disease research.
- Preliminary project review and consultation
- Support analysis and integration of diverse molecular data types including transcriptomic (e.g., microarray, RNA-Seq, single cell RNA-Seq), genomic (e.g, genotyping, exome sequencing, whole genome sequencing), proteomic (e.g., mass spectroscopy), epigenetic (methylation), immune monitoring (e.g., immune repertoire, cytokine profiling, flow cytometry and CyTOF), and phenotypic data as well as other data types depending on the projects
- Leveraging public datasets from diverse repositories such as dbGAP, GEO, ArrayExpress, ImmPort, SRA and others
- Identification of existing UCSF data collections that can be leveraged for new research
Develop novel tools, software, and analytical pipelines for the annotation, analysis, visualization, and integration of data from clinical and molecular studies of rheumatic diseases, including novel areas such as spatial -omics and large language models (LLMs). The IB Core will work with investigators to utilize their tool box of both in-house & publicly-available methods readily available for systems-level analyses of such data.
- Tools for data management, standardization and integration
- Tools for statistical analysis, data interpretation and visualization
- Data integration and functional network and pathway analysis
Integrate molecular and clinical data and leverage collaborations between the GT and CDI Cores and facilitate integrative computational analysis for a wide range of clinical, translational and basic research studies to enable precision medicine in rheumatology.
- Patient Stratification
- Identifying demographic confounders using clinical and molecular data
- Exploring comorbidities of rheumatic disease
Provide assistance with centralized data management and storage including dissemination of data for P30 associated projects including use of the UCSF Data Library developed by the Data Science CoLab
- We propose to use of the Immunology Database and Analysis Portal (ImmPort) to provide data storage, management and dissemination for the P30 related projects. The ImmPort system is the archival repository and dissemination vehicle for clinical and molecular datasets created by research consortia.
- We also collaborate closely with the Data Science CoLab to incorporate the P30 related data into the UCSF Data Library
- Work with all projects to publish data online and make it available to the UCSF and the greater research community