In addition to supporting a wide range of research studies, the HIMC is actively engaged in several research and development projects to optimize new technology platforms and develop and novel immune monitoring assays. We are always interested in new technology and welcome partnerships with industry collaborators to evaluate and develop new immune monitoring platforms. We have already engaged in several completed and ongoing research collaborations with companies including Fluidigm, Biolegend, eBioscience, Cytognos, Innova Biosciences, Glass Expansion, Curiox BioSystems,10X Genomics and CyTek. If you are interested in technology collaboration, please contact Seugnhee Kim-Schulze, our facility director.

Some of our other ongoing research and development projects include the development and optimization of reagents and workflows to improve data quality, and reproducibility and facilitate meta-analyses across CyTOF studies. We are also working to implement and optimize CITE-Seq, a novel approach that combines antibody profiling and single cell sequencing to maximize proteomic and transcriptomic profiling on single cells.

The HIMC computational team is also actively involved in the development of novel computational tools. For example, we are developing Cytutils, an open source R package that includes a tool for FCS channel renaming and other utilities for cytometry quality control and reproducibility.

We are also actively developing novel single-cell RNAseq and CITE-seq data analysis pipelines and high-performance web-based data visualization and analysis tools in order to meet the demands of single-cell data. We are continuing to develop the open source interactive heatmap tool Clustergrammer as well as developing a WebGL version of Clustergrammer that will enable GPU accelerated visualization of large datasets. Additionally, the HIMC is focused on developing transparent, reproducible and shareable analyses tools (e.g. utilizing Jupyter notebooks) that utilize open source software where available.

Resources

Computational Tools

The HIMC is actively involved in the development of novel computational tools to facilitate processing and analysis of immunological data. Some of our tools are available in Cytutils, an open source R package that includes a tool for FCS channel renaming and other utilities for cytometry quality control and reproducibility.

Public Datasets

The CyTOF data associated with many of our publications are publicly available on FlowRepository.

The Antibody Staining Data Set is a comprehensive screen performed by the HIMC to establish the expression of 326 surface markers across all major circulating immune subsets at single-cell resolution. The data is available through an interactive web application.