Annotation of mutated peptide sequences with published or novel potential neoantigen descriptors

🌾 Zhang, et al, Nature Immunology, 2019. Use single-cell transcriptomics and proteomics to study autoimmune diseases.

Comparison of gene usage in immune repertoires under different biological conditions

R function to generate a circos-style ggplot from single-cell TCR data.

scLASER: Single-Cell Longitudinal Simulation and Time-Dependent Association Detection

The disTIL immunoprofiling toolkit

QC dashboard that polls vendor SQL Server databases for Luminex bead assay results, computes QC metrics (MFI, bead counts, controls, signal-to-noise), checks thresholds, and charts longitudinal trends in real time.

Code for Jonsson*, Zhang*, et al, TteK (Granzyme K+ CD8 T cells), Science Translational Medicine, 2022: the core population of inflamed human tissue-associated CD8 T cells.

Targeted Whole Exome Sequencing (WES) pipeline isolating and functionally classifying structural somatic/germline variants across the Drosophila melanogaster Toll and Relish/IMD innate immune pathways.

Code for Zhang, Wei, Slowikowski, Fonseka, Rao, et al, Nature Immunology, 2019. Single-cell transcriptomics and proteomics data analysis and integration for rheumatoid arthritis synovial tissue. These integrative strategies can be generalized to any other diseases.