The AstroPath Pipeline was developed to process whole slide multiplex immunofluorescence data from microscope to database at single cell resolution.

Constructing Neoantigen Vaccine Pipeline with pVACtools

the peptide immune annotator pipeline (PIA-P) a collection of bash and Python scripts used running peptide HLA interaction from a variety of inputs

Immunopeptidogenomics — cryptic peptide database construction from RNA-seq. An nf-core-style port of the 31-step IPG pipeline (Scull et al. Mol Cell Proteomics 2021), built for the Li and Purcell Labs at Monash University.

Transfer learning framework (CoGAPS + projectR) quantifying cross-species conservation of tumor microenvironment transcriptional programs between mouse models and human melanoma, with immunotherapy response prediction (AUC = 0.917).

Scientific framework and immunological rationale for individualized brain tumor immunotherapy protocols.

Operator-theoretic spatial biology framework for tumor–immune interface analysis using Hodge decomposition, antisymmetric commutator geometry, and graph operator dynamics. Validated across HCC, IMC, CABO/NIVO, and a pan-cancer Visium cohort (26 sections, 118k+ spots, 6 cancer types).

The Co-culture Efficacy Score (CES) is a quantitative framework for measuring drug activity in complex multicellular systems. It integrates cumulative activity and maximal efficacy into a single interpretable score, separating general toxicity from true effector-mediated cytotoxicity.