immuno-oncology

IOBR is an R package to perform comprehensive analysis of tumor microenvironment and signatures for immuno-oncology. https://iobr.github.io/IOBR/

Detect loss of heterozygosity (LOH) in the MHC in tumor.

This repository provides the MATLAB scripts for our quantitative systems pharmacology model published in Front. Bioeng. Biotechnol., where we conduct an in silico clinical trial in breast cancer using anti-PD-1, anti-CTLA-4 antibody and an epigenetic modulator.

This repository contains the latest QSP platform for TNBC/NSCLC developed by the Popel Systems Biology Laboratory

Structure-based paralog selectivity counter-screen for the immuno-oncology target ENPP1 against ENPP2 (autotaxin) and ENPP3 — ranked by cross-paralog margin, not raw affinity.

A bioinformatics portfolio showcasing variant analysis, single-cell RNA-seq, and spatial transcriptomics pipelines

Machine learning to distinguish two types of T-cell receptor subregions.

The disTIL immunoprofiling toolkit

Open hotspot-guided de novo protein binder design pipeline integrating OpenMM, BindCraft, ProteinMPNN, and AlphaFold2.

Bit-exact, multithreaded Python+Rust acceleration layer for IOBRpy — CIBERSORT, signature scoring, TPM, EPIC, quanTIseq, MCP-counter, ESTIMATE at 23–26× speed with bit-identical outputs

A model-agnostic confidence and reproducibility layer for spatial-omics models: know when to trust a spatial score and when to abstain. pip-installable, tested, CI.

Personal academic site of Seongyong Park — computational immuno-oncology, cell–cell communication, and secreted-protein activity inference (CDSL, NCI/CCR, NIH)

⚡ Rust-accelerated IOBRpy: TME analysis (ssGSEA, deconvolution, LR pairs) — up to 364× faster, pandas-native API, graceful pure-Python fallback

Reproducibility package for the Gastrointestinal Immune Evolution Atlas and immune–tumor uncoupling framework.

FAIR single-cell RNA-seq pipeline mapping nerve–tumour–immune ligand–receptor crosstalk in glioblastoma across 170 donors (CELLxGENE Census, two sequencing-depth arms). Compartment integrity enforced as build gates against a held-out annotation. Snakemake + scvi-tools + scanpy + LIANA + marimo.

Deconvolve bulk expression into immune cell-type fractions by non-negative least squares (the CIBERSORT idea).

Multi-analyte ADC PK/PD and exposure-driven dose selection — therapeutic window and OBD from conjugate efficacy vs. free-payload toxicity, the toxicology paradigm (not MABEL).

TargetIntel-IO is an explainable, rule-based tool that ranks and classifies candidate targets in anti-PD-1-resistant melanoma by therapeutic intent: antibody/IO-combination, biomarker, or small-molecule strategy, with evidence-based reasoning and benchmark-checked accuracy behind every call.

Compass Therapeutics — independent third-party profile of a public API surface, by API Evangelist. Compass Therapeutics is a clinical-stage biopharmaceutical company developing proprietary antibody-based therapeutics for the treatment of cancer. Its research is grounded in understanding the tumor microenvironment, designing candidates that optimize

Oncimmune — independent third-party profile of a public API surface, by API Evangelist. Oncimmune is a biotechnology company specializing in antibody and autoantibody biomarker discovery for precision medicine. Its proprietary ImmunoINSIGHTS platform screens against 9,000+ human antigens using Luminex xMAP bead-based multiplexed immunoassay technol