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

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.

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

The disTIL immunoprofiling toolkit

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.

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 the components required for an effective anti-tumor immune response and bridge innate and…

Trillium Therapeutics was a Toronto-based clinical-stage immuno-oncology biopharmaceutical company developing cancer therapeutics (notably CD47-targeting agents). It was acquired by Pfizer in August 2021 for approximately $2.2B and no longer operates as an independent entity.

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).

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 technology, minimal sample volumes, high-throughput automated robotic workflows, and…

Mechanistic first-in-human dosability screen for tumor-targeted bispecific antibodies — go/no-go and dosability-margin ranking computed from binding parameters, before any dose exists.

Transcriptome-based immune phenotyping and survival stratification in TCGA lung adenocarcinoma

Normunity is a clinical-stage biotechnology company developing novel anti-cancer therapies that work at the interface of the immune system and the tumor. In collaboration with the Lieping Chen lab at the Yale School of Medicine, Normunity has identified a novel class of "Immuno-smart targets" — tumor-specific, cell-surface proteins co-opted by…

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.

Intrepida Bio, Inc. is a preclinical biotechnology company (founded 2019, headquartered in Encinitas / San Diego, CA) developing medicines that modulate the innate immune system to fight cancer and other diseases.

Trishula Therapeutics is a privately held, clinical-stage immuno-oncology company developing cancer immunotherapies that target immune-evasion mechanisms in the tumor microenvironment.

ArsenalBio is a privately held, clinical-stage biotechnology company in South San Francisco developing programmable, integrated cell therapies for solid tumors. Its platform engineers autonomous CAR-T cells using large-scale genome engineering and computational biology to create multi-functional therapies.