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.

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.

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

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…

Forty Seven, Inc. was an immuno-oncology biotechnology company founded in 2015 to commercialize CD47 immune-evasion research licensed from Stanford University (Irv Weissman and colleagues).

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).

Grey Wolf Therapeutics (Greywolf Therapeutics) is a clinical-stage biotechnology company developing a new therapeutic class of immunotherapies through antigen modulation, aimed at treating people living with cancers and autoimmune disorders.

A2 Biotherapeutics (A2 Bio) is a clinical-stage biotechnology company headquartered in Agoura Hills, California, founded in 2018 by Alexander Kamb, Michael Gallo and Paul Kang. It develops logic-gated cell therapies for solid tumors on its proprietary Tmod platform, a two-receptor activator/blocker design that lets an engineered T cell attack…

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.

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.

Cofactor Genomics is a precision-medicine biotechnology company that applies RNA-sequencing and machine learning to build predictive immuno-oncology diagnostics. Its flagship OncoPrism assay is designed to predict which cancer patients will respond to immunotherapy, and the company runs the multi-center PREDAPT clinical trial across more than 24…

Forty Seven, Inc. was a clinical-stage immuno-oncology biopharmaceutical company developing therapies that target cancer immune-evasion pathways, based on technology licensed from Stanford University.