precision-oncology

Personal Cancer Genome Reporter (PCGR)

Open-source precision oncology platform that ranks FDA-approved and repurposing drug candidates from a patient's variant profile using OncoKB, AlphaMissense, OpenTargets and ChEMBL evidence. Blinded 50-case oncologist holdout: Hit@3 0.900, zero false positives.

Open-source software for clinical trial matching from Dana-Farber Cancer Institute: MatchMiner Genomics, MatchMiner-AI, and MatchMiner Dashboard.

Patient-Specific Modeling in Python

cBioPortal is a data visualization tool for cancer genomics. This repository contains all components to deploy the customized version of cBioPortal used in the PM4Onco use case of the Medical Informatics Initiative Germany.

preon (PREcision Oncology Normalization) is a fuzzy search tool for medical entities.

A text-based computational framework for patient -specific modeling for classification of cancers. iScience (2022).

This repository contains the code and data related to the CIViC-Fact project

AI/ML project using DepMap RNA-seq data to predict Trametinib response and identify predictive gene signatures.

MIRACUM-Pipe is a whole exome and panel sequencing pipeline for precision oncology (https://github.com/AG-Boerries/MIRACUM-Pipe). This repository is a port of the pipeline running inside a singularity container.

Clinical VCF variant annotation platform integrating Ensembl VEP, ClinVar, 3D PDB structural mapping, pharmacogenomics (PGx), and precision oncology clinical trials.

Cancer prognosis with shallow tumor RNA sequencing

Fusion Oncology fuses XGBoost drug-sensitivity models with DNABERT-2 genomic embeddings, then routes predictions through digital twin simulation, PK/PD pharmacokinetics, GNN scoring, and Bayesian uncertainty to produce confidence-scored companion diagnostic reports.

Proof of concept for a connected Microsoft IQ intelligence layer in a research AMC across Foundry IQ, Fabric IQ, Work IQ, and Web IQ.

Reference-free detection of chromosomal breakpoints from NGS data. Identifies structural variations linked to cancer without reference genome dependency. Published in Bioinformatics (2014). Direct sample-to-sample comparison for precision oncology applications.

Research framework for POLE c.138del (p.Leu46Phefs*8); Confirmed germline pathogenic frameshift variant clinically consistent w/ PPAP (reported ultra-hypermutated; tumour signature confirmation pending). Mechanistic models, differential diagnosis, therapeutic strategies, and experimental priorities.

Computational phenotyping used in the paper "A Computational Pathology Model to Predict Docetaxel Benefit in Localized High-Risk and Metastatic Prostate Cancer"

Mechanistic digital twin for CRC molecular subtyping (CMS1-4) via Hopfield attractor dynamics — RT-qPCR-only panel, calibrated against real cohorts.

💊 Advanced Drug Response Prediction & Multi-Omics Platform Interactive computational biology dashboard with ML integration, synthetic CCLE/GDSC data, dose-response modeling, and biomarker discovery. Features 6-tab Streamlit interface, Random Forest predictions, and publication-quality visualizations.

Free oncology decision support for tumor boards: cited treatment-plan drafts and Onco Wiki across 100+ diseases, 800+ indications and 400+ regimens. Clinician review required.