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.
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.
spora [bench] is a benchmark for spatial proteomics foundation models.
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
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
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.
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.
Computational phenotyping used in the paper "A Computational Pathology Model to Predict Docetaxel Benefit in Localized High-Risk and Metastatic Prostate Cancer"
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.
Mechanistic digital twin for CRC molecular subtyping (CMS1-4) via Hopfield attractor dynamics — RT-qPCR-only panel, calibrated against real cohorts.
End-to-end multi-omics cancer subtype classifier XGBoost, pathway-aware deep fusion network (mRNA/miRNA/methylation/CNV), KEGG attention, SHAP/IG explainability, and a Streamlit demo. TCGA BRCA & COAD. PyTorch.
The repository can re-generate the learning curves, wall-clock times and policy heat-maps reported in the article: "Physics-guided deep reinforcement learning for personalized PDE control in cancer therapy optimization."
Beam-search + heuristic drug regimen ranking (MDCOE/HCOS) for TNBC — bug-fixed search algorithm, validated against a real patient's genomic profile.
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