Personal Cancer Genome Reporter (PCGR)

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

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.

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.

Research framework for POLE c.138del (p.Leu46Phefs*8) — an ultra-rare frameshift variant causing PPAP with ultra-hypermutated tumor phenotype (TMB >100 mut/Mb). Mechanistic models, therapeutic strategies, and experimental priorities.

💊 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.

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.

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

Official implementation: A Clinical Informatics Framework for Myeloid Oncology. Integrates Scalable AI (GBDT, LSTM) and LLMs (Agentic AI) for precision oncology trial management, patient stratification, and automated FDA 21 CFR Part 11 compliance.

High-accuracy ML model for leukemic stem cell (LSC) identification from single-cell multi-omics data (TEA‑seq, CITE‑seq, scRNA‑seq).

R/Bioconductor pipeline for Breast Cancer biomarker discovery using Limma and Random Forest.

Multimodal AI Platform for Precision Oncology — CT Tumor Detection · Cellpose Microscopy · Drug Synergy · PK/PD Modeling

A statistical framework for detecting significant drug combination synergies in cancer. By leveraging tissue-specific reference null distributions across multiple synergy metrics, we compute empirical p-values to standardize synergy detection, uncover novel interactions, and enable rigorous evaluation of drug combinations.

Bio-Resonant Restoration - Epigenetic Memory Reactivation via Piezoelectric Resonance: A Mechanistic Framework for Cellular Restoration

Bayesian framework for identifying expression-driven genetic dependencies across cancer cell lineages. BEACON integrates JAGS-based MCMC inference with pan-cancer expression and CRISPR dependency data to reveal precision oncology targets.