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.

💊 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.

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

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.

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.

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

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

ML-driven platform for Glioblastoma drug recommendation using GDSC data. Features multi-model prediction (RF, XGBoost, NN, SVM, KNN), molecular similarity analysis (Tanimoto, MCS, GCN), pathway enrichment, drug interaction checking, and combination therapy optimization with interactive dashboard.

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.

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

Pan Cancer Pan Treatment Github Repository