Computational oncology researcher · miRNA biomarkers · pancreatic cancer · kidney disease · deep learning histopathology
Based in Beirut, Lebanon · Faculty of Medicine, American University of Beirut · mkm25@aub.edu.lb
I write reproducible, open-source pipelines for biomarker discovery and functional interpretation in solid tumors, primarily pancreatic cancer and renal cell carcinoma, using multi-omics data, machine learning, and clinical cohort analysis.
| Repository | What it does | |
|---|---|---|
| 🔬 | GPRC5A-paradox-PDAC | 5-aim pipeline resolving the GPRC5A prognostic paradox in pancreatic cancer via subtype stratification, treatment deconfounding, CPTAC proteomics, AlphaFold2, and ML role-state classification · manuscript in preparation |
| 📄 | RNA-harmonization-AI | Batch-harmonized ML framework for cross-cohort RNA biomarker discovery in PDAC · bioRxiv 2025 |
| 🧬 | mirBottleneck | Bioconductor R package scoring miRNAs by transcriptome-stabilizing activity (VSS + coherence induction). Composite bottleneck index predicts OS in TCGA-PAAD (HR=6.55, p=1.43×10⁻⁸, C-index=0.699) · manuscript in preparation |
| 🔬 | miRNA-diagnostic-platform | R Shiny platform for clinical miRNA qPCR analysis in RCC — ΔΔCt, geNorm stability, Wilcoxon testing, ROC-AUC, elastic net multi-miRNA classifier |
| 🫁 | TCGA-KIRC-vs-KIRP-miRNA-Random-Forest-Classifier | Random Forest classifier for kidney cancer subtype discrimination (KIRC vs KIRP) using TCGA miRNA expression data |
| 🔭 | trichrome-analyzer | AI-powered quantification of interstitial fibrosis from trichrome-stained kidney biopsy images |
| 🏥 | kidney-fibrosis-grader | ResNet-FPN deep learning classifier for kidney biopsy fibrosis grading (4 classes) with LLM-generated pathology reports — Streamlit app |
| 🧪 | cDNA-Synthesis-Calculator | Interactive calculator for cDNA synthesis reaction setup |
Languages: R · Python
Bioinformatics: TCGAbiolinks · DESeq2 · survival · limma · edgeR · sva · Bioconductor
ML / DL: caret · xgboost · randomForest · glmnet · pROC · PyTorch · scikit-learn
Apps: R Shiny · Streamlit
Other: ggplot2 · AlphaFold2 · GDC API · CPTAC Data Portal · Zenodo
Markarian MB. Batch-harmonized machine learning framework for cross-cohort RNA biomarker discovery in pancreatic adenocarcinoma. bioRxiv. 2025. doi:10.1101/2025.11.14.688421
Markarian MB. mirBottleneck: A Dual-Score Framework for Identifying Transcriptome-Stabilizing miRNAs and Predicting Survival in Pancreatic Adenocarcinoma. Manuscript in preparation. 2026.