Crohn’s scRNA Inflammation Prediction

Team project for CMU's 02-620: ML pipeline predicting inflamed vs non-inflamed Crohn's disease biopsies from single-cell RNA-seq (49 pre-treatment biopsies, GEO: GSE282122). I led the XGBoost modelling: grouped cross-validation by patient to prevent leakage, training on both raw gene features and PCA-reduced features, with feature importance analysis. XGBoost outperformed the kNN baseline. 

Skills: Python, XGBoost, scikit-learn, PCA, Pandas

Network-Based Drug Repurposing

Team project for CMU's 02-604: network-based drug repurposing pipeline for cardiovascular disease that integrates GWAS data, STRING protein-protein interactions, and DGIdb drug-target data to surface repurposable compounds. I formalized the computational problem, built the STRING PPI network, and designed the randomization test that validated hub connectivity. The pipeline recovered both established CVD drugs and non-obvious candidates like ribavirin. 

Skills: Python, NetworkX, STRING, DGIdb, GWAS data

Adrenal-Pancreas Open Chromatin Comparative Project

Team project for CMU's 03-713: Comparative epigenomics pipeline identifying conserved and species-specific OCRs between human and mouse pancreas, then linking them to GO biological processes, promoter/enhancer classes, and TF motifs. I built Task 3, partitioning OCRs into conserved vs species-specific sets using bedtools-based reciprocal overlap analysis on HAL liftover outputs. The resulting BED files fed all downstream functional analyses. 

Skills: Shell scripting, bedtools, HAL, rGREAT, HOMER, BED files

HP Fold Arduino

A bioinformatics project that physically visualizes protein folding energy using an Arduino Uno and the HP lattice model.

Over the course of a few days, I wanted to see if I could make protein folding tangible. Most HP model implementations are purely software. I wanted the energy trajectory to actually drive something physical. So I built a system where a Python simulation runs the folding algorithm and streams the energy in real time to an Arduino. The Arduino then translates it into servo movement, LEDs, and a buzzer.

Skills: C++, Python, Arduino, serial communication

Leaky Fire Integrate Arduino

A beginner-friendly Arduino project that simulates a neuron using a pushbutton and LED.

Over spring break, I wanted to see if I could get an Arduino to behave like a neuron. I didn't just want it to blink an LED, I wanted it to actually model the integrate-and-fire dynamics that computational neuroscientists use to describe how real neurons work.

Skills: C++, Arduino