Bioinformatics

Topological Data Analysis of Protein-Protein Interaction Networks (2023-2024) Developing a TDA-based methodology to predict protein complex formation from PPI data using persistent homology with Vietoris-Rips filtration.

RNA-seq Pipeline (nf-core) (2025) Recreation of a standard RNA-seq analysis pipeline using Nextflow and nf-core best practices.

CellCNN: Spatial Transcriptomics (2024) Recreating CellCNN paper results for single-cell gene expression analysis using convolutional neural networks.

Gene Regulatory Network Modeling (2020-2022) Comparative study of ML approaches for GRN inference from Glioma transcriptome data.

Computational Drug Discovery (2022) ML pipeline for drug activity prediction targeting SARS coronavirus 3C-like protease using molecular fingerprints.

Whole Exome Sequencing Pipeline (2020) End-to-end WES analysis including QC, alignment, variant calling per GATK best practices.

Microarray Transcription Profiling (2020) Differential gene expression analysis on HIV/HCV data with 86% replication of original publication.

Burrows-Wheeler Transform Seminar (2022) Seminar on Bowtie2 and sequence mapping algorithms.

ROSALIND Solutions Solutions to computational biology problems from ROSALIND.

Machine Learning

COVID-19 Fake News Detection (2021) Multimodal classification approach comparing Logistic Regression, SVM, KNN, and Bi-LSTM.

Reinforcement Learning

optimal-puck An experimental research repository for running Reinforcement Learning experiments on the LaserHockey environment for the RL course by Dr. Georg Martius. It provides the implementations and training, tuning and evaluation pipelines for the DDPG and TD3 algorithms with custom enhancements like Prioritzed Experience Replay and ablation of different noise injections for exploration. Setup supports both standard and self-play training and is well-logged into Weights&Biases.

Teaching & Tools

Scripting for Bioinformatics (2021) Introduction to Python, Bash, and Perl for bioinformatics applications.

Introduction to Bash Workshop (2021) Workshop materials I delivered for HacKSU student club at Kent State University.