Selected research, scientific software, and infrastructure spanning computational genomics, biological networks, HPC, and biomedical data and knowledge integration. View more on GitHub and in publications.
Selected Projects
PAH-NETWORK-ANALYSIS
An in-progress PAH analysis that combines WGCNA co-expression modules, PANDA gene regulatory networks, and TF/pathway activity inference to prioritize interpretable disease regulatory programs.
A reproducible analysis of transcriptomic and phenotypic data from an ME/CFS cohort, supporting precision interpretation of rare monogenic variation and disease-associated pathways.
KG-LLM-BIO
A Neo4j and LLM template for biomedical knowledge graph applications, using PrimeKG to connect disease biology, graph traversal, and literature-aware bioinformatics reasoning.
OOD-HPC-DASH
A Flask-based Open OnDemand dashboard that makes HPC jobs, software modules, and cluster resources easier for scientists to inspect and manage in shared research computing environments.
A Python client library for programmatic access to the Harmonizome API, supporting large-scale gene-attribute queries and dataset integration.
An R package for simplified and standardized microbiome analysis workflows, supporting reproducible exploration of microbial community data.
A Python package for ortholog analysis and visualization, designed to lower barriers for comparative genomics analyses.
A reproducible scientific infrastructure framework for computational biology labs, standardizing project structure, workflow organization, and experiment tracking so analyses are easier to reuse and audit.
See additional projects for a broader inventory of open-source software, tutorials, templates, and community resources.