Knowledge Graph Engineer | Semantic Engineer | AI/ML | Data Science | Data Engineering
Building systems that bridge structured knowledge, biomedical data, and machine learning — from ontology embeddings and interaction networks to clinical data pipelines and publication-ready manuscript generation.
| Project | What it does |
|---|---|
| academic-manuscript-skill | Claude Code skill for generating scientific manuscripts with real CrossRef references and Zotero field codes |
| PPIExtractor | Automated protein-protein interaction network extraction pipeline |
| biomodelize | Web app for simulating SBML models with RoadRunner — upload, run, visualize, download |
| ontoembed | Ontology embedding methods for knowledge graph representation |
| slicerGUI | Dockerized 3D Slicer with VNC/noVNC web interface for medical image visualization |
| eGBIM | Extended graph-based interaction model |
| Mendoza | Biochemical reaction network simulation using the Mendoza equation with SBML model generation |
Knowledge Graphs & Semantics — ontology embeddings, interaction networks, graph neural networks, entity linking
Biomedical Computing — SBML simulation, spine parameter modeling, medical image processing (3D Slicer), protein interaction extraction
ML/AI — GNNs, tabular diffusion, missing data imputation, neural architecture search
Data Engineering — REDCap pipelines, Apache NiFi workflows, object storage hierarchies
Python TypeScript Vue C++ Docker Node.js Graph Neural Networks SBML OpenSim 3D Slicer
