PEPMatch
Rust + PythonFast, exact peptide and epitope search against whole proteomes, with configurable mismatches. Rust engine, Python frontend.
github.com/IEDB/PEPMatch →01 Selected work
Arborist / Protein Tree
IEDBSelects the best proteome per species across 1,600+ species and assigns a parent protein to every antigen, turning tens of thousands of isoforms into a navigable tree.
github.com/IEDB/arborist →Antigen Feature Project
in progressA meta-analysis pulling apart the molecular features that distinguish autoantigens, cancer antigens, and allergens — sequence, structure, PTMs, conservation, and more.
research · paper in progressUniProtPy
PythonA Python library that interfaces with UniProt — clean programmatic access to protein records, sequences, and metadata.
github.com/dmx2/uniprotpy →Also contributes to CEDAR, the cancer epitope database, and CMI-Flu, an influenza vaccine-response study.
02 Skills
Languages
- Python · expert
- Rust
- C++
Infra
- Linux
- Docker
- Postgres / pgvector
- nginx
- systemd
- Multi-agent / MCP
Bioinformatics
- Epitope / antigen analysis
- MHC binding prediction
- Sequence homology / BLAST
- RNA-seq
- Structural & biophysical analysis
- Post-translational modifications
- Proteome-scale pipelines
- Ontologies & databases
- UniProt
- NCBI
ML / Data
- Feature engineering
- Classification models
- Statistical / enrichment analysis
- Model evaluation (ROC / AUC)
- Embeddings / RAG
- Vector databases (pgvector)
- polars / pandas