Full-stack genome engineer & vibe coder (wet-lab + AI/ML/Quantum) | Doctoral Researcher, Gene Therapy Lab, VIT Vellore
I combine hands-on gene therapy and virology with machine learning and quantum-inspired circuits to design DNA, viral vectors, and genome-writing enzymes. Trained in the wet lab, now vibe-coding the computational tools that make genome engineering faster and smarter. The future of science is AI‑assisted. I’m living it. Wet-lab genome engineer → computational tool builder.
- Gene therapy & virology - AAV/lentiviral vector design, packaging, transduction, and titer optimization
- Plasmid & construct engineering - multi-cassette vectors, promoter/UTR tuning, reporter systems, Gibson & Golden Gate assembly
- Molecular biology - PCR, cloning, Sanger/NGS prep, qPCR, gel electrophoresis
- Mammalian cell culture - transfection, transduction, functional assays across HEK293, HeLa, and primary lines
- ML & GNNs for genome-writing enzyme discovery and link prediction (GraphSAGE/GAT + ESM-2 embeddings)
- Quantum circuits for DNA thermodynamics encoding and sequence feature extraction (Qiskit, PennyLane)
- Automated design pipelines for recombinase and base editor library engineering
- Languages & tools - Python, PyTorch, scikit-learn, networkx, Qiskit, PennyLane, Biopython, Shell/Bash
| Project | What it does |
|---|---|
| genome-atlas | Programmable genome-writing knowledge graph + GNN toolkit for CRISPR/CAST/Fanzor enzymes with ESM-2 and link prediction |
| mech-class | Mechanism classification framework for DNA-modifying enzymes using ML and sequence-structure features |
| pen-score | ML scoring and ranking of candidate recombinase constructs (PEN Suite) |
| pen-assemble | Automated design & scoring engine for molecular bridge-recombinase libraries (PEN Suite) |
| pen-compare | Benchmarking and comparison framework for recombinase and editor designs (PEN Suite) |
- Email: ahmedaneesm@gmail.com;
- Institute: Gene Therapy Lab, Vellore Institute of Technology