I build computational frameworks to accelerate the future of programmable gene therapy.
AI-Native Architect | Bioinformatics & Synthetic Biology | Doctoral Researcher, Gene Therapy Lab, VIT Vellore
I am an AI-Native Architect specializing in Genetic Engineering. I don't write syntax; I build systems. I leverage agentic workflows to translate domain-specific logic into production-grade software. My focus is on architecture, validation, and solving complex problems in the Genetics space at a speed that traditional teams can’t match.
Bioengineer turned AI-Native Architect. I bridge the gap between bench-side molecular biology and computational design. By integrating wet-lab expertise in gene therapy and virology with agentic AI workflows, I build high-velocity platforms for DNA synthesis, viral vector design, and genome-writing enzyme optimization. I don’t just write code; I architect intelligent systems that accelerate the future of genome engineering. 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