Most of biotechnology runs on a handful of domesticated organisms. I work on the rest — thermophiles and other extremophiles that carry chemistry worth having but arrive with annotation nobody has checked, no genetic parts, and no pipeline built for them. Nearly everything below began as a step in that problem with no tool attached to it, so I wrote one.

Research Professor · Dept. of Biotechnology, Yonsei University · Seoul, Korea
Working on — synthetic and systems biology of non-model thermophiles, genome editors beyond Cas9, protein engineering through orthogonal replication
Mostly with — Geobacillus, Fervidobacterium, and their thermophilic neighbours

• DNMB — One GenBank in, a domestication-ready picture out: functional annotation in a readable table, codon usage, and ribosome-binding-site preference and spacing.
• DNMBsuite — The same pipeline as a Docker image. You supply GenBank files; it fetches and caches the module databases itself.
• DNMBcluster — Pan-genome clustering with the comparative figures already drawn.
• BPGAconverter — Turns BPGA pan-genome output into tables you can actually analyse.
• MethREfinder — Methylation-sensitive restriction sites checked against REBASE — the barrier that quietly kills transformation.
• ChimeraXbridge — Puts an AI assistant inside ChimeraX: natural-language control with the session as context, plus quick actions for sequence, motif and interface work.
• GeneStudio — A plasmid workbench that runs from one HTML file: circular and linear maps, digests with a simulated gel, PCR, Gibson and Golden Gate, guide design, and .ab1 review. Builds are public; the source is not.

_{Happy to talk about non-model bacteria, editor discovery, or anything that makes a stubborn organism tractable — o3wodbs@gmail.com · KakaoTalk}