Physician | Computational Biologist | Systems thinker with a molecular lens
Curious about life's code and driven to rewrite it for better health and a better planet.
I'm a physician with an eye on the molecular world and a foot firmly in computational biology.
Born in Nigeria, trained in medicine, and drawn to oncology, spatial genomics, and structural immunoinformatics,
I see coding and biology as two dialects of the same language — both capable of transformation.
My research sits at the intersection of computational oncology, spatial genomics, and host-pathogen structural biology.
Whether it's modelling how immune receptors read pathogen structure or building microbial systems for Mars, I pursue problems with both rigor and creativity.
- 🧫 Structure-based modelling of HLA–peptide and receptor–ligand interactions using AlphaFold3 and PRODIGY
- 🗺️ Spatial transcriptomics approaches to bacterial effector–host receptor interactions (Visium)
- 🦠 Structural reassessment of molecular mimicry in vaccine-associated myocarditis
- 🧪 nf-core DSL2 pipeline development and contributions to the open-source bioinformatics ecosystem
| Category | Tools & Languages |
|---|---|
| Languages | Python, R, Bash, Nextflow DSL2, Markdown, LaTeX |
| Structure Prediction | AlphaFold3, ESMFold, SWISS-MODEL |
| Binding & Interfaces | PRODIGY (BonvinLab/WeNMR), Foldseek, TM-align, pymol-open-source |
| Bioinformatics | Biopython, NCBI EDirect, BLAST, Clustal Omega, ElliPro (IEDB) |
| Pipeline Development | nf-core/tools, nf-test, pre-commit, Nextflow DSL2 |
| Data Science & Viz | Pandas, Matplotlib, Seaborn, ggplot2, tidyverse |
| Genomics | Ensembl, UCSC Genome Browser, SRA Toolkit, FASTA/FASTQ, BEDTools, NetMHCpan |
| Linux & CLI | Arch Linux, Ubuntu, Git, Shell scripting |
| Public Databases | NCBI (GenBank, GEO, RefSeq), UniProt, PDB, COSMIC, KEGG |
| Version Control | Git, GitHub, Git CLI |
| Others | Zotero, Jupyter, VS Code, ResearchRabbit, Anki |
- 🔬 GRIMER — nf-core DSL2 module contribution for metagenomics contamination visualisation, built for the May 2026 nf-core × VirJenDB Virus Bioinformatics Hackathon
- 🦠 metaViraVerse — viral protein structure subworkflow contribution, EBI-Metagenomics
- 🧫 Regolyx — codon optimization pipeline for perchlorate-reducing enzymes in B. subtilis, targeting Martian regolith bioremediation
- 🧬 TRACE — update repo link
- 💊 RareXDrug — update repo link
- 🤖 RepurposAI — update repo link
I've pursued rigorous learning from institutions like Wellcome Connecting Science, Bio-Rad, The Jackson Laboratory, USAID, Helix Biogen, and others.
📂 certifications-and-learning →
I'm always open to research collaborations, open-source work, and projects at the intersection of health and code.
📫 Email: johnnaadedeji2018@gmail.com
"We inherit the genetic script. But what we do with it — that's the future I'm coding for."
— Adedeji John //@genome-alchemist