Bioinformatics Handbook
An open book on bioinformatics for human genetics, from molecular biology to biobank-scale association studies
Role: author and maintainer · 2026 – present
Links: Read online · Repository
Why I wrote it
I came to bioinformatics from data engineering and finance, and I learned it on the job: molecular biology, statistics, file formats, biobanks and association studies, one question at a time. For years I kept working notes on every topic I had to master. This book turns those notes into a structured reference, organized so that each chapter answers one practical question.
What’s inside
17 chapters and 4 appendices, with Mermaid diagrams, commands and checklists:
| Part | Topics |
|---|---|
| I — Foundations | Molecular biology, genetic variation, statistics for describing data, statistical inference |
| II — Data and Infrastructure | Lab and sequencing methods, file formats, computing environment (HPC, cloud), biobanks |
| III — Genetic Association Studies | Genotype QC, relatedness and population structure, GWAS, SAIGE, rare variants, meta-analysis, post-GWAS |
| IV — Applications | Pharmacogenomics, knowledge graphs |
| Appendices | Cheat sheets, templates, reading path, glossary |
What makes it different
- Practical by design. Each chapter answers one question someone actually asks when running a study, with the commands and checklists to do it.
- Public data only. Examples use public resources (1000 Genomes, public summary statistics, PharmGKB). No data, results or infrastructure details from private cohorts appear in the book.
- Same method as the SaaS Handbook: a Quarto book published to GitHub Pages, with the repository open to issues, discussions and pull requests.
- Open licenses: text under CC BY 4.0, code under MIT.
Stack
Quarto · Mermaid · GitHub Actions · GitHub Pages