Computational genomics, bioinformatics, AI systems, and the search for meaningful explanations.

I am Joseph Chao-Chung Kuo, a computational genomics researcher and bioinformatics lead based in Aachen. This site brings together practical notes from research and software work, project updates, and longer reflections on how biology, computation, and truth-seeking intersect.

Focus Areas

Genomics and Bioinformatics

Applied work on sequencing analysis, workflow design, quality control, and computational methods for real-world genomics projects.

AI and Software Systems

Practical notes on machine learning, infrastructure, APIs, DSLs, Python tooling, and the engineering choices behind reliable research software.

Research and Publications

A record of scientific contributions, ongoing ideas, and selected projects that connect methods development with biological questions.

Science and Faith

Reflections on the relationship between scientific discovery, meaning, and a Christian view of truth.

Start Here

• Read the About page for background and research direction.
• Browse Projects for active software and applied work.
• See Publications for peer-reviewed research.
• Explore Archives, Categories, and Tags to navigate the writing.

Selected Projects

• GenomKit: Python tooling for genomic file formats and analysis workflows.
• GPM: A command-line framework for managing end-to-end bioinformatics projects and sequencing applications.
• Seqmon: A lightweight dashboard for monitoring sequencing runs and demultiplexing metrics.

Recent Writing

• From APIs to DSLs: How AI Is Reshaping the Way We Build Software · 2026-03-30

• Choosing the Right License for Your Bioinformatics Python Package · 2025-03-03

• Modern Python Packaging: Say Goodbye to setup.py · 2025-03-02

• A Beginner’s Guide to the Nix Ecosystem · 2025-02-04

• An Overview of 10X Genomics Platforms · 2025-02-04

What You Will Find Here

This is not only a blog. It is a working notebook, project hub, and research profile. Some posts are polished tutorials, some are technical field notes, and some are broader essays about how scientific and computational work fits into a larger worldview.