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biomystery/README.md

👋 Hi, I'm Frank (Zhang Cheng)

Director of Data Science · Computational Biology · Scientific Software

Connecting biological questions with actionable analyses and usable systems.

📍 San Diego, CA 🌊

GitHub followers LinkedIn Profile views

🧬 About Me

I'm a computational biologist and data science leader with 15+ years spanning genomics, epigenomics, single-cell multi-omics, and therapeutic data science. I combine scientific depth with hands-on software development, working across teams to turn complex questions into analyses and systems people can use.

🔭 Working on    → Scientific data platforms · Multi-omics · CAR-Treg cell therapy
🛠️ Building      → Reproducible workflows · Knowledge tools · AI-assisted automation
💬 Ask me about  → Computational biology · Cross-functional data science · Scientific software

🌟 Highlighted Public Work

🧠 LLM Wiki + KG Starter

Build an LLM-maintained knowledge base in Obsidian, with linked notes, source provenance, and review status.

🔗 Obsidian · Open Knowledge Format · Python

Inside: example pages, an ingest/query/lint skill, and a deterministic linter. Publish with wiki-hosting-project.

📚 wiki-hosting-project

Turn an Obsidian vault into a searchable static website, with wikilinks, aliases, and backlinks.

🐍 Python · MkDocs · Docker · nginx

Inside: sample vault, Docker quickstart, and link-resolver tests.

🤖 claude-skills

Reusable agent skills for data documentation, document conversion, and knowledge management.

🧠 Agent workflows · Markdown · Obsidian

Start here: data-dictionary — Prisma + SQLite → Markdown documentation.

🔬 atacCNV

Call copy-number variation from ATAC-seq, from coverage processing to CNV regions and segment plots.

📊 R · Shell · Genomics

Inside: documented read filtering, coverage smoothing, and CNV workflow.

🏢 Science & Data @ Sonoma Biotherapeutics

As Director of Data Science, I work across scientific and operational questions in CAR-Treg cell therapy.

Focus What I contribute
🔗 Data integration Bring data across functions into a manufacturing data portal to support investigation and analysis
🧬 Multi-omics Develop workflows that connect biological measurements with interpretable outputs
🔎 Scientific analysis Contribute to efficacy-related and biomarker analyses with scientific colleagues

🏛️ Scientific Roots

  • Illumina — Led a team developing NGS analysis applications.
  • Bing Ren Lab · UC San Diego (2017–2020) — Contributed to NGS infrastructure and analysis workflows for epigenomics and gene regulation. Explore the lab's public work at epigen-UCSD.
  • 25+ peer-reviewed publications, alongside presentations on cell therapy and multi-omics.

🛠️ Technical Toolkit

Genomics & Scientific Computing
Python R Shell Nextflow Snakemake

Data Platforms & Web
TypeScript React Next.js FastAPI SQL Docker AWS

AI & Knowledge Workflows
Claude Agent Skills Obsidian MkDocs

📊 GitHub Stats

Frank's GitHub Stats Top Languages

🤝 Let's Connect

Open to conversations about scientific data platforms, reproducible bioinformatics, and practical AI workflows across R&D.

Connect on LinkedIn

Pinned Loading

  1. epigen-UCSD/epigen_ucsd_django epigen-UCSD/epigen_ucsd_django Public

    Python 1 1

  2. CA-HIV-infection-model CA-HIV-infection-model Public

    A stochastic agent-based model to demonstrate two types of HIV transmission.

    Python 2

  3. epigen-UCSD/atac_seq_pipeline epigen-UCSD/atac_seq_pipeline Public

    Python 6

  4. epigen-UCSD/bcl2fastq_undetermined_parser epigen-UCSD/bcl2fastq_undetermined_parser Public

    Parse the result from bcl2fastq and get the undermined barcode info

    Python 1 1

  5. research_ai_service research_ai_service Public

    Python

  6. claude-skills claude-skills Public

    Reusable Claude Code skills (slash commands) for repeatable workflows

    Python 1 1