Building the data infrastructure that turns cells into cures.
Computational biologist and bioinformatics leader with 15+ years spanning genomics, epigenomics, single-cell multi-omics, and therapeutic data science. I build the pipelines, platforms, and AI-powered tools that make biological data reproducible and actionable — from academic research to clinical CAR-T development.
🔭 Current focus → CAR-T manufacturing QC | Multi-omics | LLM tooling
🌱 Growing in → Data engineering (Dagster/DBT) | AI-assisted pipelines
💬 Ask me about → scRNA-seq · snATAC-seq · Snakemake · R Shiny · Cell therapy
📍 Based in → San Diego, CA
Genomics & Bioinformatics
Data Engineering & Web
AI & Agentic
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Personal Claude AI skills and prompt engineering collection. |
Production RNA-seq pipeline: Snakemake + Kallisto. |
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Mathematical modeling of innate immune signaling (MATLAB/ODE). |
Python microservice bridging LLMs and biomedical research workflows. |
🔬 atacCNVCNV calling from bulk ATAC-seq data in R. |
Director of Bioinformatics building the company’s full data infrastructure for CAR-T cell therapy — from raw NGS to clinical dashboards across 14+ internal repos.
| System | Description | Stack |
|---|---|---|
| CMC Data Platform | Full-stack manufacturing analytics: ETL, Prisma/DBML schema, SDK, web frontend for CAR-T QC reporting | Python · TypeScript |
| Clinical LIMS | Sample tracking system (v0.15.2, 17 releases) with AI module, Dockerized | TypeScript · Docker |
| Clinical Data Pipelines | Dagster + dbt orchestrated pipelines for clinical trial data; R and Python variants | Python · R · Dagster · dbt |
| Patient Safety Monitor | R Shiny app for real-time safety monitoring with EDC and ADAM datasets | R · Shiny |
| Internal Datahub | Data sharing portal with Nextflow NGS pipelines and reproducible dataset registry | Nextflow · Shell |
| Translational Omics | scRNA-seq + CAR construct integration, Treg fingerprinting, clinical reports | R · Jupyter |
| Cloud Bioinformatics | AWS bioinformatics environment and document data extraction automation | Python · AWS |
🔒 All repositories above are private. Details available upon request.
Contributed to the Bing Ren epigenomics lab at UCSD, building core NGS infrastructure and analysis pipelines for chromatin accessibility and gene regulation research.
| Project | Description | Stack |
|---|---|---|
| Lab Management System | Django-based web app for NGS job tracking, barcode validation, sequencing status, and run management | Python · Django |
| ATAC-seq Pipeline | Production ATAC-seq processing pipeline (6 ★) | Python · Shell |
| ChIP-seq Pipeline | ChIP-seq analysis pipeline with BDS workflow engine | Java · Shell |
| BCL Demux QC | Parser for bcl2fastq undetermined barcodes — Illumina sequencing QC | Python |
| snATAC Tools | Index designer, preprocessing pipeline, and motif analysis for single-nucleus ATAC-seq | Python · Shell · R |
| Hi-C Scripts | Processing scripts for Hi-C 3D genome data (3 ★) | Jupyter · Shell |
| Nat. Genetics 2021 | Analysis notebooks for peer-reviewed publication (4 ★) | Jupyter |
| C Bioinformatics Tools | Adapted lsgkm (gkm-SVM) and kentUtils for regulatory sequence analysis | C |
Work spans 2017–2021. Repos are public at github.com/epigen-UCSD.
Personal AI tooling lab — building agentic productivity systems with Claude AI, TypeScript, and Obsidian.
| Project | Description | Stack |
|---|---|---|
| Job Applier Skill Suite | Claude Code agentic skill: CV → tailored resume PDF + cover letter + JD match + interview prep, fully automated | Shell · Claude AI |
| Job Seeker Copilot | Full-stack TypeScript UI for end-to-end job application management | TypeScript |
| AI-Powered Second Brain | Obsidian Cognitive OS: AI-collaborative PKM with Cursor rules. Published EN & CN editions (MIT) | TypeScript · Python · Obsidian |
| Journal-to-Graph | Python pipeline: journal entries → knowledge graph | Python |
~40 additional private repos: personal multi-omics clinical projects, systems biology manuscripts, and AI/LLM tooling experiments.
