Yangyi (Frank) Liu

Education

1. 2023–2025

   B.S. Molecular and Cell Biology, University of California San Diego

   Eleanor Roosevelt College. Conferred December 13, 2025. GPA 3.927.

   Vi and Quang Pham ’06 Alumni Scholarship.Eleanor Roosevelt College Honors Project, on strigolactone synthetic biology in the Li Lab, Fall 2024.Cum laude.Provost Honors, in six quarters.

   CeDiD 26TK-4GJI-YCUT, verifiable at diploma.ucsd.edu.

Experience

1. 2026–present

   Founder, AmadeusBio.ai (AmadeusBio, PBC)

   Sole founder, building LLM-powered tools for biological research: Model Context Protocol (MCP) servers for PyMOL and napari, Claude Code plugins, and Molecular Animation, an open-source framework with automated tests and CI.

2. Jan–Dec 2025

   Undergraduate researcher, Jin Lab, UC San Diego

   Genes that maintain the shape of C. elegans touch-receptor neurons: genetic crosses, PCR and Sanger genotyping, fluorescence microscopy. First-author poster at the 2025 International Worm Meeting.

3. Winter 2025

   Instructional apprentice, Biological Sciences, UC San Diego

   Undergraduate teaching assistant for BIBC 102, Metabolic Biochemistry, under Professor Feng.

4. Jun–Aug 2024

   Summer K–12 research mentor, OPALS, Institute of Engineering in Medicine, UC San Diego

   Mentored high-school interns studying MSBP1 and calcium signaling in engineered yeast; they presented the work at the Biomedical Engineering Society poster expo.Poster: doi:10.6084/m9.figshare.30254713

5. Feb 2024–Jan 2025

   Undergraduate researcher, Li Lab, UC San Diego

   Strigolactone synthetic biology in a yeast and E. coli consortium, and Arabidopsis BBX31 in campesterol-producing yeast. First-author poster at the 2024 ASCB Annual Meeting.

Selected work

1. Oct 2026

   Molecular Animation. AmadeusBio.ai · open source, Apache-2.0.

   An open framework that turns a scientific brief into a molecular film with Blender. Every film comes with a production record that states, beat by beat, what is experimental and what is illustrative. The channelrhodopsin film took about two hours from idea to final render.

2. Jul–Sep 2026

   Human-gated music agents. Personal · open source.

   Claude Code skills that compose and arrange electric-guitar tablature. The model writes the tab, a validator parses and lints it, and I audition every chunk before it is accepted.

Skills

AI agents

Agent architectures and tool use, Model Context Protocol (MCP) servers (PyMOL, napari), Claude Code skills and plugins, evals with graders, RAG, model fine-tuning

Software and ML

Python (NumPy, pandas, pytest), PyTorch, Hugging Face, TypeScript, React, SQL, Docker, AWS, GCP, CI/CD

Computational biology

AlphaFold 3, PDB/mmCIF structure analysis, PyMOL, ChimeraX, R (Seurat, Bioconductor), Scanpy, Fiji/ImageJ, statistics, Blender (Python API) for 3D visualization

Wet lab

Cloning, PCR and qPCR, mammalian cell culture, yeast and E. coli strain engineering, flow cytometry, protein expression and purification, Western blot, ELISA, LC-MS, fluorescence microscopy, Benchling

Languages

English, Mandarin (fluent), Japanese (intermediate)