Stanford Researchers Release Paper2Agent: Turning Research Papers Into AI Agents That Reproduce Results and Run on New Data


Paper2Agent turns a research paper and its codebase into a tested AI agent. You don't have to clone repos, install dependencies or debug environments before using a paper's method.

It builds an MCP server from the paper's code, then generates and runs tests against the paper's own reference outputs. Tools that keep failing are excluded, so every tool in the final server has passed validation.

You can connect the server to Claude Code or any MCP-compatible agent and ask it to apply the paper's method to your own data in plain language.

On the AlphaGenome paper, Paper2Agent built 22 validated tools in about 45 minutes for US $14. The resulting agent scored 100% on 15 novel queries, compared with 78.7% for Claude Code with direct repo access and 56.0% for Biomni.

Across 100 computational biology papers from bioRxiv, 74 were agentified and 593 of 599 proposed tools passed validation. On 300 benchmark questions, it reached 91.2% accuracy at US $0.20 per query.

Learn more with the following resources:

📰 Full breakdown: https://www.marktechpost.com/2026/09/16/stanford-researchers-release-paper2agent-turning-research-papers-into-ai-agents-that-reproduce-results-and-run-on-new-data/

📄 Paper:
https://www.nature.com/articles/s41586-026-11044-y

⭐ GitHub:
https://github.com/jmiao24/Paper2Agent

🤗 AlphaGenome MCP server:
https://huggingface.co/spaces/Paper2Agent/alphagenome_mcp

🧪 Try it:
https://paper2agent.ai/live