Reimagining Research Papers as Interactive and Reliable AI Agents (New Journal Article)

The article linked below was published today by Nature.

Title

Reimagining Research Papers as Interactive and Reliable AI Agents

Authors

Jiacheng Miao
Stanford University

Joe R. Davis
Stanford University

Yaohui Zhang
Stanford University

Jonathan K. Pritchard
Stanford University

James Zou
Stanford University

Source

Nature
16 September 2026
DOI: 10.1038/s41586-026-11044-y

Abstract

Here we introduce Paper2Agent, an automated framework that converts research papers into artificial intelligence (AI) agents. Paper2Agent transforms research output from passive artefacts into active systems that accelerate use and discovery. Conventional research papers require readers to understand and adapt the paper’s code, data and methods to their work, creating barriers to dissemination and reuse. Paper2Agent addresses this challenge by converting a paper into an AI agent that functions as a virtual corresponding author, exposing its manuscript, supplementary materials, datasets, code and workflows as active, agent-native knowledge rather than static text. It analyses the paper and codebase using multiple agents to construct a model context protocol (MCP) server, then generates and runs tests to refine and increase robustness of the MCP. These paper MCPs can be connected to a chat agent (such as Claude Code) to carry out complex scientific queries through natural language while invoking tools and workflows from the paper. We demonstrate Paper2Agent’s effectiveness through case studies. Paper2Agent created an agent that leveraged AlphaGenome¹ to interpret genomic variants and agents based on Scanpy² and TISSUE (transcript imputation with spatial single-cell uncertainty estimation)³ to conduct single-cell and spatial transcriptomics analyses. We validate that these agents reproduce the results of the original papers and carry out novel user queries. Paper2Agent created multiple agents that collaborate to prioritize a causal gene for psoriasis. By turning static papers into interactive AI agents, Paper2Agent introduces a paradigm for knowledge dissemination and a collaborative ecosystem of AI co-scientists.

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