Awesome bioagent papers

This repository, autonomously updated daily by our Pantheon agent system, collects papers on the applications of LLM-based agents in biology and medicine.

Agent papers

• [2023.11 Preprint] Validation of an LLM-based Multi-Agent Framework for Protein Engineering in Dry Lab and Wet Lab
• [2023.12 Nature] Autonomous chemical research with large language models
• [2023.12 Preprint] Leveraging large language models for data analysis automation
• [2024.03 Advanced Science] BioinspiredLLM: Conversational Large Language Model for the Mechanics of Biological and Bio-Inspired Materials
• [2024.03 Preprint] BioDiscoveryAgent: An AI Agent for Designing Genetic Perturbation Experiments
• [2024.04 Preprint] CRISPR-GPT: An LLM Agent for Automated Design of Gene-Editing Experiments
• [2024.04 Preprint] Replicating a High-Impact Scientific Publication Using Systems of Large Language Models
• [2024.05 Preprint] Agent Hospital: A Simulacrum of Hospital with Evolvable Medical Agents
• [2024.05 Nature Machine Intelligence] Augmenting large language models with chemistry tools
• [2024.06 Preprint] CellAgent: An LLM-driven Multi-Agent Framework for Automated Single-cell Data Analysis
• [2024.06 Nature] A multimodal generative AI copilot for human pathology
• [2024.06 Preprint] BioInformatics Agent (BIA): Unleashing the Power of Large Language Models to Reshape Bioinformatics Workflow
• [2024.06 Nature Methods] Omega — harnessing the power of large language models for bioimage analysis
• [2024.06 Preprint] MedAgents: Large Language Models as Collaborators for Zero-shot Medical Reasoning
• [2024.08 Nature Methods] BioImage.IO Chatbot: a community-driven AI assistant for integrative computational bioimaging
• [2024.09 Preprint] Simplifying bioinformatics data analysis through conversation
• [2024.10 Preprint] Multimodal learning of transcriptomes and text enables interactive single-cell RNA-seq data exploration with natural-language chats
• [2024.10 Preprint] MMedAgent: Learning to Use Medical Tools with Multi-modal Agent
• [2024.10 Preprint] RNA-GPT: Multimodal Generative System for RNA Sequence Understanding
• [2024.11 Preprint] The Virtual Lab: AI Agents Design New SARS-CoV-2 Nanobodies with Experimental Validation
• [2024.11 Advanced Science] An AI Agent for Fully Automated Multi-Omic Analyses
• [2024.11 Nature Medicine] Collaboration between clinicians and vision–language models in radiology report generation
• [2024.11 eBioMedicine] Generative AI agents are transforming biology research: high resolution functional genome annotation for multiscale understanding of life
• [2024.11 Preprint] DrugAgent: Automating AI-aided Drug Discovery Programming through LLM Multi-Agent Collaboration
• [2024.11 Preprint] PIORS: Personalized Intelligent Outpatient Reception based on Large Language Model with Multi-Agents Medical Scenario Simulation
• [2024.12 Advanced Materials] SciAgents: Automating Scientific Discovery Through Bioinspired Multi-Agent Intelligent Graph Reasoning
• [2024.12 Nature Machine Intelligence] LLM-based agentic systems in medicine and healthcare
• [2024.12 Preprint] AI-HOPE: An AI-Driven conversational agent for enhanced clinical and genomic data integration in precision medicine research
• [2025.01 Preprint] KG4Diagnosis: A Hierarchical Multi-Agent LLM Framework with Knowledge Graph Enhancement for Medical Diagnosis
• [2025.01 Preprint] Agent Laboratory: Using LLM Agents as Research Assistants
• [2025.01 Preprint] A Multi-Modal AI Copilot for Single-Cell Analysis with Instruction Following
• [2025.01 Preprint] BioAgents: Democratizing Bioinformatics Analysis with Multi-Agent Systems
• [2025.01 Preprint] BioMaster: Multi-agent System for Automated Bioinformatics Analysis Workflow
• [2025.02 Preprint] scBaseCamp: an AI agent-curated, uniformly processed, and continually expanding single cell data repository
• [2025.02 Preprint] Towards an AI co-scientist
• [2025.02 Preprint] Spike sorting AI agent
• [2025.03 Nature communications] DrBioRight 2.0: an LLM-powered bioinformatics chatbot for large-scale cancer functional proteomics analysis
• [2025.03 Preprint] FlowAgent: A Modular Agent-Based System for Automated Workflow Management and Data Interpretation
• [2025.03 Preprint] TxAgent: An AI Agent for Therapeutic Reasoning Across a Universe of Tools
• [2025.03 Preprint] IAN: An Intelligent System for Omics Data Analysis and Discovery
• [2025.03 Preprint] PharmAgents: Building a Virtual Pharma with Large Language Model Agents
• [2025.03 Preprint] CompBioAgent: An LLM-powered agent for single-cell RNA-seq data exploration
• [2025.07 Preprint] GenoMAS: A Multi-Agent Framework for Scientific Discovery via Code-Driven Gene Expression Analysis [code] [website]

Benchmarks

• [2024.06 MLCB 2025 Oral] GenoTEX: An LLM Agent Benchmark for Automated Gene Expression Data Analysis [code] [website]
• [2025.03 Preprint] BioMaze: Benchmarking and Enhancing Large Language Models for Biological Pathway Reasoning
• [2025.03 Preprint] BixBench: a Comprehensive Benchmark for LLM-based Agents in Computational Biology
• [2025.03 Preprint] MicroVQA: A Multimodal Reasoning Benchmark for Microscopy-Based Scientific Research

Reviews

• [2023.05 Arquivos Brasileiros de Cirurgia Digestiva] Future of the Language Models in Healthcare: The Role of ChatGPT
• [2023.11 Preprint] A Survey of Large Language Models in Medicine: Progress, Application, and Challenge
• [2023.07 Lancet] The promise of large language models in health care
• [2024.04 npj Digital Medicine] Evaluating large language models as agents in the clinic
• [2024.05 iScience] The application of large language models in medicine: A scoping review
• [2024.06 Preprint] Bioinformatics and Biomedical Informatics with ChatGPT: Year One Review
• [2024.07 Preprint] Empowering Biomedical Discovery with AI Agents
• [2024.07 Nature Medicine] Evaluating the clinical benefits of LLMs
• [2024.07 arXiv] Large Language Models in Healthcare and Medical Domain: A Review
• [2024.10 Cell] Empowering biomedical discovery with AI agents
• [2024.10 JCO Precision Oncology] Expert-Guided Large Language Models for Clinical Decision Support in Precision Oncology
• [2024.11 Preprint] A Review of Large Language Models and Autonomous Agents in Chemistry
• [2024.11 PLOS Digital Health] Large language models in medicine: A review of current clinical trials across healthcare applications
• [2024.12 Computational and Structural Biotechnology Journal] Large language models and their applications in bioinformatics
• [2024.12 Springer] Large language models in medical and healthcare fields: applications, advances, and challenges
• [2024.08 Springer Link] Large models for genomics
• [2024.05 PMC] Clinical and Surgical Applications of Large Language Models: A Systematic Review
• [2024.09 Artificial Intelligence Review] Large language models in medical and healthcare fields: applications, advances, and challenges
• [2024.12 Nature Cancer] How AI agents will change cancer research and oncology
• [2025.02 The Lancet] The rise of agentic AI teammates in medicine
• [2025.03 Trends in Biotechnology] Large language model for knowledge synthesis and AI-enhanced biomanufacturing