Publications & Preprints

Our research outputs span knowledge graph development, AI applications in microbiology, and computational approaches to microbial cultivation.

đź“„ Preprints

KG-Microbe - Building Modular and Scalable Knowledge Graphs for Microbiome and Microbial Sciences

Brook E. Santangelo, Harshad Hegde, J. Harry Caufield, Justin Reese, Tomas Kliegr, Lawrence E. Hunter, Catherine A. Lozupone, Christopher J. Mungall, Marcin P. Joachimiak (2025)
bioRxiv preprint
https://doi.org/10.1101/2025.02.24.639989

đź›  Software Publications

CultureBotAI Organization Repositories

Repository Collection: github.com/CultureBotAI

Various repositories within this organization contain tools and resources for AI-driven microbial cultivation. Each repository will have its own specific citation format and documentation.

kg-microbe: Software Package and Knowledge Graph

Repository: github.com/Knowledge-Graph-Hub/kg-microbe
License: BSD-3-Clause License

📬 Citation Information

Primary Citation for CultureBotAI Work

@article{santangelo2025kgmicrobe,
  title={KG-Microbe - Building Modular and Scalable Knowledge Graphs for Microbiome and Microbial Sciences},
  author={Santangelo, Brook E and Hegde, Harshad and Caufield, J Harry and Reese, Justin and Kliegr, Tomas and Hunter, Lawrence E and Lozupone, Catherine A and Mungall, Christopher J and Joachimiak, Marcin P},
  journal={bioRxiv},
  year={2025},
  doi={10.1101/2025.02.24.639989},
  url={https://www.biorxiv.org/content/10.1101/2025.02.24.639989v1}
}

Software Citation

Software citations will vary by specific GitHub repository within the CultureBotAI organization. Please refer to individual repository documentation for proper citation formats.

📧 Publication Updates

Stay updated on our latest publications:

🤝 Collaboration & Co-authorship

We welcome collaboration opportunities and are open to:

  • Joint research projects combining AI and experimental microbiology
  • Data sharing initiatives for large-scale cultivation studies
  • Method development for computational microbiology tools
  • Review articles synthesizing advances in the field

Contact: MJoachimiak@lbl.gov for collaboration inquiries.