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title Publications
description Research publications and preprints by Dr. Marcin P. Joachimiak on KG-Microbe knowledge graph development and AI applications in microbial cultivation.
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Publications by Dr. Marcin P. Joachimiak — KG-Microbe and AI for Microbiology

Our research outputs led by Dr. Marcin P. Joachimiak span KG-Microbe knowledge graph development, AI applications in microbiology, and computational approaches to microbial cultivation.

📄 Preprints

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

Full Citation (APA): Santangelo, B. E., Hegde, H., Caufield, J. H., Reese, J., Kliegr, T., Hunter, L. E., Lozupone, C. A., Mungall, C. J., & Joachimiak, M. P. (2025). KG-Microbe - Building Modular and Scalable Knowledge Graphs for Microbiome and Microbial Sciences. bioRxiv. https://doi.org/10.1101/2025.02.24.639989

DOI: 10.1101/2025.02.24.639989

Preprint URL: https://www.biorxiv.org/content/10.1101/2025.02.24.639989v1

🛠 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

Software Citation (APA): Joachimiak, M. P., Santangelo, B. E., Hegde, H., Caufield, J. H., Reese, J., Kliegr, T., Hunter, L. E., Lozupone, C. A., & Mungall, C. J. (2025). kg-microbe: Modular knowledge graph for microbiome and microbial sciences (Version 1.0) [Computer software]. GitHub. https://github.com/Knowledge-Graph-Hub/kg-microbe

📬 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.

Frequently Asked Questions

How do I cite CultureBotAI's work?

Cite the primary publication: Santangelo, B. E., et al. (2025). KG-Microbe - Building Modular and Scalable Knowledge Graphs for Microbiome and Microbial Sciences. bioRxiv. https://doi.org/10.1101/2025.02.24.639989

What is the DOI for the KG-Microbe preprint?

The DOI is 10.1101/2025.02.24.639989, available at https://doi.org/10.1101/2025.02.24.639989

Where can I find Dr. Joachimiak's publications?

Dr. Joachimiak's publications are listed on Google Scholar at https://scholar.google.com/citations?user=zSlIlYQAAAAJ&hl=en and ORCID at https://orcid.org/0000-0001-8175-045X

What license is kg-microbe released under?

kg-microbe is released under the BSD-3-Clause License, allowing free use, modification, and distribution with proper attribution.

Can I use CultureBotAI's software in my research?

Yes, kg-microbe and related tools are open-source and freely available for research use. Please cite the appropriate publications when using these resources.

Who are the co-authors on the KG-Microbe paper?

Co-authors include Brook E. Santangelo, Harshad Hegde, J. Harry Caufield, Justin Reese, Tomas Kliegr, Lawrence E. Hunter, Catherine A. Lozupone, Christopher J. Mungall, and Marcin P. Joachimiak.