Dr. Marcin P. Joachimiak — Principal Investigator

Dr. Marcin P. Joachimiak leads CultureBotAI and the development of KG-Microbe, a groundbreaking knowledge graph for microbiology research. As a staff researcher at Lawrence Berkeley National Laboratory (LBNL) and member of the Berkeley Bioinformatics Open-source Projects (BBOP), Dr. Joachimiak bridges artificial intelligence and microbial cultivation to advance microbiological discoveries.

Research Focus

Dr. Joachimiak’s research centers on developing AI-powered solutions for microbial research, with particular emphasis on:

  • Knowledge Graph Development: Leading the creation of KG-Microbe, a modular and scalable knowledge graph for microbiome and microbial sciences
  • AI for Cultivation: Applying machine learning and artificial intelligence methods for growth preference prediction and culture optimization
  • Data Integration: Developing frameworks for integrating diverse microbial data sources into unified, queryable knowledge systems
  • Ontology Development: Creating standardized vocabularies like METPO (Microbial Experimental and Theoretical Preference Ontology) for microbiology research

Professional Affiliations

Lawrence Berkeley National Laboratory (LBNL)

  • Division: Environmental Genomics and Systems Biology Division
  • Role: Staff Scientist and Principal Investigator
  • Focus: Computational biology and bioinformatics for microbial systems

Berkeley Bioinformatics Open-source Projects (BBOP)

  • Role: Core team member
  • Contribution: Development of open-source bioinformatics tools and resources
  • Mission: Advancing biological research through collaborative, open-source software development

Key Projects

CultureBotAI

Principal investigator and founder of CultureBotAI, developing AI-powered solutions for microbial research, cultivation, and analysis that enhance laboratory workflows and accelerate microbiological discoveries.

KG-Microbe Knowledge Graph

Lead developer of KG-Microbe, a comprehensive knowledge graph that integrates diverse microbial data sources to enable AI-driven insights for growth preference prediction and culture optimization.

METPO Ontology

Creator of the Microbial Experimental and Theoretical Preference Ontology, providing standardized vocabulary for growth preferences and experimental conditions in microbiology research.

Selected Publications

Recent Preprint

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

This comprehensive preprint describes the development, architecture, and applications of KG-Microbe, demonstrating its potential for advancing microbiology research through AI-driven knowledge discovery.

Contact Information

  • Email: mjoachimiak@lbl.gov
  • Institution: Lawrence Berkeley National Laboratory
  • Division: Environmental Genomics and Systems Biology
  • GitHub: CultureBotAI Organization

Advancing microbiology through the convergence of artificial intelligence, knowledge graphs, and open science.