Marcin Joachimiak

Dr. Marcin P. Joachimiak is a Staff Researcher and Principal Investigator in the Environmental Genomics and Systems Biology Division at Lawrence Berkeley National Laboratory (LBNL). Trained in biophysics at the University of California, San Francisco, with postdoctoral work in computational genomics at UC Berkeley, he develops AI and knowledge-engineering methods for the microbial sciences. He leads CultureBot, an AI-driven microbial cultivation engineering project that includes KG-Microbe, a modular knowledge graph integrating microbial traits, genomic functions, cultivation evidence, and metabolic capabilities, and MicroGrowAgents, an agentic AI framework for recommending organism-specific cultivation conditions and experimental designs. In addition, he leads the Datasheets for Datasets Working Group within the NIH Bridge2AI consortium as well as AIO and METPO ontology development. Broader, long-term community contributions include MicrobesOnline, DOE KBase, KG-Hub, and the Biolink Model. His current research integrates knowledge graphs, graph transformers (KOGUT), agentic curation pipelines (X-Mechs), and autonomous agents for applications in novel isolate cultivation, microbial communities, biomanufacturing, and biological recovery of critical minerals. With over 70 publications, he has helped establish KG-Microbe as the most comprehensive and standardized set of FAIR, AI-ready knowledge graphs for microbial complex traits, metabolic capabilities, and cultivation, and CultureBot/MicroGrowAgents as the first integrated agentic AI system for microbial cultivation engineering. Research support comes from the U.S. DOE, LBNL, and NIH Bridge2AI programs.