Ron Caspi

Senior scientific database curator, Artificial Intelligence Center

Ron Caspi, Ph.D., is a biologist working as a database curator in the field of bioinformatics. He has a broad knowledge of biochemistry, metabolism, and molecular biology, which he has been applying since 2004 towards curation of thousands of metabolic pathways, reactions, and enzymes in MetaCyc, the largest and richest metabolic knowledge base available. He has also curated numerous organism-specific Pathway/Genome Databases for important microbes that are part of the BioCyc database collection.

 Dr. Caspi is a member of the Enzyme Commission (EC), an international group formed in 1958 to ensure proper naming of enzymes and is the secretary of the IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN).

Dr. Caspi received his B.Sc. cum laude in geology and biology from the Hebrew University in Jerusalem and his PhD in marine microbiology and molecular biology from the Scripps Institution of Oceanography, University of California in San Diego.

Key projects

Recent publications

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  • Revisiting the y-ome of Escherichia coli

    EcoCyc.org, the most comprehensive curated genome database for the model microorganism E. coli K-12, has implemented a new categorization schema that indicates the degree to which a gene has been…

  • Visual Analysis of Multi-Omics Data

    Abstract We present a tool for multi-omics data analysis that enables simultaneous visualization of up to four types of omics data on organism-scale metabolic network diagrams. The tool’s interactive web-based…

  • The Comparative Genome Dashboard

    The Comparative Genome Dashboard is a web-based software tool for interactive exploration of the similarities and differences in gene functions between organisms.

  • An Evaluation of ChatGPT and Bard (Gemini) in the Context of Biological Knowledge Retrieval

    We evaluate the effectiveness of chatbots in retrieving biological knowledge for curation and research purposes.

  • The EcoCyc Database (2023)

    The long-term goal of the project is to describe the complete molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to…

  • BioCyc: Metabolic Pathway Databases and Informatics Tools

    This article describes a coordinated set of bioinformatics databases and software tools designed to solve multiple problems faced by metabolic engineers and microbiologists related to metabolic pathways.

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