[3] He is an internationally known scholar,[1][4] focused on computational biology, knowledge-driven extraction of information from the primary biomedical literature,[5] the semantic integration of knowledge resources in molecular biology, and the use of knowledge in the analysis of high-throughput data, as well as for his foundational work in computational biology, which led to the genesis of the major professional organization in the field and two international conferences.

[6] Hunter completed his PhD at Yale University in 1989 with a thesis on Knowledge Acquisition Planning: Gaining Expertise Through Experience, on diagnosis of lung cancer from histological images using Case-based reasoning,[7] under the guidance of Roger Schank.

[2] Faced with a choice between careers in the main applications of artificial intelligence---game programming and defense work—Hunter chose an emerging new discipline, bioinformatics.

[citation needed] Throughout his career Hunter has researched and directed research groups investigating the development and application of advanced computational techniques for biomedicine to high-throughput assays, particularly the application of statistical and knowledge-based techniques, in particular bio-ontologies,[13] to the analysis of high-throughput data and of biomedical texts.

He has argued for expansion data science activities in biomedicine to include knowledge-based methods.