Hong Cui's research focuses on machine learning applications for semantic annotation of semi-structured information, with a current focus on biodiversity literature. She develops and evaluates machine learning and natural language processing algorithms for converting born-digital and digitized taxonomic descriptions into new Semantic Web formats. More recently her research has led to ontology building in biology domain. Her work has an explicit impact on how scientific information can be retrieved and used in the digital era by turning the wealth of human-readable scientific information into something that can be understood and read by computers. She is the principal investigator or co-PI of a number of National Science Foundation-funded projects. The methodology developed by Dr. Cui has been adopted by several other research groups in the US and abroad. She leads the biosemantics research group in the iSchool.