An approach to automatic classification of text for information retrieval. - Hong Cui; P. Bryan Heidorn; Hong Zhang (JCDL, 2002)

MARTT: Using induced knowledge base to automatically mark up plant taxonomic descriptions with XML. - Hong Cui (ASIST, 2005)

How Do Search Engines Handle Chinese Queries? - Haidar Moukdad; Hong Cui (Webology, 2005)

Automating Semantic Markup of Semi-Structured Text via an Induced Knowledge Base: A Case Study Using Floras - Hong Cui (2005)

Automated concept discovery in corpora of morphological descriptions. - Hong Cui; Richard M. McCourt; Monique Feist (ASIST, 2006)

The reusability of induced knowledge for the automatic semantic markup of taxonomic descriptions. - Hong Cui; P. Bryan Heidorn (J. Assoc. Inf. Sci. Technol., 2007)

Unsupervised Structure Discovery for Biodiversity Information. - Hong Cui; Richard M. McCourt; Monique Feist (Bull. IEEE Tech. Comm. Digit. Libr., 2007)

Unsupervised semantic markup of literature for biodiversity digital libraries. - Hong Cui (JCDL, 2008)

Application of semantic annotation for quality insurance in biosystematics publishing. - Hong Cui; Chunshui Yu; James A. Macklin (ASIST, 2009)

Intelligent feature extraction and knowledge mining by multivariate analyses. - Yisong Chen; Hong Cui (CIDM, 2009)

An Application for Semantic Markup of Biodiversity Documents. - Hong Cui (Bull. IEEE Tech. Comm. Digit. Libr., 2009)

Unsupervised extraction of text segments from heterogeneous document collections. - Hong Cui (ASIST, 2010)

From text to RDF triple store: An application for biodiversity literature. - Hong Cui; Kenneth (Yang) Jiang; Partha Pratim Sanyal (ASIST, 2010)

Tools for Semantic Annotation of Taxonomic Descriptions. - Hong Cui; Partha Pratim Sanyal; Chunshui Yu (KES (4), 2010)

Semantic annotation of morphological descriptions: an overall strategy. - Hong Cui (BMC Bioinform., 2010)

Competency evaluation of plant character ontologies against domain literature. - Hong Cui (J. Assoc. Inf. Sci. Technol., 2010)

Semantic annotation of biosystematics literature without training examples. - Hong Cui; David Boufford; Paul Selden (J. Assoc. Inf. Sci. Technol., 2010)

Combine unsupervised learning and heuristic rules to annotate organism morphological descriptions. - Hong Cui; Sriramu Singaram; Alyssa Janning (ASIST, 2011)

OTO: Ontology term organizer. - Fengqiong Huang; James A. Macklin; Paul J. Morris; Partha Pratim Sanyal; Robert A. Morris 002; Hong Cui (ASIST, 2012)

Mapping of glossary terms from the Flora of North America to the Plant Ontology enhances both resources. - Ramona L. Walls; Hong Cui; James A. Macklin; Chris Mungall; Laurel Cooper; Dennis W. Stevenson; Pankaj Jaiswal (ICBO, 2012)

Evaluating the botanical coverage of PATO using an unsupervised learning algorithm. - Alyssa Janning; Hong Cui (iConference, 2012)

Applications of Natural Language Processing in Biodiversity Science. - Anne E. Thessen; Hong Cui; Dmitry Mozzherin (Adv. Bioinformatics, 2012)

CharaParser for fine-grained semantic annotation of organism morphological descriptions. - Hong Cui (J. Assoc. Inf. Sci. Technol., 2012)

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. - Cecilia N. Arighi; Ben Carterette; K. Bretonnel Cohen; Martin Krallinger; W. John Wilbur; Petra Fey; Robert J. Dodson; Laurel Cooper; Ceri E. Van Slyke; Wasila M. Dahdul; Paula M. Mabee; Donghui Li; et al. (Database J. Biol. Databases Curation, 2013)

Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. - Wasila M. Dahdul; Hong Cui; Paula M. Mabee; Christopher J. Mungall; David Osumi-Sutherland; Ramona L. Walls; Melissa A. Haendel (J. Biomed. Semant., 2014)

CharaParser+EQ: Performance evaluation without gold standard. - Hong Cui; Wasila M. Dahdul; T. Alexander Dececchi; Nizar Ibrahim; Paula M. Mabee; James P. Balhoff; Hariharan Gopalakrishnan (ASIST, 2015)

OTO: Ontology Term Organizer. - Fengqiong Huang; James A. Macklin; Hong Cui; Heather A. Cole; Lorena Endara (BMC Bioinform., 2015)

MultiLayerMatrix: Visualizing Large Taxonomic Datasets. - Dang Tuan Nhon; Hong Cui; Angus G. Forbes (EuroVA@EuroVis, 2016)

MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions. - Carrine E. Blank; Hong Cui; Lisa R. Moore; Ramona L. Walls (J. Biomed. Semant., 2016)

Introducing Explorer of Taxon Concepts with a case study on spider measurement matrix building. - Hong Cui; Dongfang Xu; Steven S. Chong; Martin Ramirez; Thomas Rodenhausen; James A. Macklin; Bertram Ludäscher; Robert A. Morris 002; Eduardo M. Soto; Nicolás Mongiardino Koch (BMC Bioinform., 2016)

Microbial phenomics information extractor (MicroPIE): a natural language processing tool for the automated acquisition of prokaryotic phenotypic characters from text sources. - Jin Mao; Lisa R. Moore; Carrine E. Blank; Elvis Hsin-Hui Wu; Marcia Ackerman; Sonali Ranade; Hong Cui (BMC Bioinform., 2016)

Using Shallow Semantic Analysis to Implement Automated Quality Assessment of Web Health Care Information. - Yanjun Zhang; Robert E. Mercer; Jacquelyn A. Burkell; Hong Cui (CICLing (2), 2018)

A Natural Language Processing Pipeline to Extract Phenotypic Data from Formal Taxonomic Descriptions with a Focus on Flagellate Plants. - Lorena Endara; J. Gordon Burleigh; Laurel Cooper; Pankaj Jaiswal; Marie-Angélique Laporte; Hong Cui (ICBO, 2018)

Where Are iSchools Heading? - Vikas Yadav; Farig Sadeque; P. Bryan Heidorn; Hong Cui (iConference, 2018)

Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems. - Wasila M. Dahdul; Prashanti Manda; Hong Cui; James P. Balhoff; T. Alexander Dececchi; Nizar Ibrahim; Hilmar Lapp; Todd J. Vision; Paula M. Mabee (Database J. Biol. Databases Curation, 2018)

Identifying bacterial biotope entities using sequence labeling: Performance and feature analysis. - Jin Mao; Hong Cui (J. Assoc. Inf. Sci. Technol., 2018)

Accelerating the Large-Scale Study of Prokaryotic Phenotypes and Niche Space Evolution Through Time Using the MicrO Ontology, MicroPIE, and MicroPIEDigester Software. - Carrine E. Blank; Hong Cui; Jin Mao; Lisa R. Moore; Robert W. Thacker; Ramona L. Walls (Application of Semantic Technology in Biodiversity Science, 2018)

Developing community phenotype ontologies: Understanding users' preferences. - Limin Zhang 001; Zuleima Cota; Hong Cui; Hsin-liang Oliver Chen; Bruce Ford; Joel Sach; Jocelyn E. Pender; James A. Macklin; Anton Reznicek; Julian R. Starr (ASIST, 2019)

Enabling Authors to Produce Computable Phenotype Measurements: Usability Studies on the Measurement Recorder. - Limin Zhang 001; Hong Cui; Bruce Ford; Hsin-liang Cheng; James A. Macklin; Anton Reznicek; Julian R. Starr (HCI (48), 2020)

Innovative UX Methods for Information Access Based on Interdisciplinary Approaches: Practical Lessons from Academia and Industry. - Fei Yu 013; Laura Ruel; Ryan Tyler; Qian Xu; Hong Cui; Stan Karanasios; Ba Xuan Nguyen; Anna Keilbach; Javed Mostafa (Data Inf. Manag., 2020)

A Peek into the US Informal STEM Landscape through Theconnectory.org. - Sebastian Deimen; Hong Cui; Michelle Higgins (ASIST, 2021)

Internet of Samples. - Stephen M. Richard; David Vieglais; Hong Cui; Neil Davies 002; John Deck; Quan Gan; Eric C. Kansa; Sarah Whitcher Kansa; John A. Kunze; Danny Mandel; Christopher Meyer; Thomas Orrell; et al. (ASIST, 2021)

Which methods are the most effective in enabling novice users to participate in ontology creation? A usability study. - Limin Zhang 001; Xingyi Yang; Zuleima Cota; Hong Cui; Bruce Ford; Hsin-liang Oliver Chen; James A. Macklin; Anton Reznicek; Julian R. Starr (Database J. Biol. Databases Curation, 2021)

P3H4 Overexpression Serves as a Prognostic Factor in Lung Adenocarcinoma. - Xiangfeng Jin; Haiqing Zhou; Jianfang Song; Hong Cui; Yiren Luo; Haiping Jiang (Comput. Math. Methods Medicine, 2021)

Authors' attitude toward adopting a new workflow to improve the computability of phenotype publications. - Hong Cui; Bruce Ford; Julian R. Starr; Anton Reznicek; Limin Zhang 001; James A. Macklin (Database J. Biol. Databases Curation, 2022)

From Noisy Data to Useful Color Palettes: One Step in Making Biodiversity Data FAIR. - Hong Cui; Noah Giebink; Julian R. Starr; Dylan Longert; Bruce Ford; Étienne Léveillé-Bourret (iConference (1), 2023)

MAG: a smart gloves system based on multimodal fusion perception. - Hong Cui; Zhiquan Feng; Jinglan Tian; Dehui Kong; Zishuo Xia; Weina Li (CCF Trans. Pervasive Comput. Interact., 2023)

PenLab: Towards Understanding of Active Collaboration for Solid Geometry Teaching. - Dehui Kong; Hongyue Wang; Sijie Zhou; Hong Cui; Zhiquan Feng (CHI Extended Abstracts, 2024)

Helping authors produce FAIR taxonomic data: evaluation of an author-driven phenotype data production prototype. - Limin Zhang 001; Julian R. Starr; Bruce Ford; Anton Reznicek; Yuxuan Zhou; Étienne Léveillé-Bourret; Étienne Lacroix-Carignan; Jacques Cayouette; Tyler W. Smith; Donald Sutherland; Paul Catling; Jeffery M. Saarela; et al. (Database J. Biol. Databases Curation, 2025)

Adopting Maximum Pupil Diameter to Detect Subtle Usability Issues of a Smartphone Application, Conflict Solver. - Limin Zhang 001; Hong Cui (Int. J. Hum. Comput. Interact., 2025)