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Licong Cui, PhD

Assistant Professor

Licong Cui, Ph.D. joined the UTHealth School of Biomedical Informatics (SBMI) in January of 2019 as a tenure-track assistant professor. Prior to this position, she was a tenure-track assistant professor in the Department of Computer Science and a member of Institute for Biomedical Informatics at the University of Kentucky.

Dr. Cui’s primary research goal is to develop algorithms and software tools to solve data science problems in biomedicine. Dr. Cui’s research interests include ontologies and terminologies, big data analytics, large-scale data integration and management, information extraction and information retrieval. Dr. Cui has published over 50 peer-reviewed research papers and served as the principal investigator for a number of grants funded by NSF and NIH.

As a well-trained Computer Scientist specialized in Biomedical Informatics, Dr. Cui has strong grounding in algorithms and computational methodologies. For instance, she has designed and developed scalable algorithms for analyzing biomedical data, including extracting epilepsy phenotypes from clinical narratives for patient cohort identification, computing non-lattice subgraphs and detecting relation reversals in the SNOMED CT, mining lexical patterns in non-lattice subgraphs for detecting missing hierarchical relations and concepts in SNOMED CT, Gene Ontology and NCI Thesaurus, performing cross-ontology hierarchical relation examination in the Unified Medical Language System, and mining diverse clinical datasets from the National Sleep Research Resource. At the same time, Dr. Cui has considerable experience in applied informatics, particularly the lifecycle of web-based software development. For example, she has designed, developed and deployed a cross-cohort query system for the National Sleep Research Resource and a data integration system for Sudden Unexpected Death in Epilepsy research. Dr. Cui has conducted collaborative work in multidisciplinary team settings with sleep researchers, epilepsy researchers, cancer researchers, and other informaticians.

“As increasingly large amounts of digital data have been produced by the biomedical research community, ontologies and terminologies have been widely used for orchestrating the coding, management, exchange, and sharing of biomedical data. My research interest spans from the theoretical and computational aspects for analyzing biomedical ontologies (e.g., ontology quality assurance) to the application of ontologies to solve large-scale data science problems in biomedicine (e.g., information extraction and retrieval, data integration and management, and data mining). I am passionate at conducting data science related research in collaboration with biomedical and clinical domain experts.”

Contact

Licong.Cui@uth.tmc.edu
Phone: 713-500-3791
Fax: 713-500-3929

Staff Support

Leticia Flores
Phone: 713-500-3912

Education

  • PhD, Computer Science, Case Western Reserve University, 2014
  • MS, Pure Mathematics, Shaanxi Normal University, 2008
  • BS, Information and Computing Science, Shaanxi Normal University, 2005

Areas of Expertise

  • Ontologies and terminologies
  • Big data analytics
  • Neuroinformatics
  • Health information extraction and retrieval

Selected Publications

[1] Cui L, Bodenreider O, Shi J, Zhang GQ, Auditing SNOMED CT Hierarchical Relations Based on Lexical Features of Concepts in Non-lattice Subgraphs. Journal of Biomedical Informatics, 2018;78:177-184.

[2] Zhang GQ, Cui L, Mueller R, Tao S, Kim M, Rueschman M, Mariani S, Mobley D, Redline S. The National Sleep Research Resource: Towards a Sleep Data Commons. Journal of the American Medical Informatics Association, 2018;25(10):1351-1358.

[3] Cui L, Zeng N, Kim M, Mueller R, Hankosky ER, Redline S, Zhang GQ. X-search: an open access interface for cross-cohort exploration of the National Sleep Research Resource. BMC Medical Informatics and Decision Making, 2018;18:99.

[4] Zheng F, Cui L. Exploring Deep Learning-based Approaches for Predicting Concept Names in SNOMED CT. 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 808-813.

[5] Abeysinghe R, Qu X, Cui L. Identifying Similar Non-Lattice Subgraphs in Gene Ontology based on Structural Isomorphism and Semantic Similarity of Concept Labels. AMIA Annual Symp Proc 2018, pp. 1186-1195. [Student Paper Award Finalists].

[6] Cui L, Zhu W, Tao S, Case JT, Bodenreider O, Zhang GQ. Mining Non-Lattice Subgraphs for Detecting Missing Hierarchical Relations and Concepts in SNOMED CT. Journal of the American Medical Informatics Association, 2017;24(4): 788-798.

[7] Abeysinghe R, Brooks MA, Talbert J, Cui L. Quality Assurance of NCI Thesaurus by Mining Structural-Lexical Patterns. AMIA Annual Symp Proc 2017, pp. 364-373.

[8] Cui L, Tao S, Zhang GQ. Biomedical Ontology Quality Assurance Using a Big Data Approach. ACM Transactions on Knowledge Discovery from Data, 2016;10(4):41.

[9] Cui L, Huang Y, Tao S, Lhatoo SD, Zhang GQ. ODaCCI: Ontology-guided Data Curation for Multisite Clinical Research Data Integration in the NINDS Center for SUDEP Research. AMIA Annual Symp Proc 2016, pp. 441-450.

[10] Cui L. COHeRE: Cross-Ontology Hierarchical Relation Examination for Ontology Quality Assurance. AMIA Annual Symp Proc 2015, pp. 456-465.

[11] Cui L. Sahoo SS, Lhatoo SD, Garg G, Rai P, Bozorgi A, Zhang GQ. Complex Epilepsy Phenotype Extraction from Narrative Clinical Discharge Summaries. Journal of Biomedical Informatics, 2014; 51:272-279.

[12] Cui L. Carter R, Zhang GQ. Evaluation of a Novel Conjunctive Exploratory Navigation Interface for Consumer Health Information: A Crowdsourced Comparative Study. Journal of Medical Internet Research, 2014;16(2):e45.