Peer-reviewed Journal Publications

(* indicates corresponding author)
  1. 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. [paper]
  2. Li X, Cui L, Tao S, Chen J, Zhang X, Zhang GQ. HyCLASSS: A Hybrid Classifier for Automatic Sleep Stage Scoring. IEEE Journal of Biomedical and Health Informatics, 2017. [doi:10.1109/JBHI.2017.2668993]
  3. 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. [paper]
  4. Dean DA, Goldberger AL, Mueller R, Kim M, Rueschman M, Mobley D, Sahoo SS, Jayapandian CP, Cui L, Morrical MG, Surovec S, Zhang GQ, Redline S. Scaling up Scientific Discovery in Sleep Medicine: The National Sleep Research Resource. SLEEP, 2016;39(5):1151-1164. [paper]
  5. Xing G, Zhang GQ, Cui L*. FEDRR: Fast, Exhaustive Detection of Redundant Hierarchical Relations for Quality Improvement of Large Biomedical Ontologies. BioData Mining, 2016;9:31. [paper]
  6. Zhang GQ, Tao S, Xing G, Lhatoo SD, Mozes J, Zonjy B, Lhatoo SD, Cui L*. NHash: Randomized N-Gram Hashing for Distributed Generation of Validatable Unique Study Identifiers in Multi-center Research. JMIR Medical Informatics, 2015;3(4):e35. [paper]
  7. Luo Z, Zhang GQ, Wentz S, Cui L, Xu R. SimQ: Real-Time Retrieval of Similar Consumer Health Questions. Journal of Medical Internet Research, 2015; 17(2):e43. [paper]
  8. 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. [paper]
  9. Cui L, Xu R, Luo Z, Wentz S, Scarberry K, Zhang GQ. Multi-topic Assignment for Exploratory Navigation of Consumer Health Information in NetWellness using Formal Concept Analysis. BMC Medical Informatics and Decision Making, 2014;14:63. [paper]
  10. 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. [paper]
  11. Sahoo SS, Lhatoo SD, Gupta DK, Cui L, Zhao M, Jayapadian C, Bozorgi A, Zhang GQ. Epilepsy and Seizure Ontology: Towards an Epilepsy Informatics Infrastructure for Clinical Research and Patient Care. Journal of American Medical Informatics Association, 2014;21(1):82-9. [paper]
  12. Sahoo SS, Tao S, Parchman A, Luo Z, Cui L, Mergler P, Lanese R, Barnholtz-Sloan JS, Meropol NJ, Zhang GQ. Trial Prospector: Matching Patients with Cancer Research Studies Using an Automated and Scalable Approach. Cancer Informatics, 2014;13:157-166. [paper]
  13. Sun J, Bogie KM, Teagno J, Sun YH, Carter RR, Cui L, Zhang GQ. Design and Implementation of a Comprehensive Web-based Survey For Ovarian Cancer Survivorship With Analysis of Pre-diagnostic Symptoms via Text Mining. Cancer Informatics, 2014;Suppl. 3:113-123. [paper]
  14. Zhang GQ, Cui L*. A set coverage problem. Information Processing Letters, 2010;110(4): 158-159. [paper]
  15. Cui L*, Li Y, Zhang X. Intuitionistic fuzzy linguistic quantifiers based on intuitionistic fuzzy-valued fuzzy measures and integrals. International Journal of Uncertainty, Fuzziness and Knowledge-Based Systems, 2009;17(3): 427-448. [paper]
  16. Cui L*, Li Y. Linguistic quantifiers based on Choquet integrals. International Journal of Approximate Reasoning, 2008;48: 559-582. [paper]
Peer-reviewed Conference Publications

  1. Abeysinghe R, Brooks MA, Talbert J, Cui L*. Quality Assurance of NCI Thesaurus by Mining Structural-Lexical Patterns. AMIA Annual Symp Proc 2017. [Accepted]
  2. Zhang GQ, Huang Y, Cui L. Can SNOMED CT Changes Be Used as a Surrogate Standard for Evaluating the Performance of Its Auditing Methods? AMIA Annual Symp Proc 2017. [Accepted]
  3. Tao S, Cui L, Wu X, Zhang GQ. Facilitating Cohort Discovery by Enhancing Ontology Exploration, Query Management and Query Sharing for Large Clinical Data Repositories. AMIA Annual Symp Proc 2017. [Accepted]
  4. Zhu W, Cui L, Zhang GQ. Spark-MCA: Large-scale, Exhaustive Formal Concept Analysis for Evaluating the Semantic Completeness of SNOMED CT. AMIA Annual Symp Proc 2017. [Accepted]
  5. Li X, Cui L, Tao S, Zeng N, Zhang GQ. SpindleSphere: A Web-based Platform for Large-scale Sleep Spindle Analysis and Visualization. AMIA Annual Symp Proc 2017. [Accepted]
  6. Tao S, Zeng N, Wu X, Li X, Zhu W, Cui L, Zhang GQ. A Data Capture Framework for Large-scale Interventional Studies with Survey Workflow Management. AMIA Joint Summits on Translational Science 2017, pp. 278-286.
  7. 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.
  8. Zhu W, Luo L, Jain T, Boxer RS, Cui L, Zhang GQ. DCDS: A Real-time Data Capture and Personalized Decision Support System for Heart Failure Patients in Skilled Nursing Facilities. AMIA Annual Symp Proc 2016, pp. 2100-2109.
  9. Sun M, Zhu W, Tao S, Cui L, Zhang GQ. COBE: A Conjunctive Ontology Browser and Explorer for Visualizing SNOMED CT Fragments. AMIA Annual Symp Proc 2015, pp. 2092-2100. [paper]
  10. Cui L*. COHeRE: Cross-Ontology Hierarchical Relation Examination for Ontology Quality Assurance. AMIA Annual Symp Proc 2015, pp. 456-465. [paper]
  11. Zhu W, Zhang GQ, Tao S, Sun M, Cui L*. NEO: Systematic Non-Lattice Embedding of Ontologies for Comparing the Subsumption Relationship in SNOMED CT and in FMA Using MapReduce. AMIA Joint Summits on Translational Science 2015, pp. 216-220. [paper]
  12. Tao S, Cui L, Zhu W, Sun M, Bodenreider O, Zhang GQ. Mining Relation Reversals in the Evolution of SNOMED CT Using MapReduce. AMIA Joint Summits on Translational Science 2015, pp. 46-50. [paper]
  13. Zhang GQ, Zhu W, Sun M, Tao S, Bodenreider O, Cui L*. MaPLE: A MapReduce Pipeline for Lattice-based Evaluation and Its Application to SNOMED CT. IEEE International Conference on Big Data 2014 (IEEE BigData 2014), pp. 754-759. [paper]
  14. Cui L, Tao S, Zhang GQ. A Semantic-based Approach for Exploring Consumer Health Questions Using UMLS. AMIA Annual Symp Proc 2014, pp. 432-441. [paper]
  15. Zhang GQ, Cui L, Lhatoo S, Schuele S, Sahoo S. MEDCIS: Multi-Modality Epilepsy Data Capture and Integration System. AMIA Annual Symp Proc 2014, pp. 1248-1257. [paper]
  16. Cui L, Mueller R, Sahoo SS, Zhang GQ. Querying Complex Federated Clinical Data Using Ontological Mapping and Subsumption Reasoning. IEEE International Conference on Healthcare Informatics 2013 (ICHI 2013), pp. 351-360. [paper]
  17. Zhang GQ, Cui L*, Teagno J, Kaebler D, Koroukian S, Xu R. Merging Ontology Navigation with Query Construction for Web-based Medicare Data Exploration. AMIA Summit on Clinical Research Informatics (CRI) 2013, pp. 285-289. [paper]
  18. Cui L*, Bozorgi A, Lhatoo SD, Zhang GQ, Sahoo SS. EpiDEA: Extracting Structured Epilepsy and Seizure Information from Patient Discharge Summaries for Cohort Identification. AMIA Annual Symp Proc 2012, pp. 1191-1200. [paper]
  19. Cui L, Zhang GQ. A generalized non-pumping lemma for regular languages. World Scientific Proceedings Series on Computer Engineering and Information Science (QUANTITATIVE LOGIC AND SOFT COMPUTING 2012), pp. 420-427. [paper]
  20. Zhang GQ, Zhou X, Fraser R, Cui L. Concatenation and Kleene Star on Deterministic Finite Automata. World Scientific Proceedings Series on Computer Engineering and Information Science (QUANTITATIVE LOGIC AND SOFT COMPUTING 2012), pp. 410-419. [paper]
  21. Sahoo SS, Ogbuji C, Luo L, Dong X, Cui L, Redline SS, Zhang GQ. MiDas: Automatic Extraction of a Common Domain of Discourse in Sleep Medicine for Multi-center Data Integration. AMIA Annual Symp Proc 2011, pp. 1196-1205. [paper]
Peer-reviewed Workshop Publications

  1. Abeysinghe R, Hinderer EW, Moseley HNB, Cui L*. Auditing Subtype Inconsistencies among Gene Ontology Concepts. The 2nd International Workshop on Semantics-Powered Data Analytics (SEPDA 2017) -- in conjunction with IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2017. [Accepted]
  2. Abeysinghe R, Cui L*. Query-constraint-based Association Rule Mining from Diverse Clinical Datasets in the National Sleep Research Resource. The 2nd International Workshop on Semantics-Powered Data Analytics (SEPDA 2017) -- in conjunction with IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2017. [Accepted]
  3. Zeng N, Zhang GQ, Cui L*. Evaluation of Relational and NoSQL Approaches for Patient Cohort Identification from Heterogeneous Data Sources. 2017 International Workshop on Biomedical and Health Informatics (BHI) -- in conjunction with IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2017. [Accepted]
  4. Xing G, Cui L, Zhang GQ. FEDRR: Fast, Exhaustive Detection of Redundant Hierarchical Relations in Large Biomedical Ontologies. International Workshop on Biomedical Data Mining, Modeling, and Semantic Integration: A Promising Approach to Solving Unmet Medical Needs (BDM2I@ISWC 2015). [paper]
Abstracts

  1. Hayes JH, Antoniol G, Cui L, Yu T. Too Little for Big Data? Grand Challenges of Traceability: The Next Ten Years, 2017; p25.
  2. Cui L, Zhu W, Tao S, Case JT, Bodenreider O, Zhang GQ. Detecting Misaligned and Missing Concepts in SNOMED CT using Structural and Lexical Patterns. SNOMED CT Expo 2016. [presentation abstract]
  3. Zhang GQ, Zhu W, Tao S, Cui L. A Web-based, Interactive Graph-visualization Workbench for Collaborative Sensemaking of SNOMED CT Fragments. SNOMED CT Expo 2016. [poster abstract]