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Editorial Journal Publications (3)

  1. Agrawal A, Cui L*. Quality Assurance and Enrichment of Biological and Biomedical Ontologies and Terminologies. BMC Medical Informatics and Decision Making, 2020;20(Suppl 10):301.
  2. Kim Y, Jiang X, Lhatoo SD, Zhang GQ, Tao S, Cui L, Li X, Jolly III RD, Chen L, Phan M, Ha C, Detranaltes M, Zhang J. A community effort for automatic detection of postictal generalized EEG suppression in epilepsy. BMC Medical Informatics and Decision Making, 2020; 20(Suppl 12):328.
  3. Geller J, Perl Y, Cui L, Zhang GQ. Quality Assurance of Biomedical Terminologies and Ontologies. Journal of Biomedical Informatics, 2018;86:106-108.

Peer-reviewed Journal Publications (32)

(* indicates corresponding author)

  1. Zheng F, Shi J, Yang Y, Zheng WJ, Cui L*. A Transformation-based Method for Auditing the IS-A Hierarchy of Biomedical Terminologies in the Unified Medical Language System (UMLS). Journal of the American Medical Informatics Association, 2020;27(10):1568-1575.
  2. Zheng F, Abeysinghe R, Sioutos N, Whiteman L, Remennik L, Cui L*. Detecting missing IS-A relations in the NCI Thesaurus using an enhanced hybrid approach. BMC Medical Informatics and Decision Making, 2020;20(Suppl 10):273.
  3. Vance C, Kim Y, Zhang GQ, Lhatoo S, Tao S, Cui L, Li X, Jiang X. Learning to detect the onset of slow activity after a generalized tonic-clonic seizure. BMC Medical Informatics and Decision Making, 2020; 20(Suppl 12):330.
  4. Amith M, Lin R, Cui L, Wang D, Zhu A, Xiong G, Xu H, Roberts K, Tao C. Conversational Ontology Operator: Patient-Centric Vaccine Dialogue Management Engine for Spoken Conversational Agents. BMC Medical Informatics and Decision Making, 2020;20(Suppl 4):259.
  5. Tao S, Zeng N, Hands I, Hurt-Mueller J, Durbin EB, Cui L, Zhang GQ. Web-based interactive mapping from data dictionaries to ontologies, with an application to cancer registry. BMC Medical Informatics and Decision Making, 2020;20(Suppl 10):271.
  6. Bharath LP, Agrawal M, McCambridge G, Nicholas DA, Hasturk H, Liu J, Jiang K, Liu R, Guo Z, Deeney J, Apovian CM, Synder-Cappione J, Hawk GS, Fleeman RM, Pihl RMF, Thompson K, Belkina AC, Cui L, Proctor EA, Kern PA, Nikolajczyk BS. Metformin enhances autophagy and normalizes mitochondrial function to alleviate aging-associated inflammation. Cell Metabolism, 32:44-55.
  7. Abeysinghe R, Hinderer EW, Moseley HNB, Cui L*. SSIF: Subsumption-based Sub-term Inference Framework to Audit Gene Ontology. Bioinformatics, 2020;36(10):3207-3214.
  8. Cui L*, Abeysinghe R, Zheng F, Tao S, Zeng N, Hands I, Durbin EB, Whiteman L, Remennik L, Sioutos N, Zhang GQ. Enhancing the Quality of Hierarchic Relations in the National Cancer Institute Thesaurus to Enable Faceted Query of Cancer Registry Data. JCO Clinical Cancer Informatics, 2020(4):392-398.
  9. Li X, Tao S, Omidi SJ, Huang Y, Lhatoo SD, Zhang GQ, Cui L*. A Random Forest-based Method for Detection of Post-ictal Generalized EEG Suppression. JMIR Medical Informatics, 2020;8(2):e17061.
  10. Zhang GQ*, Tao S, Zeng N, Cui L*. Ontologies as Nested Facet Systems for Human-Data Interaction. Semantic Web, 2020;11(1):79-86.
  11. 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.
  12. Abeysinghe R, Cui L*. Query-constraint-based mining of association rules for exploratory analysis of clinical datasets in the National Sleep Research Resource. BMC Medical Informatics and Decision Making, 2018;18(Suppl 2):58.
  13. 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.
  14. 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.
  15. Zhang GQ, Xing G, Cui L. An efficient, large-scale, non-lattice-detection algorithm for exhaustive structural auditing of biomedical ontologies. Journal of Biomedical Informatics, 2018;80:106-119.
  16. 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, 2018;22(2):375-385.
  17. 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.
  18. Zeng N, Zhang GQ, Li X, Cui L*. Evaluation of Relational and NoSQL Approaches for Cohort Identification from Heterogeneous Data Sources in the National Sleep Research Resource. Journal of Health & Medical Informatics, 2017; 8:295.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. 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. [Best article in Clinical Research Informatics, 2015 IMIA Yearbook of Medical Informatics]
  28. 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.
  29. 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.
  30. Zhang GQ, Cui L*. A set coverage problem. Information Processing Letters, 2010;110(4): 158-159.
  31. 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.
  32. Cui L*, Li Y. Linguistic quantifiers based on Choquet integrals. International Journal of Approximate Reasoning, 2008;48: 559-582.

Peer-reviewed Conference Publications(30)

  1. Zheng F, Shi J, Cui L*. A lexical-based approach for exhaustive detection of missing hierarchical IS-A relations in SNOMED CT. AMIA Annual Symp Proc 2020, pp. 1392-1401.
  2. Zhu W, Tao S, Cui L, Zhang GQ. Web-based Interactive Visualization of Non-Lattice Subgraphs in SNOMED CT. AMIA Jt Summits Transl Sci Proc 2020, pp. 740–749.
  3. Abeysinghe R, Brooks MA, Cui L*. Leveraging Non-lattice Subgraphs to Audit Hierarchical Relations in NCI Thesaurus. AMIA Annual Symp Proc 2019, pp. 982-991. [Student Paper Award Finalist]
  4. Kim Y, Jiang X, Chen L, Li X, Cui L. Discriminative Sleep Patterns of Alzheimer's Disease vis Tensor Factorization. AMIA Annual Symp Proc 2019, pp. 542-551.
  5. Li X, Huang Y, Tao S, Cui L, Lhatoo SD, Zhang GQ. SeizureBank: A Repository of Analysis-ready Seizure Signal Data. AMIA Annual Symp Proc 2019, pp. 1111-1120.
  6. Liu J, Abeysinghe R, Zheng F, Cui L*. Pattern-based Extraction of Disease Drug Combination Knowledge from Biomedical Literature. The 7th IEEE International Conference on Healthcare Informatics (ICHI2019), pp. 1-7.
  7. Sun Q, Zhang GQ, Zhu W, Cui L*. Validating Auto-Suggested Changes for SNOMED CT in Non-lattice Subgraphs Using Relational Machine Learning. Studies in Health Technology and Informatics 2019;264:378-82.
  8. 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.
  9. 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]
  10. 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.
  11. 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, pp. 1886-1895.
  12. 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, pp. 1668-1677.
  13. 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, pp.1914-1923.
  14. 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, pp. 1159-1168.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. Cui L*. COHeRE: Cross-Ontology Hierarchical Relation Examination for Ontology Quality Assurance. AMIA Annual Symp Proc 2015, pp. 456-465.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. 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.

Peer-reviewed Workshop Publications (11)

  1. Qu X, Wu Y, Liu J, Cui L*. HRV-Spark: Computing Heart Rate Variability Measures Using Apache Spark. 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) -- 11th International Workshop on High Performance Bioinformatics and Biomedicine (HiBB), pp. 2235-2241.
  2. Zheng F, Cui L*. A Lexical-based Formal Concept Analysis Method to Identify Missing Concepts in the NCI Thesaurus. 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) -- The 5th International Workshop on Semantics-Powered Data Mining and Analytics (SEPDA 2020), pp. 1757-1760.
  3. Amith M, Cui L, Roberts K, Tao C. Towards an ontology-based medication conversational agent for PrEP and PEP. ACL 2020 -- The First Workshop on Natural Language Processing for Medical Conversations, pp. 31-40.
  4. Zheng F, Abeysinghe R, Cui L*. A Hybrid Method to Detect Missing Hierarchical Relations in NCI Thesaurus. 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) -- The 2nd International Workshop on Quality Assurance and Enrichment of Biological and Biomedical Ontologies and Terminologies, pp. 1948-1953.
  5. Wu Y, Li X, Liu J, Cui L*. Hadoop-EDF: Large-scale Distributed Processing of Electrophysiological Signal Data in Hadoop MapReduce. 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) -- 10th International Workshop on High performance Bioinformatics and Biomedicine (HiBB), pp. 2265-2271.
  6. Amith M, Lin R, Cui L, Wang D, Zhu A, Xiong G, Xu H, Roberts K, Tao C. An Ontology-Powered Dialogue Engine for Patient Communication of Vaccines. The 4th International Workshop on Semantics-Powered Data Mining and Analytics (SEPDA 2019), pp. 24-30.
  7. Abeysinghe R, Zheng F, Hinderer EW, Moseley HNB, Cui L*. A Lexical Approach to Identifying Subtype Inconsistencies in Biomedical Terminologies. 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), The 1st International Workshop on Quality Assurance of Biological and Biomedical Ontologies and Terminologies, pp. 1982-1989.
  8. Abeysinghe R, Hinderer EW, Moseley HNB, Cui L*. Auditing Subtype Inconsistencies among Gene Ontology Concepts. 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2nd International Workshop on Semantics-Powered Data Analytics (SEPDA 2017), pp. 1242-1245.
  9. Abeysinghe R, Cui L*. Query-constraint-based Association Rule Mining from Diverse Clinical Datasets in the National Sleep Research Resource. 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2nd International Workshop on Semantics-Powered Data Analytics (SEPDA 2017), pp. 1238-1241.
  10. Zeng N, Zhang GQ, Cui L*. Evaluation of Relational and NoSQL Approaches for Patient Cohort Identification from Heterogeneous Data Sources. 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2017 International Workshop on Biomedical and Health Informatics (BHI), pp. 1135-1140.
  11. 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).