Publications

  1. Zong N, Chowdhury S, Zhou S, Rajaganapathy S, Yu Y, Wang L, Dai Q, Li P, Liu X, Bielinski SJ, Chen J, Chen Y, Cerhan JR. Advancing Efficacy Prediction for EHR-based Emulated Trials in Repurposing Heart Failure Therapies. medRxiv. 2024 Nov 1 Epub 2024 Nov 01
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  2. Chowdhury S, Chen Y, Li P, Rajaganapathy S, Wen A, Ma X, Dai Q, Yu Y, Fu S, Jiang X, He Z, Sohn S, Liu X, Bielinski SJ, Chamberlain AM, Cerhan JR, Zong N. Stratifying heart failure patients with graph neural network and transformer using Electronic Health Records to optimize drug response prediction. J Am Med Inform Assoc. 2024 Aug 1; 31 (8):1671-1681
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  3. Chowdhury S, Rajaganapathy S, Yu Y, Tao C, Vassilaki M, Zong N. Matching Patients to Clinical Trials using LLaMA 2 Embeddings and Siamese Neural Network. medRxiv. 2024 Jun 30 Epub 2024 June 30
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  4. Fu S, Wang L, He H, Wen A, Zong N, Kumari A, Liu F, Zhou S, Zhang R, Li C, Wang Y, St Sauver J, Liu H, Sohn S. A taxonomy for advancing systematic error analysis in multi-site electronic health record-based clinical concept extraction. J Am Med Inform Assoc. 2024 Jun 20; 31 (7):1493-1502
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  5. Shaika, Yongbin, Xiao Ma, Qiying, Yue Yu, Nansu . Evaluating Drug Effectiveness for Antihypertensives in Heart Failure Prognosis: Leveraging Composite Clinical Endpoints and Biomarkers from Electronic Health Records BCB '23: Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. 2023.
  6. Bhattarai K, Rajaganapathy S, Das T, Kim Y, Chen Y, Dai Q, Li X, Jiang X, Zong N, Alzheimer's Disease Neuroimaging Initiative//Australian Imaging Biomarkers and Lifestyle Flagship Study of Ageing. Using artificial intelligence to learn optimal regimen plan for Alzheimer's disease. J Am Med Inform Assoc. 2023 Sep 25; 30 (10):1645-1656
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  7. Fu S, Wang L, Moon S, Zong N, He H, Pejaver V, Relevo R, Walden A, Haendel M, Chute CG, Liu H. Recommended practices and ethical considerations for natural language processing-assisted observational research: A scoping review. Clin Transl Sci. 2023 Mar; 16 (3):398-411 Epub 2022 Dec 26
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  8. Xiao G, Pfaff E, Prud'Hommeaux E, Booth D, Sharma DK, Huo N, Yu Y, Zong N, Ruddy KJ, Chute CG, Jiang G. FHIR-Ontop-OMOP: querying OMOP clinical databases as FHIR-compliant clinical knowledge graphs. CEUR Workshop Proceedings. 2023; 3415:165-6
  9. Bhattarai K, Rajaganapathy S, Das T, Kim Y, Chen Y, Dai Q, Li X, Jiang X, Zong N. Learning physician's treatment for Alzheimer's disease based on electronic health records and reinforcement learning. Proceedings - 2023 IEEE 11th International Conference on Healthcare Informatics, ICHI 2023. 2023; 525-6
  10. Chen Z, Yang R, Fu S, Zong N, Liu H, Huang M. Detecting Reddit users with depression using a hybrid neural network SBERT-CNN. Proceedings - 2023 IEEE 11th International Conference on Healthcare Informatics, ICHI 2023. 2023; 193-9
  11. Ren Y, Wu D, Khurana A, Mastorakos G, Fu S, Zong N, Fan J, Liu H, Huang M. Classification of patient portal messages with BERT-based language models. Proceedings - 2023 IEEE 11th International Conference on Healthcare Informatics, ICHI 2023. 2023; 176-82
  12. Xiao G, Pfaff E, Prud'hommeaux E, Booth D, Sharma DK, Huo N, Yu Y, Zong N, Ruddy KJ, Chute CG, Jiang G. FHIR-Ontop-OMOP: Building clinical knowledge graphs in FHIR RDF with the OMOP Common data Model. J Biomed Inform. 2022 Oct; 134:104201. Epub 2022 Sep 09.
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  13. Huang M, Wen A, He H, Wang L, Liu S, Wang Y, Zong N, Yu Y, Prigge JE, Costello BA, Shah ND, Ting HH, Doubeni C, Fan JW, Liu H, Patten CA. Midwest rural-urban disparities in use of patient online services for COVID-19. J Rural Health. 2022 Sep; 38 (4):908-915 Epub 2022 Mar 08
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  14. Zhao Y, Dimou A, Shen F, Zong N, Davila JI, Liu H, Wang C. PO2RDF: representation of real-world data for precision oncology using resource description framework. BMC Med Genomics. 2022 Jul 30; 15 (1):167 Epub 2022 July 30
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  15. Zong N, Li N, Wen A, Ngo V, Yu Y, Huang M, Chowdhury S, Jiang C, Fu S, Weinshilboum R, Jiang G, Hunter L, Liu H. BETA: a comprehensive benchmark for computational drug-target prediction. Brief Bioinform. 2022 Jul 18; 23 (4)
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  16. Jiang C, Ngo V, Chapman R, Yu Y, Liu H, Jiang G, Zong N. Deep Denoising of Raw Biomedical Knowledge Graph From COVID-19 Literature, LitCovid, and Pubtator: Framework Development and Validation. J Med Internet Res. 2022 Jul 6; 24 (7):e38584 Epub 2022 July 06
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  17. Zong N, Wen A, Moon S, Fu S, Wang L, Zhao Y, Yu Y, Huang M, Wang Y, Zheng G, Mielke MM, Cerhan JR, Liu H. Computational drug repurposing based on electronic health records: a scoping review. NPJ Digit Med. 2022 Jun 14; 5 (1):77 Epub 2022 June 14
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  18. Fu S, Wen A, Pagali S, Zong N, St Sauver J, Sohn S, Fan J, Liu H. The Implication of Latent Information Quality to the Reproducibility of Secondary Use of Electronic Health Records. Stud Health Technol Inform. 2022 Jun 6; 290:173-177
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  19. Huang M, Khurana A, Mastorakos G, Wen A, He H, Wang L, Liu S, Wang Y, Zong N, Prigge J, Costello B, Shah N, Ting H, Fan J, Patten C, Liu H. Patient Portal Messaging for Asynchronous Virtual Care During the COVID-19 Pandemic: Retrospective Analysis. JMIR Hum Factors. 2022 May 5; 9 (2):e35187 Epub 2022 May 05
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  20. Yu Y, Zong N, Wen A, Liu S, Stone DJ, Knaack D, Chamberlain AM, Pfaff E, Gabriel D, Chute CG, Shah N, Jiang G. Developing an ETL tool for converting the PCORnet CDM into the OMOP CDM to facilitate the COVID-19 data integration. J Biomed Inform. 2022 Mar; 127:104002 Epub 2022 Jan 22
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  21. Huang M, Khurana A, Mastorakos G, Wen A, He H, Wang L, Liu S, Wang Y, Zong N, Prigge J, Costello B, Shah N, Ting H, Fan J, Patten C, Liu H. Patient portal messaging for asynchronous virtual care during the COVID-19 pandemic: retrospective analysis. JMIR Human Factors. 2022; 9 (2):e35187
  22. Zong N, Ngo V. Computational drug target prediction: benchmark and experiments. Proceedings - 2022 IEEE 10th International Conference on Healthcare Informatics, ICHI 2022. 2022; 559-60
  23. Na J, Zong N, Wang C, Midthun DE, Luo Y, Yang P, Jiang G. Characterizing phenotypic abnormalities associated with high-risk individuals developing lung cancer using electronic health records from the All of Us researcher workbench. J Am Med Inform Assoc. 2021 Oct 12; 28 (11):2313-2324
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  24. Zong N, Ngo V, Stone DJ, Wen A, Zhao Y, Yu Y, Liu S, Huang M, Wang C, Jiang G. Leveraging Genetic Reports and Electronic Health Records for the Prediction of Primary Cancers: Algorithm Development and Validation Study. JMIR Med Inform. 2021 May 25; 9 (5):e23586
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  25. Liu S, Luo Y, Stone D, Zong N, Wen A, Yu Y, Rasmussen LV, Wang F, Pathak J, Liu H, Jiang G. Integration of NLP2FHIR Representation with Deep Learning Models for EHR Phenotyping: A Pilot Study on Obesity Datasets AMIA Jt Summits Transl Sci Proc. 2021 (in press). 2021.
  26. Zong N, Wong RSN, Yu Y, Wen A, Huang M, Li N. Drug-target prediction utilizing heterogeneous bio-linked network embeddings. Brief Bioinform. 2021 Jan 18; 22 (1):568-580
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  27. Liu S, Luo Y, Stone D, Zong N, Wen A, Yu Y, Rasmussen LV, Wang F, Pathak J, Liu H, Jiang G. Integration of NLP2FHIR Representation with Deep Learning Models for EHR Phenotyping: A Pilot Study on Obesity Datasets. AMIA Jt Summits Transl Sci Proc. 2021; 2021:410-419 Epub 2021 May 17
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  28. Zong N, Stone DJ, Sharma DK, Wen A, Wang C, Yu Y, Huang M, Liu S, Liu H, Shi Q, Jiang G. Modeling cancer clinical trials using HL7 FHIR to support downstream applications: A case study with colorectal cancer data. Int J Med Inform. 2021 Jan; 145:104308 Epub 2020 Oct 22
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  29. Yu Y, Ruddy K, Mansfield A, Zong N, Wen A, Tsuji S, Huang M, Liu H, Shah N, Jiang G. Detecting and Filtering Immune-Related Adverse Events Signal Based on Text Mining and Observational Health Data Sciences and Informatics Common Data Model: Framework Development Study. JMIR Med Inform. 2020 Jun 12; 8 (6):e17353 Epub 2020 June 12
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  30. Zong N, Wen A, Stone DJ, Sharma DK, Wang C, Yu Y, Liu H, Shi Q, Jiang G. Developing an FHIR-Based Computational Pipeline for Automatic Population of Case Report Forms for Colorectal Cancer Clinical Trials Using Electronic Health Records. JCO Clin Cancer Inform. 2020 Mar; 4:201-209.
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  31. Yu Y, Ruddy KJ, Wen A, Zong N, Tsuji S, Chen J, Shah ND, Jiang G. Integrating Electronic Health Record Data into the ADEpedia-on-OHDSI Platform for Improved Signal Detection: A Case Study of Immune-related Adverse Events. AMIA Jt Summits Transl Sci Proc. 2020; 2020:710-719 Epub 2020 May 30
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  32. Zong N, Sharma DK, Yu Y, Egan JB, Davila JI, Wang C, Jiang G. Developing a FHIR-based Framework for Phenome Wide Association Studies: A Case Study with A Pan-Cancer Cohort. AMIA Jt Summits Transl Sci Proc. 2020; 2020:750-759 Epub 2020 May 30
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  33. Chen X, Gururaj AE, Ozyurt B, Liu R, Soysal E, Cohen T, Tiryaki F, Li Y, Zong N, Jiang M , Rogith D, Salimi M, Kim H, Rocca-Serra P, Gonzalez-Beltran A, Farcas C, Johnson T, Margolis R, Alter G, Sansone SA, Fore LM, Ohno-Machado L, Grethe JS, Xu H. DataMed–an open source discovery index for finding biomedical datasets Journal of the American Medical Informatics Association. 2018; 25(3):300-308.
  34. Zong N, Kim HG, Nam S. Constructing faceted taxonomy for heterogeneous entities based on object properties in linked data Data & Knowledge Engineering. 2017; 112:79-93.
  35. Ahn J, Eom JH, Nam S, Zong N, Im DH, Kim HG. xStore: Federated temporal query processing for large scale RDF triples on a cloud environment Neurocomputing. 2017; 256:5-12.
  36. Zong N, Kim H, Ngo V, Harismendy O. Deep mining heterogeneous networks of biomedical linked data to predict novel drug-target associations. Bioinformatics. 2017 Aug 1; 33 (15):2337-2344
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  37. Zong N, Lee S, Ahn J, Kim HG. Supporting inter-topic entity search for biomedical Linked Data based on heterogeneous relationships Computers in biology and medicine. 2017; 87:217-229.
  38. Sansone SA, Gonzalez-Beltran A, Rocca-Serra P, Alter G, Grethe JS, Xu H, Fore LM, Lyle J, Gururaj AE, Chen X, Kim H, Zong N, Li Y, Liu R, Ozyurt IB, Ohno-Machado L. DATS, the data tag suite to enable discoverability of datasets Scientific data. 2017; 4(1):1-8.
  39. Ohno-Machado L, Sansone SA, Alter G, Fore L, Grethe J, Xu H, Gonzalez-Beltran A, Rocca-Serra P, Gururaj A, Bell E, Soysal E, Zong N, Kim H. Finding useful data across multiple biomedical data repositories using DataMed Nature genetics. 2017; 49(6):816-819.
  40. Kim Y, Lee S, Zong N, Kahng J. Clinical progress of human papillomavirus genotypes and their persistent infection in subjects with atypical squamous cells of undetermined significance cytology: Statistical and latent Dirichlet allocation analysis Experimental and therapeutic medicine. 2017; 13(6):3032-3038.
  41. Nam S, Jeong S, Kim SK, Kim HG, Ngo V, Zong N. Structuralizing biomedical abstracts with discriminative linguistic features Computers in biology and medicine. 2016; 79:276-285.
  42. Zong N, Lee S, Kim HG. Discovering expansion entities for keyword-based entity search in linked data Journal of Information Science. 2015; 41(2):209-227.
  43. Zong N, Nam S, Eom JH, Ahn J, Joe H , Kim HG. Aligning ontologies with subsumption and equivalence relations in Linked Data Knowledge-Based Systems. 2015; 76:30-41.
  44. Ahn J, Im DH, Eom JH, Zong N, Kim HG. G-diff: a grouping algorithm for RDF change detection on MapReduce Joint International Semantic Technology Conference. 2014; 230-235.
  45. Zong N, Lee S, Kim HG. A comparison of unsupervised taxonomical relationship induction approaches for building ontology in RDF resources Joint International Semantic Technology Conference. 2013; 445-459.
  46. Zong N, Im DH, Yang S , Hyun N, Kim HG. Dynamic generation of concepts hierarchies for knowledge discovering in bio-medical linked data sets Proceedings of the 6th International Conference on Ubiquitous Information Management and Communication. 2012; 1-5.
  47. Im DH, Zong N, Kim E, Yun S, Kim HG. A hypergraph-based storage policy for RDF version management system Proceedings of the 6th International Conference on Ubiquitous Information Management and Communication. 2012; 1-5.
  48. Jung JU, Im DH, Lee KM, Zong N, Kim HG. The design and implementation of integrated linked data and Open API connection system for semantic web mashup service Proceedings of the Korean Information Science Society Conference. 2012; 71-73.
  49. Zong N, Yang S, Hyun N, Kim HG. Discovering and ranking new links for linked data supplier Joint International Semantic Technology Conference. 2011; 358-365.
  50. Zong N, Zheng Y, Qian P. The knowledge representation and semantic reasoning realization of the mandarin fish disease diagnosis based on the SWRL Journal of the China Society for Scientific and Technical Information. 2010; 29(3):414-421.
  51. Zong N, Zheng Y, Wang Z. A SWRL rules parser algorithm based on the topic semantic comparability and ant colony algorithm 2009 Sixth International Conference on Fuzzy Systems and Knowledge Discovery. 2009; 2:161-167.
  52. Zheng Y, Li Z, He Q, Huang Q, Zong N. Construction and Preliminary Application of Agricultural Production Techniques and Market Information Ontology Agriculture Network Information. 2009; 8.