Publications

  1. Duan T, Wang Z, Li F, Doretto G, Adjeroh DA, Yin Y, Tao C. Online continual decoding of streaming EEG signal with a balanced and informative memory buffer. Neural Netw. 2024 Aug; 176:106338 Epub 2024 Apr 25
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  2. Li Y, Zhao J, Li M, Dang Y, Yu E, Li J, Sun Z, Hussein U, Wen J, Abdelhameed AM, Mai J, Li S, Yu Y, Hu X, Yang D, Feng J, Li Z, He J, Tao W, Duan T, Lou Y, Li F, Tao C. RefAI: a GPT-powered retrieval-augmented generative tool for biomedical literature recommendation and summarization. J Am Med Inform Assoc. 2024 Jun 10 Epub 2024 June 10
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  3. He J, Li F, Li J, Hu X, Nian Y, Xiang Y, Wang J, Wei Q, Li Y, Xu H, Tao C. Prompt Tuning in Biomedical Relation Extraction. J Healthc Inform Res. 2024 Jun; 8 (2):206-224 Epub 2024 Feb 29
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  4. Bilotta I, Tonidandel S, Liaw WR, King E, Carvajal DN, Taylor A, Thamby J, Xiang Y, Tao C, Hansen M. Examining Linguistic Differences in Electronic Health Records for Diverse Patients With Diabetes: Natural Language Processing Analysis. JMIR Med Inform. 2024 May 23; 12:e50428
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  5. Fu S, Jia H, Vassilaki M, Keloth VK, Dang Y, Zhou Y, Garg M, Petersen RC, St Sauver J, Moon S, Wang L, Wen A, Li F, Xu H, Tao C, Fan J, Liu H, Sohn S. FedFSA: Hybrid and federated framework for functional status ascertainment across institutions. J Biomed Inform. 2024 Apr; 152:104623 Epub 2024 Mar 06
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  6. Li Y, Tao W, Li Z, Sun Z, Li F, Fenton S, Xu H, Tao C. Artificial intelligence-powered pharmacovigilance: A review of machine and deep learning in clinical text-based adverse drug event detection for benchmark datasets. J Biomed Inform. 2024 Apr; 152:104621 Epub 2024 Mar 05
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  7. Dally D, Amith M, Mauldin RL, Thomas L, Dang Y, Tao C. A Semantic Approach to Describe Social and Economic Characteristics That Impact Health Outcomes (Social Determinants of Health): Ontology Development Study. Online J Public Health Inform. 2024 Mar 13; 16:e52845
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  8. Zhang X, Feng Y, Li F, Ding J, Tahseen D, Hinojosa E, Chen Y, Tao C. Evaluating MedDRA-to-ICD terminology mappings. BMC Med Inform Decis Mak. 2024 Feb 7; 23 (Suppl 4):299 Epub 2024 Feb 07
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  9. Li F, Rasmy L, Xiang Y, Feng J, Abdelhameed A, Hu X, Sun Z, Aguilar D, Dhoble A, Du J, Wang Q, Niu S, Dang Y, Zhang X, Xie Z, Nian Y, He J, Zhou Y, Li J, Prosperi M, Bian J, Zhi D, Tao C. Dynamic Prognosis Prediction for Patients on DAPT After Drug-Eluting Stent Implantation: Model Development and Validation. J Am Heart Assoc. 2024 Feb 6; 13 (3):e029900 Epub 2024 Jan 31
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  10. Wang X, Li J, Liang T, Hasan WU, Zaman KT, Du Y, Xie B, Tao C. Promoting Personalized Reminiscence Among Cognitively Intact Older Adults Through an AI-Driven Interactive Multimodal Photo Album: Development and Usability Study. JMIR Aging. 2024 Jan 23; 7:e49415
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  11. Sankaranarayanapillai M, Wang S, Ji H, Song HY, Tao C. Lessons learned from annotation of VAERS reports on adverse events following influenza vaccination and related to Guillain-Barre syndrome. BMC Med Inform Decis Mak. 2024 Jan 5; 23 (Suppl 4):298 Epub 2024 Jan 05
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  12. Li Y, Lundin SK, Li J, Tao W, Dang Y, Chen Y, Tao C. Unpacking adverse events and associations post COVID-19 vaccination: a deep dive into vaccine adverse event reporting system data. Expert Rev Vaccines. 2024 Jan-Dec; 23 (1):53-59 Epub 2023 Dec 14
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  13. Li Y, Li J, He J, Tao C. AE-GPT: Using Large Language Models to extract adverse events from surveillance reports-A use case with influenza vaccine adverse events. PLoS One. 2024; 19 (3):e0300919 Epub 2024 Mar 21
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  14. Zhang M, Sankaranarayanapillai M, Du J, Xiang Y, Manion FJ, Harris MR, Stansbury C, Pham HA, Tao C. Machine learning-based donor permission extraction from informed consent documents. BMC Bioinformatics. 2023 Dec 15; 24 (Suppl 3):477
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  15. Dang Y, Li F, Hu X, Keloth VK, Zhang M, Fu S, Amith MF, Fan JW, Du J, Yu E, Liu H, Jiang X, Xu H, Tao C. Systematic design and data-driven evaluation of social determinants of health ontology (SDoHO). J Am Med Inform Assoc. 2023 Aug 18; 30 (9):1465-1473
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  16. Zhang X, Lin RZ, Amith MT, Wang C, Light J, Strickley J, Tao C. DEVO: an ontology to assist with dermoscopic feature standardization. BMC Med Inform Decis Mak. 2023 Aug 18; 23 (Suppl 1):162
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  17. Hao X, Li X, Zhang GQ, Tao C, Schulz PE, Cui L, Alzheimer's Disease Neuroimaging Initiative. An ontology-based approach for harmonization and cross-cohort query of Alzheimer's disease data resources. BMC Med Inform Decis Mak. 2023 Aug 4; 23 (Suppl 1):151 Epub 2023 Aug 04
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  18. Li F, Nian Y, Sun Z, Tao C. Advancing Biomedicine with Graph Representation Learning: Recent Progress, Challenges, and Future Directions. Yearb Med Inform. 2023 Aug; 32 (1):215-224 Epub 2023 Dec 26
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  19. He Z, Pfaff E, Guo SJ, Guo Y, Wu Y, Tao C, Stiglic G, Bian J. Enriching Real-world Data with Social Determinants of Health for Health Outcomes and Health Equity: Successes, Challenges, and Opportunities. Yearb Med Inform. 2023 Aug; 32 (1):253-263 Epub 2023 Dec 26
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  20. Wang S, Dang Y, Sun Z, Ding Y, Pathak J, Tao C, Xiao Y, Peng Y. An NLP approach to identify SDoH-related circumstance and suicide crisis from death investigation narratives. J Am Med Inform Assoc. 2023 Jul 19; 30 (8):1408-1417
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  21. Wijarnpreecha K, Li F, Lundin SK, Suresh D, Song MW, Tao C, Chen VL, Lok ASF. Higher mortality among lean patients with non-alcoholic fatty liver disease despite fewer metabolic comorbidities. Aliment Pharmacol Ther. 2023 May; 57 (9):1014-1027 Epub 2023 Feb 23
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  22. Sun F, Yao J, Du S, Qian F, Appleton AA, Tao C, Xu H, Liu L, Dai Q, Joyce BT, Nannini DR, Hou L, Zhang K. Social Determinants, Cardiovascular Disease, and Health Care Cost: A Nationwide Study in the United States Using Machine Learning. J Am Heart Assoc. 2023 Mar 7; 12 (5):e027919 Epub 2023 Feb 21
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  23. Nguyen E, Amith M, Nordberg A, Tang L, Harris MR, Tao C. CRENO: An ontology to model concepts relating to culture, race, ethnicity, and nationality for health data. AMIA Jt Summits Transl Sci Proc. 2023; 2023:398-407 Epub 2023 June 16
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  24. Zhang X, Xie Z, Xiang Y, Baig I, Kozman M, Stender C, Giancardo L, Tao C. Issues in Melanoma Detection: Semisupervised Deep Learning Algorithm Development via a Combination of Human and Artificial Intelligence. JMIR Dermatol. 2022 Dec 12; 5 (4):e39113
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  25. Nian Y, Hu X, Zhang R, Feng J, Du J, Li F, Bu L, Zhang Y, Chen Y, Tao C. Mining on Alzheimer's diseases related knowledge graph to identity potential AD-related semantic triples for drug repurposing. BMC Bioinformatics. 2022 Sep 30; 23 (Suppl 6):407 Epub 2022 Sept 30
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  26. Manuel W, Abeysinghe R, He Y, Tao C, Cui L. Identification of missing hierarchical relations in the vaccine ontology using acquired term pairs. J Biomed Semantics. 2022 Aug 13; 13 (1):22
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  27. Amith MT, Cui L, Zhi D, Roberts K, Jiang X, Li F, Yu E, Tao C. Toward a standard formal semantic representation of the model card report. BMC Bioinformatics. 2022 Jul 14; 23 (Suppl 6):281 Epub 2022 July 14
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  28. Luo C, Du J, Cuker A, Lautenbach E, Asch DA, Poland GA, Tao C, Chen Y. Comparability of clinical trials and spontaneous reporting data regarding COVID-19 vaccine safety. Sci Rep. 2022 Jun 29; 12 (1):10946 Epub 2022 June 29
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  29. He J, Li F, Hu X, Li J, Nian Y, Wang J, Xiang Y, Wei Q, Xu H, Tao C. Chemical-Protein Relation Extraction with Pre-trained Prompt Tuning. IEEE Int Conf Healthc Inform. 2022 Jun; 2022:608-609 Epub 2022 Sept 08
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  30. Huang Y, Luo C, Jiang Y, Du J, Tao C, Chen Y, Hao Y. A Bayesian Network to Predict the Risk of Post Influenza Vaccination Guillain-Barre Syndrome: Development and Validation Study. JMIR Public Health Surveill. 2022 Mar 25; 8 (3):e25658
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  31. Bae KT, Tao C, Feldman R, Yu ASL, Torres VE, Perrone RD, Chapman AB, Brosnahan G, Steinman TI, Braun WE, Mrug M, Bennett WM, Harris PC, Srivastava A, Landsittel DP, Abebe KZ, CRISP and HALT PKD Consortium. Volume Progression and Imaging Classification of Polycystic Liver in Early Autosomal Dominant Polycystic Kidney Disease. Clin J Am Soc Nephrol. 2022 Mar; 17 (3):374-384 Epub 2022 Feb 25
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  32. Lu Y, Barrett LA, Lin RZ, Amith M, Tao C, He Z. Understanding Information Needs and Barriers to Accessing Health Information Across All Stages of Pregnancy: Systematic Review. JMIR Pediatr Parent. 2022 Feb 21; 5 (1):e32235
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  33. Xiang Y, Du J, Fujimoto K, Li F, Schneider J, Tao C. Application of artificial intelligence and machine learning for HIV prevention interventions. Lancet HIV. 2022 Jan; 9 (1):e54-e62 Epub 2021 Nov 08
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  34. Amith M, Onye C, Ledoux T, Xiong G, Tao C. The ontology of fast food facts: conceptualization of nutritional fast food data for consumers and semantic web applications. BMC Med Inform Decis Mak. 2021 Nov 9; 21 (Suppl 7):275 Epub 2021 Nov 09
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  35. Perrone RD, Abebe KZ, Watnick TJ, Althouse AD, Hallows KR, Lalama CM, Miskulin DC, Seliger SL, Tao C, Harris PC, Bae KT. Primary results of the randomized trial of metformin administration in polycystic kidney disease (TAME PKD). Kidney Int. 2021 Sep; 100 (3):684-696 Epub 2021 June 27
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  36. Du J, Wang Q, Wang J, Ramesh P, Xiang Y, Jiang X, Tao C. COVID-19 trial graph: a linked graph for COVID-19 clinical trials. J Am Med Inform Assoc. 2021 Aug 13; 28 (9):1964-1969
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  37. Du J, Preston S, Sun H, Shegog R, Cunningham R, Boom J, Savas L, Amith M, Tao C. Using Machine Learning-Based Approaches for the Detection and Classification of Human Papillomavirus Vaccine Misinformation: Infodemiology Study of Reddit Discussions. J Med Internet Res. 2021 Aug 5; 23 (8):e26478 Epub 2021 Aug 05
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  38. Wijarnpreecha K, Li F, Xiang Y, Xu X, Zhu C, Maroufy V, Wang Q, Tao W, Dang Y, Pham HA, Zhou Y, Li J, Zhang X, Xu H, Taner CB, Yang L, Tao C. Nonselective beta-blockers are associated with a lower risk of hepatocellular carcinoma among cirrhotic patients in the United States. Aliment Pharmacol Ther. 2021 Aug; 54(4):481-492. Epub 2021 Jul 05.
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  39. Du J, Xiang Y, Sankaranarayanapillai M, Zhang M, Wang J, Si Y, Pham HA, Xu H, Chen Y, Tao C. Extracting postmarketing adverse events from safety reports in the vaccine adverse event reporting system (VAERS) using deep learning. J Am Med Inform Assoc. 2021 Jul 14; 28 (7):1393-1400
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  40. Zhu A, Amith M, Tang L, Cunningham R, Xu A, Boom JA, Tao C. Experimenting with a Prototype Interactive Narrative Game to Improve Knowledge and Beliefs for the HPV Vaccine. HCI Int Late Break Pap (2021). 2021 Jul; 13097:186-201 Epub 2021 Nov 20
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  41. Rasmy L, Xiang Y, Xie Z, Tao C, Zhi D. Med-BERT: pretrained contextualized embeddings on large-scale structured electronic health records for disease prediction. NPJ Digit Med. 2021 May 20; 4 (1):86
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  42. Luo C, Jiang Y, Du J, Tong J, Huang J, Lo Re V 3rd, Ellenberg SS, Poland GA, Tao C, Chen Y. Prediction of post-vaccination Guillain-Barré syndrome using data from a passive surveillance system. Pharmacoepidemiol Drug Saf. 2021 May; 30(5):602-609. Epub 2021 Feb 23.
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  43. Xiang Y, Fujimoto K, Li F, Wang Q, Del Vecchio N, Schneider J, Zhi D, Tao C. Identifying influential neighbors in social networks and venue affiliations among young MSM: a data science approach to predict HIV infection. AIDS. 2021 May 1; 35 (Suppl 1):S65-S73
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  44. Huang J, Cai Y, Du J, Li R, Ellenberg S, Hennessy S, Tao C, Chen Y. Monitoring Vaccine Safety by Studying Temporal Variation of Adverse Events Using Vaccine Adverse Event Reporting System. Annals of Applied Statistics. 2021; 15(1):252-269.
  45. Tang L, Fujimoto K, Amith MT, Cunningham R, Costantini RA, York F, Xiong G, Boom JA, Tao C. "Down the Rabbit Hole" of Vaccine Misinformation on YouTube: Network Exposure Study. J Med Internet Res. 2021 Jan 5; 23 (1):e23262 Epub 2021 Jan 05
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  46. Ngantcha P, Amith M, Tao C, Roberts K. Patient-Provider Communication Training Models for Interactive Speech Devices. Digit Hum Model Appl Health Saf Ergon Risk Manag (2021). 2021; 12777:250-268
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  47. Amith M, Fujimoto K, Mauldin R, Tao C. Friend of a Friend with Benefits ontology (FOAF+): extending a social network ontology for public health. BMC Med Inform Decis Mak. 2020 Dec 15; 20 (Suppl 10):269
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  48. Zhang L, Hu J, Xu Q, Li F, Rao G, Tao C. A semantic relationship mining method among disorders, genes, and drugs from different biomedical datasets. BMC Med Inform Decis Mak. 2020 Dec 14; 20 (Suppl 4):283
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  49. Du J, Luo C, Shegog R, Bian J, Cunningham RM, Boom JA, Poland GA, Chen Y, Tao C. Use of Deep Learning to Analyze Social Media Discussions About the Human Papillomavirus Vaccine. JAMA Netw Open. 2020 Nov 02; 3(11):e2022025.
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  50. Rasmy L, Tiryaki F, Zhou Y, Xiang Y, Tao C, Xu H, Zhi D. Representation of EHR data for predictive modeling: a comparison between UMLS and other terminologies. J Am Med Inform Assoc. 2020 Oct 1; 27 (10):1593-1599
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  51. Li J, Maharjan B, Xie B, Tao C. A Personalized Voice-Based Diet Assistant for Caregivers of Alzheimer Disease and Related Dementias: System Development and Validation. J Med Internet Res. 2020 Sep 21; 22 (9):e19897 Epub 2020 Sept 21
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  52. Wang SQ, Zhang XY, Liu J, Tao C, Zhu CY, Shu C, Xu T, Jin HZ. Deep learning-based, computer-aided classifier developed with dermoscopic images shows comparable performance to 164 dermatologists in cutaneous disease diagnosis in the Chinese population. Chin Med J (Engl). 2020 Sep 5; 133 (17):2027-2036
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  53. Xie B, Tao C, Li J, Hilsabeck RC, Aguirre A. Artificial Intelligence for Caregivers of Persons With Alzheimer's Disease and Related Dementias: Systematic Literature Review. JMIR Med Inform. 2020 Aug 20; 8 (8):e18189
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  54. Xiang Y, Ji H, Zhou Y, Li F, Du J, Rasmy L, Wu S, Zheng WJ, Xu H, Zhi D, Zhang Y, Tao C. Asthma Exacerbation Prediction and Risk Factor Analysis Based on a Time-Sensitive, Attentive Neural Network: Retrospective Cohort Study. J Med Internet Res. 2020 Jul 31; 22 (7):e16981 Epub 2020 July 31
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  55. Bae KT, Shi T, Tao C, Yu ASL, Torres VE, Perrone RD, Chapman AB, Brosnahan G, Steinman TI, Braun WE, Srivastava A, Irazabal MV, Abebe KZ, Harris PC, Landsittel DP, HALT PKD Consortium. Expanded Imaging Classification of Autosomal Dominant Polycystic Kidney Disease. J Am Soc Nephrol. 2020 Jul; 31 (7):1640-1651 Epub 2020 June 02
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  56. Li F, Du J, He Y, Song HY, Madkour M, Rao G, Xiang Y, Luo Y, Chen HW, Liu S, Wang L, Liu H, Xu H, Tao C. Time event ontology (TEO): to support semantic representation and reasoning of complex temporal relations of clinical events. J Am Med Inform Assoc. 2020 Jul 1; 27 (7):1046-1056
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  57. Li F, Rao G, Du J, Xiang Y, Zhang Y, Selek S, Hamilton JE, Xu H, Tao C. Ontological representation-oriented term normalization and standardization of the Research Domain Criteria. Health Informatics J. 2020 Jun; 26 (2):726-737 Epub 2019 Mar 07
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  58. Duan R, Zhang X, Du J, Huang J, Tao C, Chen Y. On the evidence consistency of pharmacovigilance outcomes between Food and Drug Administration Adverse Event Reporting System and electronic medical record data for acute mania patients. Health Informatics J. 2020 Jun; 26 (2):753-764 Epub 2019 Mar 19
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  59. Luo J, Du J, Tao C, Xu H, Zhang Y. Exploring temporal suicidal behavior patterns on social media: Insight from Twitter analytics. Health Informatics J. 2020 Jun; 26 (2):738-752 Epub 2019 Mar 14
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  60. Rizvi RF, Vasilakes J, Adam TJ, Melton GB, Bishop JR, Bian J, Tao C, Zhang R. iDISK: the integrated DIetary Supplements Knowledge base. J Am Med Inform Assoc. 2020 Apr 1; 27 (4):539-548
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  61. Wei Q, Zhang Y, Amith M, Lin R, Lapeyrolerie J, Tao C, Xu H. Recognizing software names in biomedical literature using machine learning. Health Informatics J. 2020 Mar; 26 (1):21-33 Epub 2019 Sept 30
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  62. Zhang H, Wheldon C, Dunn AG, Tao C, Huo J, Zhang R, Prosperi M, Guo Y, Bian J. Mining Twitter to assess the determinants of health behavior toward human papillomavirus vaccination in the United States. J Am Med Inform Assoc. 2020 Feb 1; 27 (2):225-235
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  63. Wei Q, Ji Z, Li Z, Du J, Wang J, Xu J, Xiang Y, Tiryaki F, Wu S, Zhang Y, Tao C, Xu H. A study of deep learning approaches for medication and adverse drug event extraction from clinical text. J Am Med Inform Assoc. 2020 Jan 1; 27 (1):13-21
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  64. Zhang Z, Yu P, Chang HCR, Lau SK, Tao C, Wang N, Yin M, Deng C. Developing an ontology for representing the domain knowledge specific to non-pharmacological treatment for agitation in dementia. Alzheimers Dement (N Y). 2020; 6 (1):e12061 Epub 2020 Sept 01
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  65. Du J, Chen Q, Peng Y, Xiang Y, Tao C, Lu Z. ML-Net: multi-label classification of biomedical texts with deep neural networks. J Am Med Inform Assoc. 2019 Nov 1; 26 (11):1279-1285
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  66. Xiang Y, Fujimoto K, Schneider J, Jia Y, Zhi D, Tao C. Network context matters: graph convolutional network model over social networks improves the detection of unknown HIV infections among young men who have sex with men. J Am Med Inform Assoc. 2019 Nov 1; 26 (11):1263-1271
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  67. Soysal E, Warner JL, Wang J, Jiang M, Harvey K, Jain SK, Dong X, Song HY, Siddhanamatha H, Wang L, Dai Q, Chen Q, Du X, Tao C, Yang P, Denny JC, Liu H, Xu H. Developing Customizable Cancer Information Extraction Modules for Pathology Reports Using CLAMP. Stud Health Technol Inform. 2019 Aug 21; 264:1041-1045
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  68. Huang J, Zhang X, Tong J, Du J, Duan R, Yang L, Moore JH, Tao C, Chen Y. Comparing drug safety of hepatitis C therapies using post-market data. BMC Med Inform Decis Mak. 2019 Aug 08; 19(Suppl 4):147.
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  69. Amith M, Manion F, Liang C, Harris M, Wang D, He Y, Tao C. Architecture and usability of OntoKeeper, an ontology evaluation tool. BMC Med Inform Decis Mak. 2019 Aug 8; 19 (Suppl 4):152 Epub 2019 Aug 08
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  70. Ozen ME, Peltek G, Zhang Y, Tao C, Xu H, Selek S. Comparison of Social anxiety levels of Turks in Turkey and Turkish immigrants in Germany: A Social Media Study. Journal of Affective Disorders. 2019; 254:131.
  71. Bae KT, Zhou W, Shen C, Landsittel DP, Wu Z, Tao C, Chapman AB, Torres VE, Yu ASL, Mrug M, Bennett WM, Harris PC, Consortium for Radiologic Imaging Studies of Polycystic Kidney Disease (CRISP). Growth Pattern of Kidney Cyst Number and Volume in Autosomal Dominant Polycystic Kidney Disease. Clin J Am Soc Nephrol. 2019 Jun 7; 14 (6):823-833 Epub 2019 May 14
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  72. Xiang Y, Xu J, Si Y, Li Z, Rasmy L, Zhou Y, Tiryaki F, Li F, Zhang Y, Wu Y, Jiang X, Zheng WJ, Zhi D, Tao C, Xu H. Time-sensitive clinical concept embeddings learned from large electronic health records. BMC Med Inform Decis Mak. 2019 Apr 9; 19 (Suppl 2):58 Epub 2019 Apr 09
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  73. Du J, Jia P, Dai Y, Tao C, Zhao Z, Zhi D. Gene2vec: distributed representation of genes based on co-expression. BMC Genomics. 2019 Feb 4; 20 (Suppl 1):82 Epub 2019 Feb 04
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  74. Chen G, Jia Y, Zhu L, Li P, Zhang L, Tao C, Jim Zheng W. Gene fingerprint model for literature based detection of the associations among complex diseases: a case study of COPD. BMC Med Inform Decis Mak. 2019 Jan 31; 19 (Suppl 1):20
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  75. Du J, Cunningham RM, Xiang Y, Li F, Jia Y, Boom JA, Myneni S, Bian J, Luo C, Chen Y, Tao C. Leveraging deep learning to understand health beliefs about the Human Papillomavirus Vaccine from social media. NPJ Digit Med. 2019; 2:27 Epub 2019 Apr 15
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  76. Amith M, Zhu A, Cunningham R, Lin R, Savas L, Shay L, Chen Y, Gong Y, Boom J, Roberts K, Tao C. Early Usability Assessment of a Conversational Agent for HPV Vaccination. Stud Health Technol Inform. 2019; 257:17-23.
  77. Jia Y, Zhu C, Du J, Xiang Y, Chen Y, Wang W, Tao C. Investigating safety profiles of human papillomavirus vaccine across group differences using VAERS data and MedDRA. PeerJ. 2019; 7:e7490 Epub 2019 Aug 20
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  78. Amith M, Tao C. Representing vaccine misinformation using ontologies. J Biomed Semantics. 2018 Aug 31; 9 (1):22
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  79. Du J, Zhang Y, Luo J, Jia Y, Wei Q, Tao C, Xu H. Extracting psychiatric stressors for suicide from social media using deep learning. BMC Med Inform Decis Mak. 2018 Jul 23; 18 (Suppl 2):43 Epub 2018 July 23
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  80. Lin R, Amith MT, Liang C, Duan R, Chen Y, Tao C. Visualized Emotion Ontology: a model for representing visual cues of emotions. BMC Med Inform Decis Mak. 2018 Jul 23; 18 (Suppl 2):64 Epub 2018 July 23
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  81. Zhang X, Wang S, Liu J, Tao C. Towards improving diagnosis of skin diseases by combining deep neural network and human knowledge. BMC Med Inform Decis Mak. 2018 Jul 23; 18 (Suppl 2):59 Epub 2018 July 23
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  82. Lee HJ, Zhang Y, Jiang M, Xu J, Tao C, Xu H. Identifying direct temporal relations between time and events from clinical notes. BMC Med Inform Decis Mak. 2018 Jul 23; 18 (Suppl 2):49 Epub 2018 July 23
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  83. Du J, Tang L, Xiang Y, Zhi D, Xu J, Song HY, Tao C. Public Perception Analysis of Tweets During the 2015 Measles Outbreak: Comparative Study Using Convolutional Neural Network Models. J Med Internet Res. 2018 Jul 9; 20 (7):e236 Epub 2018 July 09
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  84. Wang L, Zhang Y, Jiang M, Wang J, Dong J, Liu Y, Tao C, Jiang G, Zhou Y, Xu H. Toward a normalized clinical drug knowledge base in China-applying the RxNorm model to Chinese clinical drugs. J Am Med Inform Assoc. 2018 Jul 01; 25(7):809-818.
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  85. Dad T, Abebe KZ, Bae KT, Comer D, Torres VE, Czarnecki PG, Schrier RW, Steinman TI, Moore CG, Chapman AB, Kaya D, Tao C, Braun WE, Winklhofer FT, Brosnahan G, Hogan MC, Miskulin DC, Rahbari Oskoui F, Flessner MF, Perrone RD. Longitudinal Assessment of Left Ventricular Mass in Autosomal Dominant Polycystic Kidney Disease. Kidney Int Rep. 2018 May; 3 (3):619-624 Epub 2018 Jan 06
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  86. Amith M, He Z, Bian J, Lossio-Ventura JA, Tao C. Assessing the practice of biomedical ontology evaluation: Gaps and opportunities. J Biomed Inform. 2018 Apr; 80:1-13 Epub 2018 Feb 17
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  87. Chen HW, Du J, Song HY, Liu X, Jiang G, Tao C. Representation of Time-Relevant Common Data Elements in the Cancer Data Standards Repository: Statistical Evaluation of an Ontological Approach. JMIR Med Inform. 2018 Feb 22; 6(1):e7.
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  88. Zhang Y, Shen F, Mojarad MR, Li D, Liu S, Tao C, Yu Y, Liu H. Systematic identification of latent disease-gene associations from PubMed articles. PLoS One. 2018; 13(1):e0191568. Epub 2018 Jan 26.
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  89. Huang J, Du J, Duan R, Zhang X, Tao C, Chen Y. Characterization of the Differential Adverse Event Rates by Race/Ethnicity Groups for HPV Vaccine by Integrating Data From Different Sources. Front Pharmacol. 2018; 9:539 Epub 2018 May 24
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  90. Amith M, Cunningham R, Savas LS, Boom J, Schvaneveldt R, Tao C, Cohen T. Using Pathfinder networks to discover alignment between expert and consumer conceptual knowledge from online vaccine content. J Biomed Inform. 2017 Oct; 74:33-45 Epub 2017 Aug 18
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  91. Cai Y, Du J, Huang J, Ellenberg SS, Hennessy S, Tao C, Chen Y. A signal detection method for temporal variation of adverse effect with vaccine adverse event reporting system data. BMC Med Inform Decis Mak. 2017 Jul 5; 17 (Suppl 2):76 Epub 2017 July 05
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  92. Amith M, Song HY, Zhang Y, Xu H, Tao C. Lightweight predicate extraction for patient-level cancer information and ontology development. BMC Med Inform Decis Mak. 2017 Jul 5; 17 (Suppl 2):73 Epub 2017 July 05
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  93. Du J, Xu J, Song HY, Tao C. Leveraging machine learning-based approaches to assess human papillomavirus vaccination sentiment trends with Twitter data. BMC Med Inform Decis Mak. 2017 Jul 5; 17 (Suppl 2):69 Epub 2017 July 05
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  94. Sharma DK, Solbrig HR, Tao C, Weng C, Chute CG, Jiang G. Building a semantic web-based metadata repository for facilitating detailed clinical modeling in cancer genome studies. J Biomed Semantics. 2017 Jun 5; 8 (1):19 Epub 2017 June 05
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  95. Amith M, Tao C. Modulated evaluation metrics for drug-based ontologies. J Biomed Semantics. 2017 Apr 24; 8 (1):17
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  96. Du J, Xu J, Song H, Liu X, Tao C. Optimization on machine learning based approaches for sentiment analysis on HPV vaccines related tweets. J Biomed Semantics. 2017 Mar 3; 8 (1):9 Epub 2017 Mar 03
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  97. Huang J, Zhang X, Du J, Duan R, Yang L, Moore JH, Chen Y, Tao C. Comparing Different Adverse Effects Among Multiple Drugs Using FAERS Data. Stud Health Technol Inform. 2017; 245:1268
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  98. Liu S, Wang L, Ihrke D, Chaudhary V, Tao C, Weng C, Liu H. Correlating Lab Test Results in Clinical Notes with Structured Lab Data: A Case Study in HbA1c and Glucose. AMIA Jt Summits Transl Sci Proc. 2017; 2017:221-228 Epub 2017 July 26
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  99. Du J, Cai Y, Chen Y, He Y, Tao C. Analysis of Individual Differences in Vaccine Pharmacovigilance Using VAERS Data and MedDRA System Organ Classes: A Use Case Study With Trivalent Influenza Vaccine. Biomed Inform Insights. 2017; 9:1178222617700627 Epub 2017 Apr 11
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  100. Amith M, Manion FJ, Harris MR, Zhang Y, Xu H, Tao C. Expressing Biomedical Ontologies in Natural Language for Expert Evaluation. Stud Health Technol Inform. 2017; 245:838-842
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  101. Madkour M, Benhaddou D, Tao C. Temporal data representation, normalization, extraction, and reasoning: A review from clinical domain. Comput Methods Programs Biomed. 2016 May; 128:52-68 Epub 2016 Feb 23
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  102. Kim Y, Ge Y, Tao C, Zhu J, Chapman AB, Torres VE, Yu AS, Mrug M, Bennett WM, Flessner MF, Landsittel DP, Bae KT, Consortium for Radiologic Imaging Studies of Polycystic Kidney Disease (CRISP). Automated Segmentation of Kidneys from MR Images in Patients with Autosomal Dominant Polycystic Kidney Disease. Clin J Am Soc Nephrol. 2016 Apr 7; 11 (4):576-84 Epub 2016 Jan 21
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  103. Kim Y, Bae SK, Cheng T, Tao C, Ge Y, Chapman AB, Torres VE, Yu ASL, Mrug M, Bennett WM, Flessner MF, Landsittel DP, Bae KT. Automated segmentation of liver and liver cysts from bounded abdominal MR images in patients with autosomal dominant polycystic kidney disease. Physics in Medicine and Biology. 2016; 61(22):7864-80.
  104. Wang D, Cunningham R, Boom J, Amith M, Tao C. Towards a HPV vaccine knowledgebase for patient education content. Stud Health Technol Inform. 2016; (225):432-6.
  105. Zhang Y, Wu HY, Du J, Xu J, Wang J, Tao C, Li L, Xu H. Extracting drug-enzyme relation from literature as evidence for drug drug interaction. J Biomed Semantics. 2016; 7:11 Epub 2016 Mar 07
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  106. Legaz-Garcia C, Menarguez-Tortosa M, Fernandez-Breis JT, Chute CG, Tao C. Transformation of standardized clinical models based on OWL technologies: from CEM to OpenEHR archetypes. J Am Med Inform Assoc. 2015 May; 22 (3):536-44 Epub 2015 Feb 10
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  107. Jiang G, Solbrig HR, Prud'hommeaux E, Tao C, Weng C, Chute CG. Quality Assurance of Cancer Study Common Data Elements Using A Post-Coordination Approach. AMIA Annu Symp Proc. 2015; 2015:659-68 Epub 2015 Nov 05
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  108. Hogan MC, Abebe K, Torres VE, Chapman AB, Bae KT, Tao C, Sun H, Perrone RD, Steinman TI, Braun W, Winklhofer FT, Miskulin DC, Rahbari-Oskoui F, Brosnahan G, Masoumi A, Karpov IO, Spillane S, Flessner M, Moore CG, Schrier RW. Liver involvement in early autosomal-dominant polycystic kidney disease. Clin Gastroenterol Hepatol. 2015 Jan; 13 (1):155-64.e6 Epub 2014 Aug 09
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  109. Zhang Y, Soysal E, Moon S, Wang J, Tao C, Xu H. Integrating Multiple On-line Knowledge Bases for Disease-Lab Test Relation Extraction. AMIA Jt Summits Transl Sci Proc. 2015; 2015:204-8 Epub 2015 Mar 25
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  110. Tao C, Sun J, Zheng WJ, Chen J, Xu H. Colorectal cancer drug target prediction using ontology-based inference and network analysis. Database (Oxford). 2015; 2015 Epub 2015 Mar 27
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  111. Chen G, Zhao J, Cohen T, Tao C, Sun J, Xu H, Bernstam EV, Lawson A, Zeng J, Johnson AM, Holla V, Bailey AM, Lara-Guerra H, Litzenburger B, Meric-Bernstam F, Jim Zheng W. Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature. Database (Oxford). 2015; 2015:bav034 Epub 2015 Apr 08
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  112. Zhang Y, Wu P, Luo Y, Tao C. Identification of sex-associated network patterns in Vaccine-Adverse Event Association Network in VAERS. J Biomed Semantics. 2015; 6:33 Epub 2015 Aug 19
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  113. Tao C, Du J, Cai Y, Chen Y. Trivalent Influenza Vaccine Adverse Event Analysis Based On MedDRA System Organ Classes Using VAERS Data. Stud Health Technol Inform. 2015; 216:1076
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  114. Bouamrane MM, Tao C, Sarkar IN. Managing interoperability and complexity in health systems. Methods Inf Med. 2015; 54 (1):1-4
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  115. Amith M, Gong Y, Cunningham R, Boom J, Tao C. Developing VISO: Vaccine Information Statement Ontology for patient education. J Biomed Semantics. 2015; 6:23 Epub 2015 May 01
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  116. Zhu K, Liu Q, Zhou Y, Tao C, Zhao Z, Sun J, Xu H. Oncogenes and tumor suppressor genes: comparative genomics and network perspectives. BMC Genomics. 2015; 16 Suppl 7 (Suppl 7):S8 Epub 2015 June 11
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  117. Tao C, He Y, Arabandi S. A 2013 workshop: vaccine and drug ontology studies (VDOS 2013). J Biomed Semantics. 2014 Mar 20; 5 (1):16
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  118. Clark K, Sharma D, Qin R, Chute CG, Tao C. A use case study on late stent thrombosis for ontology-based temporal reasoning and analysis. J Biomed Semantics. 2014; 5(1):49. Epub 2014 Dec 11.
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  119. Zhang Y, Tao C, Jiang G, Nair AA, Su J, Chute CG, Liu H. Network-based analysis reveals distinct association patterns in a semantic MEDLINE-based drug-disease-gene network. J Biomed Semantics. 2014; 5:33 Epub 2014 Aug 06
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  120. Zhu Q, Tao C, Shen F, Chute CG. Exploring the pharmacogenomics knowledge base (PharmGKB) for repositioning breast cancer drugs by leveraging Web ontology language (OWL) and cheminformatics approaches. Pac Symp Biocomput. 2014; 172-82
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  121. Zhang Y, Tao C. Network Analysis of Cancer-focused Association Network Reveals Distinct Network Association Patterns. Cancer Inform. 2014; 13 (Suppl 3):45-51 Epub 2014 Oct 16
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  122. Tao C, Wu P, Luo Y, Zhang Y. Linked vaccine adverse event data from VAERS for biomedical data analysis and longitudinal studies. BioData Min. 2014; 7:36 Epub 2014 Dec 31
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  123. Cao Y, Steffey S, He J, Xiao D, Tao C, Chen P, Muller H. Medical Image Retrieval: A Multimodal Approach. Cancer Inform. 2014; 13 (Suppl 3):125-36 Epub 2015 July 22
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  124. He Y, Sarntivijai S, Lin Y, Xiang Z, Guo A, Zhang S, Jagannathan D, Toldo L, Tao C, Smith B. OAE: The Ontology of Adverse Events. J Biomed Semantics. 2014; 5:29 Epub 2014 July 05
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  125. Pathak J, Bailey KR, Beebe CE, Bethard S, Carrell DC, Chen PJ, Dligach D, Endle CM, Hart LA, Haug PJ, Huff SM, Kaggal VC, Li D, Liu H, Marchant K, Masanz J, Miller T, Oniki TA, Palmer M, Peterson KJ, Rea S, Savova GK, Stancl CR, Sohn S, Solbrig HR, Suesse DB, Tao C, Taylor DP, Westberg L, Wu S, Zhuo N, Chute CG. Normalization and standardization of electronic health records for high-throughput phenotyping: the SHARPn consortium. J Am Med Inform Assoc. 2013 Dec; 20 (e2):e341-8 Epub 2013 Nov 04
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  126. Zhang Y, Tao C, He Y, Kanjamala P, Liu H. Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology. J Biomed Semantics. 2013 Nov 11; 4 (1):33
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  127. Tao C, Song D, Sharma D, Chute CG. Semantator: semantic annotator for converting biomedical text to linked data. J Biomed Inform. 2013 Oct; 46 (5):882-93 Epub 2013 July 15
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  128. Sohn S, Wagholikar KB, Li D, Jonnalagadda SR, Tao C, Komandur Elayavilli R, Liu H. Comprehensive temporal information detection from clinical text: medical events, time, and TLINK identification. J Am Med Inform Assoc. 2013 Sep-Oct; 20: (5)836-42.
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  129. Tao C, Jiang G, Oniki TA, Freimuth RR, Zhu Q, Sharma D, Pathak J, Huff SM, Chute CG. A semantic-web oriented representation of the clinical element model for secondary use of electronic health records data. J Am Med Inform Assoc. 2013 May 01; 20(3):554-62. Epub 2012 Dec 25.
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  130. Zhu Q, Freimuth RR, Lian Z, Bauer S, Pathak J, Tao C, Durski MJ, Chute CG. Harmonization and semantic annotation of data dictionaries from the Pharmacogenomics Research Network: a case study. J Biomed Inform. 2013 Apr; 46 (2):286-93 Epub 2012 Nov 29
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  131. Tao C, Pathak J, Solbrig HR, Wei WQ, Chute CG. Terminology representation guidelines for biomedical ontologies in the semantic web notations. J Biomed Inform. 2013 Feb; 46 (1):128-38 Epub 2012 Sept 28
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  132. Tao C, Li D, Shen F, Lian Z, Pathak J, Liu H, Chute CG. Phenotyping on EHR data using OWL and semantic web technologies. Lecture Notes in Computer Science. 2013; 8040 LNCS:31-2.
  133. Hulse NC, Long J, Tao C. Combining infobuttons and semantic web rules for identifying patterns and delivering highly-personalized education materials. AMIA Annu Symp Proc. 2013; 2013:638-47 Epub 2013 Nov 16
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  134. Martinez-Costa C, Bosca D, Legaz-Garcia MC, Tao C, Fernandez Breis JT, Schulz S, Chute CG. Isosemantic rendering of clinical information using formal ontologies and RDF. Stud Health Technol Inform. 2013; 192:1085.
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  135. Tao C, He Y, Yang H, Poland GA, Chute CG. Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis. J Biomed Semantics. 2012 Dec 20; 3 (1):13
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  136. He Y, Toldo L, Burns G, Tao C, Abernethy DR. A 2012 Workshop: Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012). J Biomed Semantics. 2012 Dec 18; 3(1):12.
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  137. Zhu Q, Tao C, Ding Y, Chute CG. Time-related patient data retrieval for the case studies from the pharmacogenomics research network. J Med Syst. 2012 Nov; 36 Suppl 1:S37-42 Epub 2012 Oct 18
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  138. Rea S, Pathak J, Savova G, Oniki TA, Westberg L, Beebe CE, Tao C, Parker CG, Haug PJ, Huff SM, Chute CG. Building a robust, scalable and standards-driven infrastructure for secondary use of EHR data: the SHARPn project. J Biomed Inform. 2012 Aug; 45(4):763-71. Epub 2012 Feb 04.
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  139. Wu ST, Liu H, Li D, Tao C, Musen MA, Chute CG, Shah NH. Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis. J Am Med Inform Assoc. 2012 Jun; 19 (e1):e149-56 Epub 2012 Apr 04
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  140. Song D, Chute CG, Tao C. Semantator: annotating clinical narratives with semantic web ontologies. AMIA Jt Summits Transl Sci Proc. 2012; 2012:20-9. Epub 2012 Mar 19.
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  141. Tao C, Noy NF, Solbrig HR, Shah NH, Musen MA, Chute CG. Proposed SKOS extensions for bioportal terminology services. Lecture Notes in Computer Science. 2012; 7185 LNCS:342-9.
  142. Tao C, Parker CG, Oniki TA, Pathak J, Huff SM, Chute CG. An OWL meta-ontology for representing the Clinical Element Model. AMIA Annu Symp Proc. 2011; 2011:1372-81. Epub 2011 Oct 22.
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  143. Tao C, Jiang G, Wei W, Solbrig HR, Chute CG. Towards Semantic-Web Based Representation and Harmonization of Standard Meta-data Models for Clinical Studies. AMIA Jt Summits Transl Sci Proc. 2011; 2011:59-63. Epub 2011 Mar 07.
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  144. Tao C, Solbrig HR, Chute CG. CNTRO 2.0: A Harmonized Semantic Web Ontology for Temporal Relation Inferencing in Clinical Narratives. AMIA Jt Summits Transl Sci Proc. 2011; 2011:64-8. Epub 2011 Mar 07.
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  145. Embley DW, Liddle SW, Tao C. A Web of Knowledge: A Conceptual-Modeling Perspective. Lecture Note in Computer Science. 2011; 6520:137-60.
  146. Clark KK, Sharma DK, Chute CG, Tao C. Application of a temporal reasoning framework tool in analysis of medical device adverse events. AMIA Annu Symp Proc. 2011; 2011:1366-71. Epub 2011 Oct 22.
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  147. Wei WQ, Tao C, Jiang G, Chute CG. A high throughput semantic concept frequency based approach for patient identification: a case study using type 2 diabetes mellitus clinical notes. AMIA Annu Symp Proc. 2010 Nov 13; 2010:857-61.
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  148. Tao C, Wei WQ, Solbrig HR, Savova G, Chute CG. CNTRO: A Semantic Web Ontology for Temporal Relation Inferencing in Clinical Narratives. AMIA Annu Symp Proc. 2010 Nov 13; 2010:787-91.
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  149. Tao C, Solbrig HR, Sharma DK, Wei WQ, Savova GK, Chute CG. Time-Oriented Question Answering from Clinical Narratives Using Semantic-Web Techniques. Lect Notes Comput Sci. 2010; 6497:241-56.
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  150. Embley DW, Liddle SW, Lonsdale DW, Steward A, Tao C. KBB: A Knowledge-Bundle Builder for Research Studies. Lecture Notes in Computer Science. 2010; 6413:148-157.
  151. Tao C, Embley DW. FOCIH: Form-based Ontology Creation, Information Harvesting. Lecture Notes in Computer Science. 2009 Nov; 5829:346-59.
  152. Tao C, Pathak J, Solbrig HR, Wei WQ, Chute CG. LexRDF Model: An RDF-based Unified Model for Heterogeneous Biomedical Ontologies. CEUR Workshop Proc. 2009 Oct 26; 521:3
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  153. Tao C, Embley DW. Automatic Hidden-Web Table Interpretation, Conceptualization, and Semantic Annotation. Journal of Data & Knowledge Engineering. 2009; 68(7):683-703.
  154. Embley DW, Liddle SW, Lonsdale DW, Nagy G, Tijerino Y, Clawson R, Crabtree J, Ding Y, Jha P, Lian Z, Lynn S, Padmanabhan R, Peters J, Tao C, Watts R, Woodbury C, Zitzelberger A. A Conceptual-Model-Based Computational Alembic for a Web of Knowledge. Lecture Notes in Computer Science. 2008; 5231:532-3.
  155. Tao C, Embley DW. Automatic Hidden-Web Table Interpretation by Sibling Page Comparison. Lecture Notes in Computer Science. 2007 Nov; 566-81.
  156. Tao C, Embley DW. Seed-based Generation of Personalized Bio-Ontologies for Information Extraction. Lecture Notes In Computer Science. 2007 Nov; 4802:74-84.
  157. Tao C. Toward Making Online Biological Data Machine Understandable. Lecture Notes in Computer Science. 2006 Nov; 4273:992-3.
  158. Tao C, Ding Y, Lonsdale D. Automatic Creation of Web Services from Extraction Ontologies. Lecture Notes in Computer Science. 2006 Nov; 4231:415-24.
  159. Embley DW, Tao C, Liddle SW. Automating the Extraction of Data from HTML Tables with Unknown Structure. Journal of Data & Knowledge Engineering. 2005 Jul; 54(1):3-28.
  160. Embley DW, Tao C, Liddle SW. Automatically Extracting Ontologically Specified Data from HTML Tables with Unknown Structure. Lecture Notes in Computer Science. 2002 Oct 7-11; (2573):322-27.