Publications

1. Nakai H, Suman G, Adamo DA, Navin PJ, Bookwalter CA, LeGout JD, Chen FK, Wellnitz CV, Silva AC, Thomas JV, Kawashima A, Fan JW, Froemming AT, Lomas DJ, Humphreys MR, Dora C, Korfiatis P, Takahashi N. Natural language processing pipeline to extract prostate cancer-related information from clinical notes. Eur Radiol. 2024 Dec; 34 (12):7878-7891 Epub 2024 June 06
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2. Moon S, Wu Y, Doughty JB, Wieland ML, Philpot LM, Fan JW, Njeru JW. Automated Identification of Patients' Unmet Social Needs in Clinical Text Using Natural Language Processing. Mayo Clin Proc Digit Health. 2024 Sep; 2 (3):411-420 Epub 2024 July 08
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3. Ren Y, Wu Y, Fan JW, Khurana A, Fu S, Wu D, Liu H, Huang M. Automatic uncovering of patient primary concerns in portal messages using a fusion framework of pretrained language models. J Am Med Inform Assoc. 2024 Aug 1; 31 (8):1714-1724
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4. Loor-Torres R, Duran M, Toro-Tobon D, Chavez MM, Ponce O, Jacome CS, Torres DS, Perneth SA, Montori V, Golembiewski E, Osorio MB, Fan JW, Ospina NS, Wu Y, Brito JP. A Systematic Review of Natural Language Processing Methods and Applications in Thyroidology. Mayo Clin Proc Digit Health. 2024 Jun; 2 (2):270-279 Epub 2024 May 21
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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. Jacome CS, Torres DS, Fan JW, Loor-Torres R, Duran M, Zahidy MA, Cabezas E, Borras-Osorio M, Toro-Tobon D, Wu Y, Wu Y, Ospina NS, Brito JP. Thyroid Ultrasound Appropriateness Identification Through Natural Language Processing of Electronic Health Records. Mayo Clin Proc Digit Health. 2024 Mar; 2 (1):67-74 Epub 2024 Feb 01
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7. Jacome CS, Garcia A, Golembiewski E, Loor-Torres R, Duran M, Segura D, Toro-Tobon D, Fan JW, Singh Ospina N, Brito JP. Physical Examination of the Thyroid: Accuracy in Detecting Thyroid Nodules and Frequency of Additional Findings. Endocr Pract. 2024 Jan; 30 (1):31-35 Epub 2023 Oct 05
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8. Soto Jacome C, Segura Torres D, Fan JW, Garcia-Bautista A, Golembiewski E, Duran M, Loor-Torres R, Toro-Tobon D, Singh Ospina N, Brito JP. Drivers of Thyroid Ultrasound Use: A Retrospective Observational Study. Endocr Pract. 2023 Dec; 29 (12):948-954 Epub 2023 Sept 16
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9. 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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10. Toro-Tobon D, Loor-Torres R, Duran M, Fan JW, Singh Ospina N, Wu Y, Brito JP. Artificial Intelligence in Thyroidology: A Narrative Review of the Current Applications, Associated Challenges, and Future Directions. Thyroid. 2023 Aug; 33 (8):903-917 Epub 2023 June 26
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11. Moon S, He H, Jia H, Liu H, Fan JW. Extractive Clinical Question-Answering With Multianswer and Multifocus Questions: Data Set Development and Evaluation Study. JMIR AI. 2023 Jun 20; 2:e41818 Epub 2023 June 20
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12. Moon S, Liu S, Kshatriya BSA, Fu S, Moser ED, Bielinski SJ, Fan J, Liu H. Assessing document section heterogeneity across multiple electronic health record systems for computational phenotyping: A case study of heart-failure phenotyping algorithm. PLoS One. 2023; 18 (3):e0283800 Epub 2023 Mar 31
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13. Fan JW, Wang W, Huang M, Liu H, Hooten WM. Retrospective content analysis of consumer product reviews related to chronic pain. Front Digit Health. 2023; 5:958338 Epub 2023 Apr 24
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14. 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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15. Sohn S, Moon S, Prokop LJ, Montori VM, Fan JW. A scoping review of medical practice variation research within the informatics literature. Int J Med Inform. 2022 Sep; 165:104833 Epub 2022 July 14
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16. Moon S, He H, Fan JW. Effects of Information Masking in the Task-Specific Finetuning of a Transformers-Based Clinical Question-Answering Framework. The 10th IEEE International Conference on Healthcare Informatics. 2022.
    
17. Huang M, Khurana A, Mastorakos GM, Fan J. Identification of Transportation Barriers in Patient Portal Messages via Deep Semantic Embeddings and Clustering. Stud Health Technol Inform. 2022 Jun 6; 290:794-798
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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. Huang M, Fan J, Prigge J, Shah ND, Costello BA, Yao L. Characterizing Patient-Clinician Communication in Secure Medical Messages: Retrospective Study. J Med Internet Res. 2022 Jan 11; 24 (1):e17273
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21. Fu S, Vassilaki M, Ibrahim OA, Petersen RC, Pagali S, St Sauver J, Moon S, Wang L, Fan JW, Liu H, Sohn S. Quality assessment of functional status documentation in EHRs across different healthcare institutions. Front Digit Health. 2022; 4:958539 Epub 2022 Sept 27
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22. Fan J, Jeffery MM, Hooten WM, Shah ND, McCoy RG. Trends in Pain Medication Initiation Among Patients With Newly Diagnosed Diabetic Peripheral Neuropathy, 2014-2018. JAMA Netw Open. 2021 Jan 4; 4 (1):e2035632 Epub 2021 Jan 04
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23. Wen A, Wang L, He H, Liu S, Fu S, Sohn S, Kugel JA, Kaggal VC, Huang M, Wang Y, Shen F, Fan J, Liu H. An aberration detection-based approach for sentinel syndromic surveillance of COVID-19 and other novel influenza-like illnesses. J Biomed Inform. 2021 Jan; 113:103660 Epub 2020 Dec 13
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24. Mastorakos G, Khurana A, Huang M, Fu S, Tafti AP, Fan J, Liu H. Probing Patient Messages Enhanced by Natural Language Processing: A Top-Down Message Corpus Analysis. Health Data Sci. 2021; 2021:1504854 Epub 2021 May 18
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25. Moon S, Fan J. How You Ask Matters: The Effect of Paraphrastic Questions to BERT Performance on a Clinical SQuAD Dataset. Proceedings of the 3rd Clinical Natural Language Processing Workshop. 2020.
    
26. Carlson LA, Jeffery MM, Fu S, He H, McCoy RG, Wang Y, Hooten WM, St Sauver J, Liu H, Fan J. Characterizing Chronic Pain Episodes in Clinical Text at Two Health Care Systems: Comprehensive Annotation and Corpus Analysis. JMIR Med Inform. 2020 Nov 16; 8 (11):e18659
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27. Zheng L, He Z, Wei D, Keloth V, Fan JW, Lindemann L, Zhu X, Cimino JJ, Perl Y. A review of auditing techniques for the Unified Medical Language System. J Am Med Inform Assoc. 2020 Oct 1; 27 (10):1625-1638
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28. Wen A, Shen F, Moon S, Liu H, Fan J. A Deep Profiling and Visualization Framework to Audit Clinical Assessment Variation. Proceedings of the IEEE International Symposium on Computer Based Medical Systems (CBMS). 2020; 549.
    
29. Wen A, Elwazir MY, Moon S, Fan J. Adapting and evaluating a deep learning language model for clinical why-question answering. JAMIA Open. 2020 Apr; 3 (1):16-20 Epub 2020 Feb 04
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30. Wen A, Wang Y, Kaggal VC, Liu S, Liu H, Fan J. Enhancing Clinical Information Retrieval through Context-Aware Queries and Indices. Proc IEEE Int Conf Big Data. 2019 Dec; 2019:2800-2807 Epub 2020 Feb 24
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31. Fan J. Annotating and characterizing clinical sentences with explicit why-QA cues. Proceedings of the 2nd Clinical Natural Language Processing Workshop. 2019.
    
32. Vitali F, Berghout J, Fan J, Li J, Li Q, Li H, Lussier YA. Precision drug repurposing via convergent eQTL-based molecules and pathway targeting independent disease-associated polymorphisms. Proceedings of the Pacific Symposium on Biocomputing (PSB). 2019.
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33. Wen A, Fu S, Moon S, El Wazir M, Rosenbaum A, Kaggal VC, Liu S, Sohn S, Liu H, Fan J. Desiderata for delivering NLP to accelerate healthcare AI advancement and a Mayo Clinic NLP-as-a-service implementation. NPJ Digit Med. 2019; 2:130 Epub 2019 Dec 17
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34. Li H, Fan J, Berghout J, Aberasturi D, Li J, Wilson L, Chiu W, Pumajero M, Han J, Kenost C, Koripella PC, Pouladi N, Billheimer D, Bedrick EJ, Lussier YA. Novel disease syndromes unveiled by integrative multiscale network analysis of diseases sharing molecular effectors and comorbidities. BMC Medical Genomics. 2018; 11(Suppl 6):112.
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35. Fan JW, Lussier YA. Word-of-Mouth Innovation: Hypothesis Generation for Supplement Repurposing based on Consumer Reviews. AMIA Annu Symp Proc. 2017; 2017:689-695 Epub 2018 Apr 16
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36. Fan JW, Li J, Lussier YA. Semantic Modeling for Exposomics with Exploratory Evaluation in Clinical Context. J Healthc Eng. 2017; 2017:3818302 Epub 2017 Aug 30
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37. Torii M, Tilak SS, Doan S, Zisook DS, Fan JW. Mining Health-Related Issues in Consumer Product Reviews by Using Scalable Text Analytics. Biomed Inform Insights. 2016; 8 (Suppl 1):1-11 Epub 2016 June 20
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38. Torii M, Fan JW, Yang WL, Lee T, Wiley MT, Zisook DS, Huang Y. Risk factor detection for heart disease by applying text analytics in electronic medical records. J Biomed Inform. 2015 Dec; 58 Suppl:S164-70 Epub 2015 Aug 14
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39. Jiang M, Huang Y, Fan JW, Tang B, Denny J, Xu H. Parsing clinical text: how good are the state-of-the-art parsers? BMC Med Inform Decis Mak. 2015; 15 Suppl 1:S2 Epub 2015 May 20
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40. Fan JW, Yang EW, Jiang M, Prasad R, Loomis RM, Zisook DS, Denny JC, Xu H, Huang Y. Syntactic parsing of clinical text: guideline and corpus development with handling ill-formed sentences. J Am Med Inform Assoc. 2013 Nov-Dec; 20 (6):1168-77 Epub 2013 Aug 01
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41. Xu H, AbdelRahman S, Jiang M, Fan JW, Huang Y. An initial study of full parsing of clinical text using the Stanford Parser. IEEE BIBM 2011 Workshop. 2011; 607-14.
    
42. Fan JW, Friedman C. Deriving a probabilistic syntacto-semantic grammar for biomedicine based on domain-specific terminologies. J Biomed Inform. 2011 Oct; 44 (5):805-14 Epub 2011 Apr 28
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43. Fan JW, Prasad R, Yabut RM, Loomis RM, Zisook DS, Mattison JE, Huang Y. Part-of-speech tagging for clinical text: wall or bridge between institutions? AMIA Annu Symp Proc. 2011; 2011:382-91 Epub 2011 Oct 22
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44. Fan JW, Friedman C. Generating quality word sense disambiguation test sets based on MeSH indexing. AMIA Annu Symp Proc. 2009 Nov 14; 2009:183-7
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45. Zhu X, Fan JW, Baorto DM, Weng C, Cimino JJ. A review of auditing methods applied to the content of controlled biomedical terminologies. J Biomed Inform. 2009 Jun; 42 (3):413-25 Epub 2009 Mar 12
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46. Fan JW, Friedman C. Word sense disambiguation via semantic type classification. AMIA Annu Symp Proc. 2008 Nov 6; 177-81 Epub 2008 Nov 06
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47. Fan JW, Friedman C. Semantic reclassification of the UMLS concepts. Bioinformatics. 2008 Sep 1; 24 (17):1971-3 Epub 2008 July 13
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48. Fan JW, Xu H, Friedman C. Using contextual and lexical features to restructure and validate the classification of biomedical concepts. BMC Bioinformatics. 2007 Jul 24; 8:264 Epub 2007 July 24
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49. Fan JW, Friedman C. Semantic classification of biomedical concepts using distributional similarity. J Am Med Inform Assoc. 2007 Jul-Aug; 14 (4):467-77 Epub 2007 Apr 25
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50. Xu H, Fan JW, Friedman C. Combining multiple evidence for gene symbol disambiguation. Proceedings of BioNLP. 2007; 41-8.
    
51. Xu H, Fan JW, Hripcsak G, Mendonca EA, Markatou M, Friedman C. Gene symbol disambiguation using knowledge-based profiles. Bioinformatics. 2007 Apr 15; 23 (8):1015-22 Epub 2007 Feb 21
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52. Chen HH, Chiu TH, Fan JW. Educating knowledge management professionals in the era of knowledge economy. Journal of Information & Knowledge Management. 2002; 1(2):91-98.