Publications

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2024

  • Knoll BC, Gunderson M, Rajamani G, Wick EC, Colley A, Lindemann E, Rizvi R, Diethelm M, Hultman G, Pierce L, Zhang R, Melton GB. Advanced Care Planning Content Encoding with Natural Language Processing. Stud Health Technol Inform. 2024 Jan 25;310:609-613. doi: 10.3233/SHTI231037. PMID: 38269881.
  • Silverman GM, Rajamani G, Ingraham NE, Glover JK, Sahoo HS, Usher M, Zhang R, Ikramuddin F, Melnik TE, Melton GB, Tignanelli CJ. A Symptom-Based Natural Language Processing Surveillance Pipeline for Post-COVID-19 Patients. Stud Health Technol Inform. 2024 Jan 25;310:860-864. doi: 10.3233/SHTI231087. PMID: 38269931.
  • Zhou H, Austin R, Lu SC, Silverman GM, Zhou Y, Kilicoglu H, Xu H, Zhang R. Complementary and Integrative Health Information in the literature: its lexicon and named entity recognition. J Am Med Inform Assoc. 2024 Jan 18;31(2):426-434. doi: 10.1093/jamia/ocad216. PMID: 37952122; PMCID: PMC10797266.

2023

  • Liu S, Wen A, Wang L, He H, Fu S, Miller R, Williams A, Harris D, Kavuluru R, Liu M, Abu-El-Rub N, Schutte D, Zhang R, Rouhizadeh M, Osborne JD, He Y, Topaloglu U, Hong SS, Saltz JH, Schaffter T, Pfaff E, Chute CG, Duong T, Haendel MA, Fuentes R, Szolovits P, Xu H, Liu H. An open natural language processing (NLP) framework for EHR-based clinical research: a case demonstration using the National COVID Cohort Collaborative (N3C). J Am Med Inform Assoc. 2023 Nov 17;30(12):2036-2040. doi: 10.1093/jamia/ocad134. PMID: 37555837; PMCID: PMC10654844.
  • Zhou H, Austin R, Lu SC, Silverman GM, Zhou Y, Kilicoglu H, Xu H, Zhang R. Complementary and Integrative Health Information in the literature: its lexicon and named entity recognition. J Am Med Inform Assoc. 2023 Nov 10:ocad216. doi: 10.1093/jamia/ocad216. Epub ahead of print. PMID: 37952122.
  • Sun B, Yew PY, Chi CL, Song M, Loth M, Zhang R, Straka RJ. Development and application of pharmacological statin-associated muscle symptoms phenotyping algorithms using structured and unstructured electronic health records data. JAMIA Open. 2023 Oct 24;6(4):ooad087. doi: 10.1093/jamiaopen/ooad087. PMID: 37881784; PMCID: PMC10597587.
  • Zhou S, Wang N, Wang L, Sun J, Blaes A, Liu H, Zhang R. A cross-institutional evaluation on breast cancer phenotyping NLP algorithms on electronic health records. Comput Struct Biotechnol J. 2023 Aug 22;22:32-40. doi: 10.1016/j.csbj.2023.08.018. PMID: 37680211; PMCID: PMC10480628.
  • Zhou H, Silverman G, Niu Z, Silverman J, Evans R, Austin R, Zhang R. Extracting Complementary and Integrative Health Approaches in Electronic Health Records. J Healthc Inform Res. 2023 Aug 17;7(3):277-290. doi: 10.1007/s41666-023-00137-2. PMID: 37637720; PMCID: PMC10449701.
  • Keloth VK, Banda JM, Gurley M, Heider PM, Kennedy G, Liu H, Liu F, Miller T, Natarajan K, V Patterson O, Peng Y, Raja K, Reeves RM, Rouhizadeh M, Shi J, Wang X, Wang Y, Wei WQ, Williams AE, Zhang R, Belenkaya R, Reich C, Blacketer C, Ryan P, Hripcsak G, Elhadad N, Xu H. Representing and utilizing clinical textual data for real world studies: An OHDSI approach. J Biomed Inform. 2023 Jun;142:104343. doi: 10.1016/j.jbi.2023.104343. Epub 2023 Mar 17. PMID: 36935011.
  • Melnik T, Thompson JA, Vasilakes J, Annis T, Zhou S, Schutte D, Melton GB, Pleasants S, Zhang R. Semi-automated Clinical Content Curation of COVID-19 Chatbot Remote Patient Monitoring Solution. AMIA Annu Symp Proc. 2023 Apr 29;2022:756-765. PMID: 37128405; PMCID: PMC10148278.
  • Zhang J, Kummerfield E, Hultman G, Drawz PE, Adam TJ, Simon G, Melton GB. Application of Causal Discovery Algorithms in Studying the Nephrotoxicity of Remdesivir Using Longitudinal Data from the EHR. AMIA Annu Symp Proc. 2023 Apr 29;2022:1227-1236. PMID: 37128413; PMCID: PMC10148284.
  • Su C, Hou Y, Zhou M, Rajendran S, Maasch JRMA, Abedi Z, Zhang H, Bai Z, Cuturrufo A, Guo W, Chaudhry FF, Ghahramani G, Tang J, Cheng F, Li Y, Zhang R, DeKosky ST, Bian J, Wang F. Biomedical discovery through the integrative biomedical knowledge hub (iBKH). iScience. 2023 Mar 21;26(4):106460. doi: 10.1016/j.isci.2023.106460. PMID: 37020958; PMCID: PMC10068563.
  • Dauner DG, Zhang R, Adam TJ, Leal E, Heitlage V, Farley JF. Performance of subgrouped proportional reporting ratios in the US Food and Drug Administration (FDA) adverse event reporting system. Expert Opin Drug Saf. 2023 Mar 7:1-9. doi: 10.1080/14740338.2023.2182289. Epub ahead of print. PMID: 36800190.

2022

  • 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. doi: 10.1186/s12859-022-04934-1. PMID: 36180861; PMCID: PMC9523633.
  • Schutte D, Vasilakes J, Bompelli A, Zhou Y, Fiszman M, Xu H, Kilicoglu H, Bishop JR, Adam T, Zhang R. Discovering novel drug-supplement interactions using SuppKG generated from the biomedical literature. J Biomed Inform. 2022 Jul;131:104120. doi: 10.1016/j.jbi.2022.104120. Epub 2022 Jun 13. PMID: 35709900.
  • Zhou H, Silverman G, Niu Z, Silverman J, Evans R, Austin R, Zhang R. Annotating Music Therapy, Chiropractic and Aquatic Exercise Using Electronic Health Record. IEEE Int Conf Healthc Inform. 2022 Jun;2022:610-611. doi: 10.1109/ichi54592.2022.00121. Epub 2022 Sep 8. PMID: 37073399; PMCID: PMC10110363.
  • Shen Z, Schutte D, Yi Y, Bompelli A, Yu F, Wang Y, Zhang R. Classifying the lifestyle status for Alzheimer's disease from clinical notes using deep learning with weak supervision. BMC Med Inform Decis Mak. 2022 Jul 7;22(Suppl 1):88. doi: 10.1186/s12911-022-01819-4. PMID: 35799294; PMCID: PMC9261217.
  • Singh E, Bompelli A, Wan R, Bian J, Pakhomov S, Zhang R. A conversational agent system for dietary supplements use. BMC Med Inform Decis Mak. 2022 Jul 7;22(Suppl 1):153. doi: 10.1186/s12911-022-01888-5. PMID: 35799177; PMCID: PMC9264487.
  • Barrett LA, Xing A, Sheffler J, Steidley E, Adam TJ, Zhang R, He Z. Assessing the use of prescription drugs and dietary supplements in obese respondents in the National Health and Nutrition Examination Survey. PLoS One. 2022 Jun 3;17(6):e0269241. doi: 10.1371/journal.pone.0269241. PMID: 35657782; PMCID: PMC9165812.
  • Kiogou SD, Chi CL, Zhang R, Ma S, Adam TJ. Clinical Data Cohort Quality Improvement: The Case of the Medication Data in The University of Minnesota's Clinical Data Repository. AMIA Annu Symp Proc. 2022 May 23;2022:293-302. PMID: 35854717; PMCID: PMC9285162.
  • Zhang J, Drawz PE, Zhu Y, Hultman G, Simon G, Melton GB. Validation of Administrative Coding and Clinical Notes for Hospital-Acquired Acute Kidney Injury in Adults. AMIA Annu Symp Proc. 2022 Feb 21;2021:1234-1243. PMID: 35308921; PMCID: PMC8861756.
  • Zhou S, Wang N, Wang L, Liu H, Zhang R. CancerBERT: a cancer domain-specific language model for extracting breast cancer phenotypes from electronic health records. J Am Med Inform Assoc. 2022 Jun 14;29(7):1208-1216. doi: 10.1093/jamia/ocac040. PMID: 35333345; PMCID: PMC9196678.

2021

  • Bompelli A, Wang Y, Wan R, Singh E, Zhou Y, Xu L, Oniani D, Kshatriya B, Balls-Berry J, Zhang R. Social and Behavioral Determinants of Health in the Era of Artificial Intelligence with Electronic Health Records: A Scoping Review. Health Data Science. 2021; 2021(9759016):19 pages. https://doi.org/10.34133/2021/9759016.
  • Silverman GM, Sahoo H, Ingraham N, Lupei M, Pusharich M, Usher M, Dries J, Finzel R, Murray E, Sartori J, Simon G, Zhang R, Melton GB, Pakhomv S. NLP Methods for Extraction of Symptoms from Unstructured Data for Use in Prognostic COVID-19 Analytic Models. Journal of Artificial Intelligence Research. 2021:72(2021):429-474. https://doi.org/10.1613/jair.1.12631.
  • Bompelli A, Li J, Xu Y, Wang N, Wang Y, Adam T, He Z, Zhang R. Deep Learning Approach to Parse Eligibility Criteria in Dietary Supplements Clinical Trials Following OMOP Common Data Model. AMIA Annu Symp Proc. 2021 Jan 25;2020:243-252. PMID: 33936396; PMCID: PMC8075443.
  • Zhang R, Hristovski D, Schutte D, Kastrin A, Fiszman M, Kilicoglu H. Drug Repurposing for COVID-19 Via Knowledge Graph Completion. J Biomed Inform. 2021 Mar;115:103696. doi: 10.1016/j.jbi.2021.103696. Epub 2021 Feb 8. PMID: 33571675; PMCID: PMC7869625.
  • Fan Y, Zhou S, Li Y, Zhang R. Deep Learning Approaches for Extracting Adverse Events and Indications of Dietary Supplements from Clinical Text. J Am Med Inform Assoc. 2021 Mar 1;28(3):569-577. doi: 10.1093/jamia/ocaa218. PMID: 33150942; PMCID: PMC7936508.
  • He X, Zhang R, Alpert J, Zhou S, Adam TJ, Raisa A, Peng Y, Zhang H, Guo Y, Bian J. When Text Simplification is Not Enough: Could a Graph-Based Visualization Facilitate Consumers’ Comprehension of Dietary Supplement Information? JAMIA Open. 2021 Apr 4;4(1):ooab026. doi: 10.1093/jamiaopen/ooab026. PMID: 33855274; PMCID: PMC8029346.
  • Sahoo H, Silverman GM, Ingraham N, Lupei M, Puskarich M, Finzel R, Sartori J, Zhang R, Knoll BC, Liu S, Liu H, Melton GB, Tignanelli CJ, Pakhomov S. A Fast, Resource Efficient, and Reliable Rule-Based System for COVID-19 Symptom Identification. JAMIA Open. 2021 Aug 7;4(3):ooab070. doi: 10.1093/jamiaopen/ooab070. PMID: 34423261; PMCID: PMC8374371.
  • Wang Y, Zhao Y, Schutte D, Bian J, Zhang R. Deep Learning Models in Detection of Dietary Supplement Adverse Event Signals from Twitter. JAMIA Open. 2021 Oct 8;4(4):ooab081. doi: 10.1093/jamiaopen/ooab081. PMID: 34632323; PMCID: PMC8497875.

2020

  • Bompelli A, Silverman GM, Finzel R, Vasilakes J, Knoll BC, Pakhomov S, Zhang R. Comparing NLP Systems to Extract Entities of Eligibility Criteria in Dietary Supplements Clinical Trials Using NLP-ADAPT. Artificial Intelligence in Medicine. 2020:67-77. https://doi.org/10.1007/978-3-030-59137-3_7.
  • Singh E, Bompelli A, Yang A, Wang A, Pakhomov S, Zhang R. A Prototype Conversational Agent for Dietary Supplements. 2020 IEEE International Conference on Healthcare Informatics (ICHI). 2020:1-2. doi: 10.1109/ICHI48887.2020.9374355.
  • Yi Y, Shen Z, Bompelli A, Yu F, Wang Y, Zhang R. Natural Language Processing Methods to Extract Lifestyle Exposures for Alzheimer’s Disease From Clinical Notes. 2020 IEEE International Conference on Healthcare Informatics (ICHI). 2020:pp. 1-2. doi: 10.1109/ICHI48887.2020.9374320.
  • 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. doi: 10.1093/jamia/ocz191. PMID: 31711186; PMCID: PMC7025367.
  • Rizvi R, Vasilakes J, Adam T, Melton GB, Bishop J, 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. doi: 10.1093/jamia/ocz216. PMID: 32068839; PMCID: PMC7075538.
  • Tignanelli CJ, Silverman GM, Lindemann EA, Trembley AL, Gipson JC, Beilman G, Lyng JW, Finzel R, McEwan R, Knoll BC, Pakhomov S, Melton GB. Natural language processing of prehospital emergency medical services trauma records allows for automated characterization of treatment appropriateness. J Trauma Acute Care Surg. 2020 May;88(5):607-614. doi: 10.1097/TA.0000000000002598. PMID: 31977990; PMCID: PMC8553576.
  • He Z, Barrett L, Rizvi R, Tang X, Payrovnaziri S, Zhang R. Assessing the Use and Perception of Dietary Supplements Among Obese Patients with National Health and Nutrition Examination Survey. AMIA Jt Summits Transl Sci Proc. 2020 May 30;2020:231-240. PMID: 32477642; PMCID: PMC7233063.
  • Wang Y, Zhao Y, Zhang J, Bian J, Zhang R. Detecting Association Between Dietary Supplement Intake and Sentiments within mental Disorder Tweets. Health Informatics J. 2020 Jun;26(2):803-815. doi: 10.1177/1460458219867231. Epub 2019 Sep 30. PMID: 31566452; PMCID: PMC7103532.
  • Vasilakes J, Bompelli A, Bishop J, Adam T, Bodenreider O, Zhang R. Assessing the Enrichment of Dietary Supplement Coverage in the Unified Medical Language System. J Am Med Inform Assoc. 2020 Oct 1;27(10):1547-1555. doi: 10.1093/jamia/ocaa128. PMID: 32940692; PMCID: PMC7566420.
  • Zhou S, Zhao Y, Bian J, Haynos AF, Zhang R. Exploring Eating Disorder Topics on Twitter: Machine Learning Approach. JMIR Med Inform. 2020 Oct 30;8(10):e18273. doi: 10.2196/18273. PMID: 33124997; PMCID: PMC7665945.
  • He Z, Tao C, Bian J, Zhang R. Selected Articles from the Fourth International Workshop on Semantics-Powered Data Mining and Analytics (SEPDA 2019). BMC Med Inform Decis Mak. 2020 Dec 14;20(Suppl 4):315. doi: 10.1186/s12911-020-01292-x. PMID: 33317524; PMCID: PMC7734704.

2019

  • Vasilakes JA, Rizvi RF, Zhang J, Adam TJ, Zhang R. Detecting Signals of Dietary Supplement Adverse Events from the CFSAN Adverse Event Reporting System (CAERS). AMIA Jt Summits Transl Sci Proc. 2019 May 6;2019:258-266. PMID: 31258978; PMCID: PMC6568094.
  • Hultman GM, Marquard JL, Lindemann E, Arsoniadis E, Pakhomov S, Melton GB. Challenges and Opportunities to Improve the Clinician Experience Reviewing Electronic Progress Notes. Appl Clin Inform. 2019 May;10(3):446-453. doi: 10.1055/s-0039-1692164. Epub 2019 Jun 19. PMID: 31216591; PMCID: PMC6584143.
  • Fan Y, Pakhomov S, McEwan R, Zhao W, Lindemann E, Zhang R. Using word embeddings to expand terminology of dietary supplements on clinical notes. JAMIA Open. 2019 Jul;2(2):246-253. doi: 10.1093/jamiaopen/ooz007. Epub 2019 Mar 28. PMID: 31825016; PMCID: PMC6904105.
  • Aldekhyyel RN, Bakker CJ, Pitt MB, Melton GB. The Impact of Patient Interactive Systems on the Management of Pain in an Inpatient Hospital Setting: A Systematic Review. Appl Clin Inform. 2019 Aug;10(4):580-596. doi: 10.1055/s-0039-1694002. Epub 2019 Aug 14. PMID: 31412381; PMCID: PMC6693998.
  • He Z, Bian J, Tao C, Zhang R. Selected articles from the Third International Workshop on Semantics-Powered Data Analytics (SEPDA 2018). BMC Med Inform Decis Mak. 2019 Aug 8;19(Suppl 4):148. doi: 10.1186/s12911-019-0855-3. PMID: 31391050; PMCID: PMC6686213.
  • Silverman GM, Lindemann EA, Rajamani G, Finzel RL, McEwan R, Knoll BC, Pakhomov S, Melton GB, Tignanelli CJ. Named Entity Recognition in Prehospital Trauma Care. Stud Health Technol Inform. 2019 Aug 21;264:1586-1587. doi: 10.3233/SHTI190547. PMID: 31438244; PMCID: PMC7360018.
  • Arsoniadis EG, Olsen RK, Skube S, Marquard J, Melton GB. Resident-Physician Preferences for Electronic Handoff Note Content: Implications for Implementation of a System-Wide Electronic Health Record-Integrated Handoff Tool. Stud Health Technol Inform. 2019 Aug 21;264:1121-1125. doi: 10.3233/SHTI190400. PMID: 31438099.
  • Hultman GM, Marquard JL, Kandaswamy S, Lindemann EA, Pakhomov S, Melton GB. Electronic Progress Note Reading Patterns: An Eye Tracking Analysis. Stud Health Technol Inform. 2019 Aug 21;264:1684-1685. doi: 10.3233/SHTI190596. PMID: 31438292.
  • Knoll BC, Lindemann EA, Albert AL, Melton GB, Pakhomov SVS. Recurrent Deep Network Models for Clinical NLP Tasks: Use Case with Sentence Boundary Disambiguation. Stud Health Technol Inform. 2019 Aug 21;264:198-202. doi: 10.3233/SHTI190211. PMID: 31437913; PMCID: PMC7360019.
  • Rizvi RF, Wang Y, Nguyen T, Vasilakes J, Bian J, He Z, Zhang R. Analyzing Social Media Data to Understand Consumer Information Needs on Dietary Supplements. Stud Health Technol Inform. 2019 Aug 21;264:323-327. doi: 10.3233/SHTI190236. PMID: 31437938; PMCID: PMC6792048.
  • Tourani R, Murphree DH, Melton-Meaux G, Wick E, Kor DJ, Simon GJ. The Value of Aggregated High-Resolution Intraoperative Data for Predicting Post-Surgical Infectious Complications at Two Independent Sites. Stud Health Technol Inform. 2019 Aug 21;264:398-402. doi: 10.3233/SHTI190251. PMID: 31437953; PMCID: PMC7037580.
  • Vasilakes J, Fan Y, Rizvi R, Bompelli A, Bodenreider O, Zhang R. Normalizing Dietary Supplement Product Names Using the RxNorm Model. Stud Health Technol Inform. 2019 Aug 21;264:408-412. doi: 10.3233/SHTI190253. PMID: 31437955; PMCID: PMC6792000.

2018

  • Rajamani S, Chen ES, Lindemann E, Aldekhyyel R, Wang Y, Melton GB. Representation of occupational information across resources and validation of the occupational data for health model. J Am Med Inform Assoc. 2018 Feb 1;25(2):197-205. doi: 10.1093/jamia/ocx035. PMID: 28444213; PMCID: PMC6080809.
  • Lindemann EA, Chen ES, Wang Y, Skube SJ, Melton GB. Representation of Social History Factors Across Age Groups: A Topic Analysis of Free-Text Social Documentation. AMIA Annu Symp Proc. 2018 Apr 16;2017:1169-1178. PMID: 29854185; PMCID: PMC5977721.
  • Sun D, Simon GJ, Skube S, Blaes AH, Melton GB, Zhang R. Causal Phenotyping for Susceptibility to Cardiotoxicity from Antineoplastic Breast Cancer Medications. AMIA Annu Symp Proc. 2018 Apr 16;2017:1655-1664. PMID: 29854236; PMCID: PMC5977581.
  • Winden TJ, Chen ES, Wang Y, Lindemann E, Melton GB. Residence, Living Situation, and Living Conditions Information Documentation in Clinical Practice. AMIA Annu Symp Proc. 2018 Apr 16;2017:1783-1792. PMID: 29854249; PMCID: PMC5977617.
  • Aldekhyyel RN, Melton GB, Hultman G, Pitt MB. Using a Bedside Interactive Technology to Solicit and Record Pediatric Pain Reassessments: Parent and Nursing Perspectives on a Novel Workflow. AMIA Jt Summits Transl Sci Proc. 2018 May 18;2017:300-309. PMID: 29888088; PMCID: PMC5961804.
  • Hultman G, McEwan R, Pakhomov S, Lindemann E, Skube S, Melton GB. Usability Evaluation of an Unstructured Clinical Document Query Tool for Researchers. AMIA Jt Summits Transl Sci Proc. 2018 May 18;2017:84-93. PMID: 29888047; PMCID: PMC5961783.
  • Rizvi RF, Adam TJ, Lindemann EA, Vasilakes J, Pakhomov SV, Bishop JR, Melton GB, Zhang R. Comparing Existing Resources to Represent Dietary Supplements. AMIA Jt Summits Transl Sci Proc. 2018 May 18;2017:207-216. PMID: 29888074; PMCID: PMC5961776.
  • Skube SJ, Lindemann EA, Arsoniadis EG, Akre M, Wick EC, Melton GB. Characterizing Functional Health Status of Surgical Patients in Clinical Notes. AMIA Jt Summits Transl Sci Proc. 2018 May 18;2017:379-388. PMID: 29888096; PMCID: PMC5961772.
  • Winden TJ, Chen ES, Monsen KA, Wang Y, Melton GB. Evaluation of Flowsheet Documentation in the Electronic Health Record for Residence, Living Situation, and Living Conditions. AMIA Jt Summits Transl Sci Proc. 2018 May 18;2017:236-245. PMID: 29888079; PMCID: PMC5961798.
  • Aldekhyyel RN, Melton GB, Lindgren B, Wang Y, Pitt MB. Linking Pediatrics Patients and Nurses With the Pharmacy and Electronic Health Record System Through the Inpatient Television: A Novel Interactive Pain-Management Tool. Hosp Pediatr. 2018 Sep;8(9):588-592. doi: 10.1542/hpeds.2018-0096. Epub 2018 Aug 16. PMID: 30115680; PMCID: PMC6226310.
  • Vasilakes J, Rizvi RF, Melton GB, Pakhomov SV, Zhang R. Evaluating Active Learning Methods for Annotating Semantic Predictions. JAMIA Open. 2018 Oct; 1(2):275–282. https://doi.org/10.1093/jamiaopen/ooy021.

2017

  • Arsoniadis EG, Skube SJ, Bjerke TM, Jarabek B, Melton GB. Assessing Provider-Generated Free-Text Quality in EHR-Integrated Handoff Notes. Stud Health Technol Inform. 2017;245:999-1003. PMID: 29295251.
  • Hultman G, McEwan R, Pakhomov S, Lindemann E, Skube S, Melton GB. Usability Evaluation of NLP-PIER: A Clinical Document Search Engine for Researchers. Stud Health Technol Inform. 2017;245:1269. PMID: 29295354; PMCID: PMC6188640.
  • Hultman G, McEwan R, Pakhomov S, Skube SJ, Melton GB. Usability Testing of a Clinical Document Search Engine for Researchers. AMIA Joint Summits Translational Science Proceedings. 2017: 348-349.
  • Lindemann EA, Chen ES, Rajamani S, Manohar N, Wang Y, Melton GB. Assessing the Representation of Occupation Information in Free-Text Clinical Documents Across Multiple Sources. Stud Health Technol Inform. 2017;245:486-490. PMID: 29295142; PMCID: PMC5755623.
  • Lindemann EA, Chen ES, Wang Y, Skube SJ, Melton GB. Representation of Social History Factors Acrsos Age Groups: A Topic Analysis of Free-Text Social Documentation. Proceedings of the American Medical Informatics Association Symposium. 2017. Accepted.
  • Rizvi RF, Marquard JL, Seywerd MA, Adam TJ, Elison JT, Hultman GM, Harder KA, Melton GB. Usability Evaluation of an EHR's Clinical Notes Interface from the Perspective of Attending and Resident Physicians: An Exploratory Study. Stud Health Technol Inform. 2017;245:1128-1132. PMID: 29295278.
  • Skube SJ, Hu Z, Arsoniadis EG, Simon GJ, Wick EC, Ko CY, Melton GB. Characterizing Surgical Site Infection Signals in Clinical Notes. Stud Health Technol Inform. 2017;245:955-959. PMID: 29295241; PMCID: PMC6197986.
  • Sun D, Sarda G, Skube SJ, Blaes A, Zhang R, Melton GB. A Study on Phenotyping and Visualizing Black Box Warnings of Antineoplastic Breast Cancer Medications. American Medical Informatics Association Joint Summits Translational Science Proceedings. 2017: 392-393.
  • Sun D, Simon GJ, Skube S, Blaes AH, Melton GB, Zhang R. Causal Phenotyping for Susceptibility to Cardiotoxicity from Antineoplastic Breast Cancer Medications. Proceedings of the American Medical Informatics Association Symposium. 2017. Accepted.
  • Winden TJ, Chen ES, Wang Y, Lindemann E, Melton GB. Residence, Living Situation, and Living Conditions Information Documentation in Clinical Practice. Proceedings of the American Medical Informatics Association Symposium. 2017. Accepted. 
  • Mattar A, Carlston D, Sariol G, Yu T, Almustafa A, Melton GB, Ahmed A. The prevalence of obesity documentation in Primary Care Electronic Medical Records. Are we acknowledging the problem? Appl Clin Inform. 2017 Jan 25;8(1):67-79. doi: 10.4338/ACI-2016-07-RA-0115. PMID: 28119990; PMCID: PMC5373753.
  • Aldekhyyel R, Chen ES, Rajamani S, Wang Y, Melton GB. Content and Quality of Free-Text Occupation Documentation in the Electronic Health Record. AMIA Annu Symp Proc. 2017 Feb 10;2016:1708-1716. PMID: 28269929; PMCID: PMC5333203. * Manuscript winner of the AMIA Student Paper Competition (1st place)
  • Finley GP, Pakhomov SV, McEwan R, Melton GB. Towards Comprehensive Clinical Abbreviation Disambiguation Using Machine-Labeled Training Data. AMIA Annu Symp Proc. 2017 Feb 10;2016:560-569. PMID: 28269852; PMCID: PMC5333249.
  • Hu Z, Melton GB, Moeller ND, Arsoniadis EG, Wang Y, Kwaan MR, Jensen EH, Simon GJ. Accelerating Chart Review Using Automated Methods on Electronic Health Record Data for Postoperative Complications. AMIA Annu Symp Proc. 2017 Feb 10;2016:1822-1831. PMID: 28269941; PMCID: PMC5333220.
  • Wang Y, Chen ES, Pakhomov S, Lindemann E, Melton GB. Investigating Longitudinal Tobacco Use Information from Social History and Clinical Notes in the Electronic Health Record. AMIA Annu Symp Proc. 2017 Feb 10;2016:1209-1218. PMID: 28269918; PMCID: PMC5333299.
  • Winden TJ, Chen ES, Melton GB. Representing Residence, Living Situation, and Living Conditions: An Evaluation of Terminologies, Standards, Guidelines, and Measures/Surveys. AMIA Annu Symp Proc. 2017 Feb 10;2016:2072-2081. PMID: 28269967; PMCID: PMC5333311.
  • Hu Z, Melton GB, Arsoniadis EG, Wang Y, Kwaan MR, Simon GJ. Strategies for handling missing clinical data for automated surgical site infection detection from the electronic health record. J Biomed Inform. 2017 Apr;68:112-120. Doi:10.1016/j.jbi.2017.03.009. PMID: 28323112.
  • Arsoniadis EG, Ho YY, Melton GB, Madoff RD, Le C, Kwaan MR. African Americans and Short-Term Outcomes after Surgery for Crohn's Disease: An ACS-NSQIP Analysis. J Crohns Colitis. 2017 Apr 1;11(4):468-473. doi: 10.1093/ecco-jcc/jjw175. PMID: 27683803; PMCID: PMC5881719.
  • Rajamani S, Chen ES, Lindemann E, Aldekhyyel R, Wang Y, Melton GB. Representation of occupational information across resources and validation of the occupational data for health model. J Am Med Inform Assoc. 2017 Apr 22. doi: 10.1093/jamia/ocx035.
  • Zhang R, Pakhomov SVS, Arsoniadis EG, Lee JT, Wang Y, Melton GB. Detecting clinically relevant new information in clinical notes across specialties and settings. BMC Med Inform Decis Mak. 2017 Jul 5;17(Suppl 2):68. doi: 10.1186/s12911-017-0464-y. PMID: 28699564; PMCID: PMC5506580.

2016

  • Knoll B, Melton G, Liu H, Xu H, Pakhomov S. Using Synthetic Clinical Data to Train an HMM-Based POS Tagger. 2016 IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI). 2016:252-255. doi: 10.1109/BHI.2016.7455882.
  • Rizvi R, Harder K, Hultman G, Adam TJ, Kim K, Pakhomov S, Melton GB. A comparative observational study of inpatient clinical note entry and reading/retrieval styles adopted by physicians. International Journal of Medical Informatics. 2016 Jun;90:1-11. doi: 10.1016/j.ijmedinf.2016.02.011. Epub 2016 Mar 2. PMID: 27103191.
  • Hultman G, Marquard J, Arsoniadis E, Mink P, Rizvi R, Ramer T, Khairat S, Fickau K, Melton GB. Usability Testing of Two Ambulatory EHR Navigators. Appl Clin Inform. 2016 Jun 15;7(2):502-15. doi: 10.4338/ACI-2015-10-RA-0129. PMID: 27437057; PMCID: PMC4941856.
  • McEwan R, Melton GB, Knoll BC, Wang Y, Hultman G, Dale JL, Meyer T, Pakhomov SV. NLP-PIER: A Scalable Natural Language Processing, Indexing, and Searching Architecture for Clinical Notes. AMIA Jt Summits Transl Sci Proc. 2016 Jul 20;2016:150-9. PMID: 27570663; PMCID: PMC5001745.
  • Wang Y, Chen ES, Leppik I, Pakhomov S, Sarkar IN, Melton GB. Identifying Family History and Substance Use Associations for Adult Epilepsy from the Electronic Health Record. AMIA Jt Summits Transl Sci Proc. 2016 Jul 20;2016:250-9. PMID: 27570679; PMCID: PMC5001738. * Paper was nominated for “Best Paper” for the AMIA Clinical Research Informatics Summits
  • Pakhomov SV, Finley G, McEwan R, Wang Y, Melton GB. Corpus domain effects on distributional semantic modeling of medical terms. Bioinformatics. 2016 Dec 1;32(23):3635-3644. doi: 10.1093/bioinformatics/btw529. Epub 2016 Aug 16. PMID: 27531100; PMCID: PMC5181540.

2015

  • Arsoniadis E, Tambyraja R, Khairat S, Jahansouz C, Scheppmann D, Kwaan MR, Melton GB. Characterizing Patient-Generated Clinical Data and Associated Implications for Electronic Health Records. Studies in Health Technology and Informatics (MedInfo 2015). 2015;216:158-62. PMID: 26262030.
  • Carter EW, Sarkar IN, Melton GB, Chen EC. Representation of Drug Use in Biomedical Standards, Clinical Text, and Research Measures. Proceedings of the American Medical Informatics Association Symposium. 2015: 376-85. PMID: 26958169.
  • Chen ES, Carter EW, Winden TJ, Sarkar IN, Wang Y, Melton GB. Multi-Source Development of an Integrated Model for Family Health History. Journal of the American Medical Informatics Association. 2015 22 (3): 615-620. doi: 10.1136/amiajnl-2014-003100. PMID: 25336591.
  • Chen ES, Melton GB, Wasserman RC, Rosenau PT, Howard DB, Sarkar IN. Mining and Visualizing Family History Associations in the Electronic Health Record: A Case Study for Pediatric Asthma. Proceedings of the American Medical Informatics Association Symposium. 2015: 396-405. PMID: 26958171.
  • Manohar N, Adam TJ, Pakhomov S, Melton GB, Zhang R. Evaluation of herbal and nutritional supplement resource term coverage. Studies in Health Technology and Informatics (MedInfo 2015). 2015;216:785-9. PMID: 26262159.
  • Melton GB, Wang Y, Arsoniadis E, Pakhomov SVS, Adam TJ, Kwaan MR, Rothenberger DA, Chen ES. Analyzing Operative Note Structure in Development of a Section Header Resource. Studies in Health Technology and Informatics (MedInfo 2015). 2015;216:821-6. PMID: 26262166.
  • Rajamani S, Chen ES, Akre M, Wang Y, Melton GB. Assessing the Adequacy of the HL7/LOINC Document Ontology Role Axis. Journal of the American Medical Informatics Association. 2015 22 (3): 615-620 doi: 10.1136/amiajnl-2014-003100. PMID: 25352569.
  • Wang Y, Chen ES, Pakhomov S, Arsoniadis E, Carter EW, Lindemann E, Sarkar IN, Melton GB.  Automated Extraction of Substance Use Information from Clinical Texts. Proceedings of the American Medical Informatics Association Symposium. 2015: 2121-30. PMID: 26958312.
  • Winden TJ, Chen ES, Wang, Y, Sarkar IN, Carter EW, Melton GB. Towards the Standardized Documentation of E-Cigarette Use in the Electronic Health Record for Population Health Surveillance and Research. American Medical Informatics Association Joint Summits Translational Science Proceedings. 2015 Mar 25;2015:199-203. PMID: 26306269.
  • Zhang R, Manohar N, Arsoniadis E, Wang Y, Adam TJ, Pakhomov SV, Melton GB. Evaluating Term Coverage of Herbal and Dietary Supplements in Electronic Health Records. Proceedings of the American Medical Informatics Association Symposium. 2015: 1361-70. PMID: 26958277.
  • Zhen H, Simon GJ, Arsoniadis EG, Wang Y, Kwaan MR, Melton GB. Automated Detection of Postoperative Surgical Site Infections Using Supervised Methods with Electronic Health Record Data. Studies in Health Technology and Informatics (MedInfo 2015). 2015;216:706-10. PMID: 26262143.
  • Moon S, McInnes B, Melton GB. Challenges and practical approaches with word sense disambiguation of acronyms and abbreviations in the clinical domain. Healthc Inform Res. 2015 Jan;21(1):35-42. doi: 10.4258/hir.2015.21.1.35. Epub 2015 Jan 31. PMID: 25705556.
  • Zhang R, Adam T, Simon G, Cairelli M, Rindflesch T, Pakhomov S, Melton GB. Mining Biomedical Literature to Explore Interactions between Cancer Drugs and Dietary Supplements. American Medical Informatics Association Joint Summits Translational Science Proceedings. 2015 Mar 23;2015:69-73. PMID: 26306241. *Manuscript nominated for best paper for the AMIA Translational Bioinformatics Meeting 
  • Wang Y, Pakhomov S, Ryan JO, Melton GB. Domain Adaption of Parsing for Operative Notes. Journal of Biomedical Informatics. 2015 Apr;54:1-9. doi: 10.1016/j.jbi.2015.01.016. Epub 2015 Feb 7. PMID: 25661593.

2014

  • Zhang R, Cairelli MJ, Fiszman M, Rosemblat G, Kilicoglu H, Rindflesch TC, Pakhomov SV, Melton GB. Using Semantic Predications to Uncover Drug-Drug Interactions in Clinical Data. Journal of Biomedical Informatics. 2014 Jan 19. pii: S1532-0464(14)00005-7. doi: 10.1016/j.jbi.2014.01.004. [Epub ahead of print]. PMID: 24448204.
  • Moon S, Pakhomov S, Liu N, Ryan JO, Melton GB. A sense inventory for clinical abbreviations and acronyms created using clinical notes and medical dictionary resources. J Am Med Inform Assoc. 2014 Mar-Apr;21(2):299-307. doi: 10.1136/amiajnl-2012-001506. Epub 2013 Jun 27. PMID: 23813539; PMCID: PMC3932450.
  • Wang Y, Pakhomov S, Dale JL, Chen ES, Melton GB. Application of HL7/LOINC Document Ontology to a University-Affiliated Integrated Health System Research Clinical Data Repository. AMIA Jt Summits Transl Sci Proc. 2014 Apr 7;2014:230-4. PMID: 25954591; PMCID: PMC4419769.
  • Zhang R, Pakhomov S, Melton GB. Longitudinal analysis of new information types in clinical notes. AMIA Jt Summits Transl Sci Proc. 2014 Apr 7;2014:232-7. PMID: 25717418; PMCID: PMC4333708. 232-7. *Manuscript selected finalist in AMIA Student Paper Competition
  • Zhang R, Cairelli MJ, Fiszman M, Kilicoglu H, Rindflesch TC, Pakhomov SV, Melton GB. Exploiting Literature-derived Knowledge and Semantics to Identify Potential Prostate Cancer Drugs. Cancer Inform. 2014 Oct 14;13(Suppl 1):103-11. doi: 10.4137/CIN.S13889. PMID: 25392688; PMCID: PMC4216049.
  • Bill R, Pakhomov S, Chen ES, Winden TJ, Carter EW, Melton GB. Automated extraction of family history information from clinical notes. AMIA Annu Symp Proc. 2014 Nov 14;2014:1709-17. PMID: 25954443; PMCID: PMC4419952.
  • Chen ES, Carter EW, Sarkar IN, Winden TJ, Melton GB. Examining the use, contents, and quality of free-text tobacco use documentation in the Electronic Health Record. AMIA Annu Symp Proc. 2014 Nov 14;2014:366-74. PMID: 25954340; PMCID: PMC4419995.
  • McInnes BT, Pedersen T, Liu Y, Melton GB, Pakhomov SV. U-path: An undirected path-based measure of semantic similarity. AMIA Annu Symp Proc. 2014 Nov 14;2014:882-91. PMID: 25954395; PMCID: PMC4419983.
  • Rajamani S, Chen ES, Wang Y, Melton GB. Extending the HL7/LOINC Document Ontology Settings of Care. AMIA Annu Symp Proc. 2014 Nov 14;2014:994-1001. PMID: 25954408; PMCID: PMC4419877.
  • Zhang R, Pakhomov SV, Lee JT, Melton GB. Using language models to identify relevant new information in inpatient clinical notes. AMIA Annu Symp Proc. 2014 Nov 14;2014:1268-76. PMID: 25954438; PMCID: PMC4419897.

2013

  • Wang Y, Pakhomov S, Melton GB. Predicate argument structure frames for modeling information in operative notes. Stud Health Technol Inform. 2013;192:783-7. PMID: 23920664; PMCID: PMC4662251. *Manuscript selected as a Student Paper Competition Finalist at MedInfo
  • Zhang R, Pakhomov S, Lee JT, Melton GB. Navigating longitudinal clinical notes with an automated method for detecting new information. Stud Health Technol Inform. 2013;192:754-8. PMID: 23920658; PMCID: PMC4495914. *Manuscript selected as a Student Paper Competition Finalist at MedInfo
  • Farri O, Monsen KA, Pakhomov SV, Pieczkiewicz DS, Speedie SM, Melton GB. Effects of time constraints on clinician-computer interaction: a study on information synthesis from EHR clinical notes. J Biomed Inform. 2013 Dec;46(6):1136-44. doi: 10.1016/j.jbi.2013.08.009. Epub 2013 Sep 6. PMID: 24013076.

2012

  • Bill RW, Liu Y, McInnes BT, Melton GB, Pedersen T, Pakhomov S. Evaluating semantic relatedness and similarity measures with Standardized MedDRA Queries. AMIA Annu Symp Proc. 2012;2012:43-50. Epub 2012 Nov 3. PMID: 23304271; PMCID: PMC3540472.
  • Liu Y, Bill R, Fiszman M, Rindflesch T, Pedersen T, Melton GB, Pakhomov SV. Using SemRep to label semantic relations extracted from clinical text. AMIA Annu Symp Proc. 2012;2012:587-95. Epub 2012 Nov 3. PMID: 23304331; PMCID: PMC3540517.
  • Liu Y, McInnes B, Pedersen T, Melton GB, Pakhomov S. Semantic Relatedness Study Using Second Order Co-occurrence Vectors Computed from Biomedical Corpora, UMLS and WordNet. 2nd ACM SIGHIT International Health Informatics (IHI) Symposium. 2012: 363-71.
  • Wang Y, Pakhomov S, Burkart NE, Ryan JO, Melton GB. A study of actions in operative notes. AMIA Annu Symp Proc. 2012;2012:1431-40. Epub 2012 Nov 3. PMID: 23304423; PMCID: PMC3540433.
  • Zhang R, Pakhomov S, Gladding S, Aylward M, Borman-Shoap E, Melton GB. Automated assessment of medical training evaluation text. AMIA Annu Symp Proc. 2012;2012:1459-68. Epub 2012 Nov 3. PMID: 23304426; PMCID: PMC3540577.
  • Zhang R, Pakhomov S, Melton GB. Automated identification of relevant new information in clinical narrative. 2nd ACM SIGHIT International Health Informatics (IHI) Symposium. 2012 Jan:837-41. https://doi.org/10.1145/2110363.2110467.
  • Pakhomov S, McInnes BT, Lamba J, Liu Y, Melton GB, Ghodke Y, Bhise N, Lamba V, Birnbaum AK. Using PharmGKB to train text mining approaches for identifying potential gene targets for pharmacogenomic studies. J Biomed Inform. 2012 Oct;45(5):862-9. doi: 10.1016/j.jbi.2012.04.007. Epub 2012 May 4. PMID: 22564551; PMCID: PMC3438361.
  • Farri O, Rahman A, Monsen KA, Zhang R, Pakhomov SV, Pieczkiewicz DS, Speedie SM, Melton GB. Impact of a prototype visualization tool for new information in EHR clinical documents. Appl Clin Inform. 2012 Oct 31;3(4):404-18. doi: 10.4338/ACI-2012-05-RA-0017. PMID: 23646087; PMCID: PMC3613039.

2011

  • McInnes BT, Pedersen T, Liu Y, Melton GB, Pakhomov SV. Knowledge-based method for determining the meaning of ambiguous biomedical terms using information content measures of similarity. AMIA Annu Symp Proc. 2011;2011:895-904. Epub 2011 Oct 22. PMID: 22195148; PMCID: PMC3243213.
  • McInnes B, Pedersen T, Liu Y, Melton GB, Pakhomov S. Using Second-Order Vectors in a Knowledge-Based Method for Acronym Disambiguation. Proceedings of the 15th Conference of Computational Natural Language Learning. 2011:145-153.
  • Moon S, Pakhomov S, Ryan J, Melton GB. Automated non-alphanumeric symbol resolution in clinical texts. AMIA Annu Symp Proc. 2011;2011:979-86. Epub 2011 Oct 22. PMID: 22195157; PMCID: PMC3243158.
  • Pakhomov SV, Shah ND, Van Houten HK, Hanson PL, Smith SA. The role of the electronic medical record in the assessment of health related quality of life. AMIA Annu Symp Proc. 2011;2011:1080-8. Epub 2011 Oct 22. PMID: 22195169; PMCID: PMC3243229.
  • Wang Y, Melton GB, Pakhomov S. It's about this and that: a description of anaphoric expressions in clinical text. AMIA Annu Symp Proc. 2011;2011:1471-80. Epub 2011 Oct 22. PMID: 22195211; PMCID: PMC3243152.
  • Zhang R, Pakhomov S, McInnes BT, Melton GB. Evaluating measures of redundancy in clinical texts. AMIA Annu Symp Proc. 2011;2011:1612-20. Epub 2011 Oct 22. PMID: 22195227; PMCID: PMC3243221.
  • Pakhomov SV, Pedersen T, McInnes B, Melton GB, Ruggieri A, Chute CG. Towards a framework for developing semantic relatedness reference standards. J Biomed Inform. 2011 Apr;44(2):251-65. doi: 10.1016/j.jbi.2010.10.004. Epub 2010 Oct 31. PMID: 21044697; PMCID: PMC3063326.

2010

  • Melton GB, Moon S, McInnes B, Pakhomov S. Automated identification of synonyms in biomedical acronym sense inventories. Proceedings of the NAACL HLT 2010 Second Louhi Workshop on Text and Data Mining of Health Documents. 2010:46-52.
  • Melton GB, Raman N, Chen ES, Sarkar IN, Pakhomov S, Madoff RD. Evaluation of family history information within clinical documents and adequacy of HL7 clinical statement and clinical genomics family history models for its representation: a case report. J Am Med Inform Assoc. 2010 May-Jun;17(3):337-40. doi: 10.1136/jamia.2009.002238. PMID: 20442153; PMCID: PMC2995709.
  • Melton GB, Westra BL, Raman N, Monsen KA, Kerr MJ, Hart CH, Solomon DA, Timm JE. Informing standard development and understanding user needs with omaha system signs and symptoms text entries in community-based care settings. AMIA Annu Symp Proc. 2010 Nov 13;2010:512-6. PMID: 21347031; PMCID: PMC3041407.
  • Pakhomov S, McInnes B, Adam T, Liu Y, Pedersen T, Melton GB. Semantic Similarity and Relatedness between Clinical Terms: An Experimental Study. AMIA Annu Symp Proc. 2010 Nov 13;2010:572-6. PMID: 21347043; PMCID: PMC3041430.