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  • Lu C, Payne A, Demner-Fushman D. Classification Types: A New Feature in the SPECIALIST Lexicon MIA 2019 Annual Symposium, Washington, DC, November 16-20, 2019.
  • Lu C, Aronson AR, Shooshan SE, Demner-Fushman D. Spell checker for consumer language (CSpell) Journal of the American Medical Informatics Association, Volume 26, Issue 3, 1 March 2019, Pages 211-218, https://doi.org/10.1093/jamia/ocy171 21 January 2019 (Editor's Choice)
  • Divita G, Rosemblat G, Browne AC. Building a medical Spanish lexicon. AMIA Annu Symp Proc. 2007 Oct 11:941.
  • Zhang XA, Yates A, Vasilevsky N, Gourdine JP, Callahan TJ, Carmody LC, Danis D, Joachimiak MP, Ravanmehr V, Pfaff ER, Champion J, Robasky K, Xu H, Fecho K, Walton NA, Zhu RL, Ramsdill J, Mungall CJ, Kohler S, Haendel MA, McDonald CJ, Vreeman DJ, Peden DB, Bennett TD, Feinstein JA, Martin B, Stefanski AL, Hunter LE, Chute CG, Robinson PN. Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery. NPJ Digit Med. 2019;2. pii: 32. doi: 10.1038/s41746-019-0110-4. Epub 2019 May 2.
  • Lu C, Demner-Fushman D. Improving Spelling Correction with Consumer Health Terminology Improving Spelling Correction with Consumer Health Terminology AMIA 2018 Annual Symposium, San Francisco, CA, November 3-7, 2018, p. 2053.
  • Lu C, Demner-Fushman D. Improving Spelling Correction with Consumer Health Terminology . AMIA 2018 Annual Symposium, San Francisco, CA, November 3-7, 2018, p. 2053.
  • McDonald CJ, Maglott D, Abhyankar S, Goodwin RM, Kanduru A, Lu S, Lynch P, Vreeman D, Wang Y, Wood G. US Realm, Chapter 14, Use Case – Clinical Genomics Code Systems. in HL7 Version 2.5.1 Implementation Guide: Lab Results Interface (LRI), DTSU3. HL7 International (Ann Arbor).
  • McDonald CJ, Maglott D, Abhyankar S, Goodwin RM, Kanduru A, Lu S, Lynch P, Vreeman D, Wang Y, Wood G. US Realm, Chapter 5, Use Case – Clinical Genomics Results Reporting in HL7 Version 2.5.1 Implementation Guide: Lab Results Interface (LRI), DTSU3. HL7 International (Ann Arbor).
  • McDonald CJ. Logical Observation Identifiers Names and Codes for In Vitro Diagnostic Test; Guidance for Industry and Food and Drug Administration Staff. Silver Spring, Md: Center for Devices and Radiological Health, FDA, 2018.
  • Vreeman DJ, Abhyankar S, McDonald CJ. Re: Unit conversions between LOINC codes Published June 19, 2017 [Letter]. J Am Med Inform Assoc. 2018 May 1;25(5):614-615. doi: 10.1093/jamia/ocx087.
  • Kayaalp M. Modes of De-identification. AMIA Annu Symp Proc. 2018 Apr 16;2017:1044-1050. eCollection 2017.
  • Rodriguez L, Morrison SM, Greenberg K, Demner-Fushman D. Mining the literature for genes associated with placenta-mediated maternal diseases. AMIA Annu Symp Proc. 2018 Apr 16;2017:1498-1506. eCollection 2017.
  • Tang P, McDonald CJ. Computer-Based Patient-Record Systems - Chapter 9. In Shortliffe E, Perreault L, eds. Medical Informatics. New York: springer. 2001:327-358. DOI: 10.1007/978-0-387-21721-5_9.
  • Abhyankar S, Schluter P, Bennett K, Vreeman D, McDonald CJ. Enabling Interoperability between Healthcare Devices and EHR Systems. In 2017 AMIA Symposium. Wasington DC: IEEE.
  • Lu C, Tormey D, McCreedy L, Browne AC. Enhancing LexSynonym Features in the Lexical Tools AMIA 2017 Annual Symposium, Washington, DC, November 04-08, 2017, p. 2090
  • McDonald CJ, Vreeman D, Wang K, Carr C, Colins B, Abhyankar S, Deckard J, Rubin D, Langlotz C. The LOINC/RSNA Radiology Playbook: A unified terminology for radiology procedures. . In 2017 AMIA Symposium. Washington DC.
  • Abhyankar S, Vreeman DJ, Westra BL, Delaney CW. Comments on the Use of LOINC and SNOMED CT for Representing Nursing Data [Letter]. Int J Nurs Knowl. 2017 Aug 30. doi: 10.1111/2047-3095.12183. [Epub ahead of print]
  • Raje S, Bodenreider O. Interoperability of disease concepts in clinical and research ontologies – Contrasting coverage and structure in the Disease Ontology and SNOMED CT. Stud Health Technol Inform. 2017;245:925-929.
  • Bhupatiraju R, Fung K, Bodenreider O. MetaMapLite in Excel: Biomedical named-entity recognition for non-technical users. Stud Health Technol Inform (Proc Medinfo): 1252.
  • Mrabet Y, Kilicoglu H, Demner-Fushman D. TextFlow: A Text Similarity Measure based on Continuous Sequences. Proceedings of the 55th Annual Meeting of the Association for Computational Linguistics, 2017, Vancouver, Canada, July 30 - August 4, Volume
  • Vreeman DJ, Abhyankar S, McDonald CJ. Unit conversions between LOINC codes Published June 19, 2017 [Letter]. Journal of the American Medical Informatics Association, 1–3. http://doi.org/10.1093/jamia/ocx087.
  • McDonald CJ, Maglott D, Abhyankar S, Goodwin R, Kanduru A, Lu S, Lynch P, Vreeman D, Wang Y, Wood G. HL7 Version 2.5.1 Implementation Guide: Lab Results Interface (LRI), Release 1, STU Release 4. US Realm, Chapter 5, Clinical Genomics Results Reporting. Published for May 2017 Ballot.
  • Ash J, Sittig D. Everything Electronic Medical Records: Systems, Standards and Studies Conversations with Medical Informatics Pioneers: An oral history project.
  • Raje S, Bodenreider O. Investigating the coverage of diseases across biomedical research and clinical ontologies. Proceedings of the AMIA Joint Summits on Translational Science CRI: 384-385.
  • Lu C, Tormey D, McCreedy L, Browne AC. Generating A Distilled N-Gram Set: Effective Lexical Multiword Building in the SPECIALIST Lexicon. The 10th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2017), Vol(5): HEALTHINF, PORTO, Portugal, February 21-23, 2017, p. 77-87.
  • Kury F, Baik SH, McDonald CJ. Analysis of Healthcare Cost and Utilization in the First Two Years of the Medicare Shared Savings Program Using Big Data from the CMS Enclave. AMIA Annu Symp Proc. 2017 Feb 10;2016:724-733. eCollection 2016.
  • Mrabet Y, Kilicoglu H, Roberts K, Demner-Fushman D. Combining Open-domain and Biomedical Knowledge for Topic Recognition in Consumer Health Questions. AMIA Annu Symp Proc. 2017 Feb 10;2016:914-923. eCollection 2016.
  • Workman E, Weir, C, Rindflesch TC. Differentiating Sense through Semantic Interaction Data. AMIA Annu Symp Proc. 2017 Feb 10;2016:1238-1247. eCollection 2016.
  • Bahr NJ, Nelson SD, Winnenburg R, Bodenreider O. Eliciting the Intension of Drug Value Sets - Principles and Quality Assurance Applications. Stud Health Technol Inform. 2017;245:843-847.
  • Dhombres F, Bodenreider O. Trends in Fetal Medicine: A 10-Year Bibliometric Analysis of Prenatal Diagnosis. Stud Health Technol Inform. 2017;245:853-857.
  • Yu Z, Nguyen T, Dhombres F, Johnson T, Bodenreider O. "Hybrid Topics" - Facilitating the Interpretation of Topics Through the Addition of MeSH Descriptors to Bags of Words. Stud Health Technol Inform. 2017;245:662-666.
  • Kilicoglu H. Inferring Implicit Causal Relationships in Biomedical Literature. Proc 15th Workshop on Biomedical Natural Language Processing. Pages 46-55. 2016.
  • Ben Abacha A, de Herrera A, Wang Ke, Long LR, Antani SK, Demner-Fushman D. Named entity recognition in functional neuroimaging literature. 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Kansas City, MO, 2017, pp. 2218-2220.
  • Demner-Fushman D, Elhadad N. Aspiring to Unintended Consequences of Natural Language Processing: A Review of Recent Developments in Clinical and Consumer-Generated Text Processing. IMIA Yearbook of Medical Informatics 2016.
  • Mrabet Y, Vougiouklis P, Kilicoglu H, Gardent C, Demner-Fushman D, Hare J, Simperl E. Aligning Texts and Knowledge Bases with Semantic Sentence Simplification. WebNLG 2016.
  • Mrabet Y, Kilicoglu H, Demner-Fushman D. Unsupervised Ranking of Knowledge Bases for Named Entity Recognition. ECAI 2016, The Hague, The Netherlands, 1248-1255.
  • Boyce RD, Voss EA, Huser V, Evans L, Reich C, Duke JD, Tatonetti NP, Lorberbaum T, Dumontier M, Hauben M, Wallberg M. LAERTES: An open scalable architecture for linking pharmacovigilance evidence sources with clinical data. Proc International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016). http://icbo2016.cgrb.oregonstate.edu/node/354.
  • Homer ML, Palmer NP, Bodenreider O, Cami A, Chadwick L, Mandl KD. The Drug Data to Knowledge Pipeline: Large-Scale Claims Data Classification for Pharmacologic Insight. AMIA Jt Summits Transl Sci Proc. 2016 Jul 20;2016:105-11. eCollection 2016.
  • Kilicoglu H, Ben Abacha A, Mrabet Y, Roberts K, Rodriguez L, Shooshan SE, Demner-Fushman D. Annotating named entities in consumer health questions. LREC,23-28 May 2016, Portorož.
  • Kilicoglu H. Software: Bio-SCoRes
  • Bodenreider O. Identifying missing hierarchical relations in SNOMED CT from logical definitions based on the lexical features of concept names. Proceedings of the 6th International Conference on Biomedical Ontology (ICBO 2016), 2016: p. (electronic proceedings: http://ceur-ws.org/Vol-1747/IT601_ICBO2016.pdf).
  • Kury F, Bodenreider O. Desiderata for drug classification systems for their use in analyzing large drug prescription datasets. Proceedings of the 3rd Workshop on Data Mining for Medical Informatics (DMMI 2016), 2016.
  • Cimino JJ, Huser V. Characterization of the Context of Drug Concepts in Research Protocols: An Empiric Study to Guide Ontology Development. AMIA Annu Symp Proc. 2015 Nov 5;2015:441-7. eCollection 2015.
  • Demner-Fushman D, Mork JG. Extracting Characteristics of the Study Subjects from Full-Text Articles. AMIA Annu Symp Proc. 2015 Nov 5;2015:484-91. eCollection 2015.
  • Kayaalp M, Browne AC, Sagan P, McGee T, McDonald CJ. Challenges and Insights in Using HIPAA Privacy Rule for Clinical Text Annotation. AMIA Annu Symp Proc. 2015 Nov 5;2015:707-16. eCollection 2015.
  • Kilicoglu H, Fiszman M, Roberts K, Demner-Fushman D. An Ensemble Method for Spelling Correction in Consumer Health Questions. AMIA Annu Symp Proc. 2015 Nov 5;2015:727-36. eCollection 2015.
  • Kury F, Huser V, Cimino JJ. Reproducing a Prospective Clinical Study as a Computational Retrospective Study in MIMIC-II. AMIA Annu Symp Proc. 2015 Nov 5;2015:804-13. eCollection 2015.
  • Morid MA, Jonnalagadda S, Fiszman M, Raja K, Del Fiol G. Classification of Clinically Useful Sentences in MEDLINE. AMIA Annu Symp Proc. 2015 Nov 5;2015:2015-24. eCollection 2015.
  • Pan X, Cimino JJ. Identifying the Clinical Laboratory Tests from Unspecified "Other Lab Test" Data for Secondary Use. AMIA Annu Symp Proc. 2015 Nov 5;2015:1018-23. eCollection 2015.
  • Peters LB, Bodenreider O. Approaches to Supporting the Analysis of Historical Medication Datasets with RxNorm. AMIA Annu Symp Proc. 2015 Nov 5;2015:1034-41. eCollection 2015.

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