• Antani S, Xue Z, Long LR, Bennett D, Ward S, Thoma GR. Is there a need for biomedical CBIR systems in clinical practice? Outcomes from a usability study. Proceedings of SPIE Medical Imaging 2011: Advanced PACS-based Imaging Informatics and Therapeutic Applications. Orlando, FL. February 2011;7967:796708.

  Abstract | pub2011-078.pdf

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• Bakker TA, Ryce AN, Logan RA, Tse T, Hutcherson LY. A Consumer Health Informatics (CHI) Toolbox: Challenges and Implications AMIA Annu Symp Proc. 2005:21-5

  Abstract | pub2005071.pdf | PMID:  16778994 | PMCID:  PMC1479846

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• Beaudoin DE, Longo N, Logan RA, Jones JP, Mitchell JA. Using information prescriptions to refer patients with metabolic conditions to the Genetics Home Reference website. J Med Libr Assoc. 2011 Jan;99(1):70-6. doi: 10.3163/1536-5050.99.1.012.

  Abstract | pub2011004.pdf | PMID:  21243058 | PMCID:  PMC3016649

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• Beaudoin DE, Rocha RA, Tse T. Enhancing Access to Patient Education Information: A Pilot Usability Study AMIA Annu Symp Proc. 2005:892

  Abstract | pub2005045.pdf | PMID:  16779179 | PMCID:  PMC1560886

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• Ben Abacha A, Mrabet Y, Sharp M, Goodwin T, Shooshan S, Demner-Fushman D. Bridging the Gap Between Consumers' Medication Questions and Trusted Answers. Studies in health technology and informatics, 264, pp.25-29, 2019.

  Abstract | PMID:  31437878 | URL:  https://doi.org/10.3233/SHTI190176

  AbstractExternal link
• 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.

  Abstract

  Abstract
• Bhupatiraju R, Huser V, Fung K. Phenotype modelling tools utilizing standardized EHR data in a Common Data Model format [Poster]. NIH Research Festival 2017.

  Abstract | pub9631.pdf

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• Califf RM, Zarin DA, Kramer JM, Sherman RE, Aberle LH, Tasneem A. Characteristics of clinical trials registered in ClinicalTrials.gov, 2007-2010. JAMA. 2012 May 2;307(17):1838-47. doi: 10.1001/jama.2012.3424.

  Abstract | PMID:  22550198 | URL:  http://jama.jamanetwork.com/article.aspx?articleid=1150093

  AbstractExternal link
• Chachra S, Ben Abacha A, Shooshan SE, Rodriguez L, Demner-Fushman D. A Hybrid Approach to Generation of Missing Abstracts in Biomedical Literature. Proceedings of COLING 2016, the 26th International Conference on Computational Linguistics: Technical Papers: 1093-1100.

  Abstract | pub9455.pdf

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• Collins H, Calvo SC, Greenberg K, Forman NL, Morrison SM. Using Genetics Home Reference to Reinforce Patient Education [Poster]. American College of Medical Genetics Annual Meeting, Phoenix, AZ, March 21-25, 2017.

  Abstract | pub9564.pdf

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• Collins H, Calvo SC, Greenberg K, Forman, NL, Morrison SM. Information Needs in the Precision Medicine Era: How Genetics Home Reference Can Help. Interact J Med Res 2016;5(2):e13 DOI: 10.2196/ijmr.5199

  Abstract

  Abstract
• Datta S, Rodriguez L, Shooshan SE, Demner-Fushman D, Roberts K. Understanding Spatial Language in Radiology: Representation Framework, Annotation, and Spatial Relation Extraction from Chest X-ray Reports using Deep Learning. Journal of Biomedical Informatics, 103473.

  Abstract | URL:  https://arxiv.org/pdf/1908.04485.pdf

  AbstractExternal link
• Deardorff A, Masterton K, Roberts K, Kilicoglu H, Demner-Fushman D. A protocol-driven approach to automatically finding authoritative answers to consumer health questions in online resources. JASIST, 68(7): 1724-1736. doi: 10.1002/asi.23806.

  Abstract

  Abstract
• 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.

  Abstract

  Abstract
• Demner-Fushman D, Shooshan SE, Rodriguez L, Antani SK, Thoma GR. Annotation of Chest Radiology Reports for Indexing and Retrieval. Multimodal Retrieval in the Medical Domain 2015 (MRMD 2015), Vienna, Austria, March 29, 2015

  Abstract | pub9218.pdf

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• Fomous C, Mitchell JA, McCray A. Genetics Home Reference: Helping Patients Understand the Role of Genetics in Health and Disease Community Genet. 2006;9(4):274-8

  Abstract | pub2006027.pdf

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• Gallagher ME. Improving Software Sustainability: Lessons Learned from Profiles in Science. Archiving. 2013;2013:74-79.

  Abstract | a2013001.pdf | PMID:  25267934 | PMCID:  PMC4176707

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• Gallagher ME, Moffatt C. The Profiles in Science Digital Library: Behind the Scenes. Proc ACM/IEEE Joint Conf Digit Libr. 2012: 433–434. doi: 10.1145/2232817.2232928.

  Abstract | pub2012016.pdf | PMCID:  PMC3609548

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• Gallagher ME. Keeping the Promises Associated with Your Digital Assets: Is it Possible? In: Archiving 2007 Final Program and Proceedings, pp.146-149, 2007.

  Abstract | pub2007007.pdf

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• Gallagher ME, Moffatt C. Surviving Change: The First Step Toward Sustaining Your Digital Library In: J. Trant and D. Bearman (eds.). Museums and the Web 2006: Proceedings, Toronto: Archives & Museum Informatics, published March 1, 2006.

  Abstract | pub2006006.pdf

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• Gopal AD, Desai NR, Tse T, Ross JS. Reporting of noninferiority trials in ClinicalTrials.gov and corresponding publications. JAMA. 2015 Mar 17;313(11):1163-5. doi: 10.1001/jama.2015.1697.

  Abstract | PMID:  25781447

  Abstract
• Graham L, Tse T, Keselman A. Exploring User Navigation during Online Health Information Seeking AMIA Annu Symp Proc. 2006:299-303

  Abstract | pub2006065.pdf | PMID:  17238351 | PMCID:  PMC1839467

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• Greenberg K, Calvo SC, Collins H, Foreman NL, Morrison SM. Genetics Home Reference: A point of care resource in the genomic medicine era [Poster]. American Society of Human Genetics Annual Meeting, Vancouver, British Columbia, Canada, November 18-22, 2016.

  Abstract | pub9563.pdf

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• Hartung DM, Zarin D, Guise JM, McDonagh M, Paynter R, Helfand M. Reporting discrepancies between the ClinicalTrials.gov results database and peer-reviewed publications. Ann Intern Med. 2014 Apr 1;160(7):477-83. doi: 10.7326/M13-0480.

  Abstract | PMID:  24687070 | PMCID:  PMC4617780

  Abstract
• Huston M, Williams RJ, Bergeris A, Fun J, Tse T. New style and new content for ClinicalTrials.gov. NLM Tech Bull. 2012 Jul-Aug;(387):e5.

  Abstract | URL:  http://www.nlm.nih.gov/pubs/techbull/ja12/ja12_clinicaltrials.html

  AbstractExternal link
• Ide NC, Loane RF, Demner-Fushman D. Essie: A Concept-based Search Engine for Structured BiomedicalText J Am Med Inform Assoc. 2007 May-Jun;14(3):253-63. Epub 2007 Feb 28

  Abstract | pub2007019.pdf | PMID:  17329729 | PMCID:  PMC2244877

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• Jaeger S, Karargyris A, Candemir S, Folio L, Siegelman J, Callaghan FM, Xue Z, Palaniappan K, Singh RK, Antani SK, Thoma GR, Wang Y, Lu P, McDonald CJ. Automatic tuberculosis screening using chest radiographs. IEEE Trans Med Imaging. 2014 Feb;33(2):233-45. doi: 10.1109/TMI.2013.2284099. Epub 2013 Oct 1.

  Abstract | 2014_TMI_Automatic Tuberculosis.pdf | PMID:  24108713

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• Kayaalp M, Browne AC, Dodd ZA, Sagan P, McDonald CJ. An Easy-to-Use Clinical Text De-identification Tool for Clinical Scientists: NLM Scrubber [Poster]. Proceedings of the Annual American Medical Informatics Association Fall Symposium: 1522.

  Abstract

  Abstract
• Kilicoglu H. Dataset: Consumer Health Spelling Error Dataset

  Abstract | URL:  https://ceb.nlm.nih.gov/ridem/infobot_docs/CHQA_SpellCorrection_Dataset.zip

  AbstractExternal link
• 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.

  Abstract | pub9349.pdf

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• 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.

  Abstract | PMID:  26958208 | PMCID:  PMC4765565

  Abstract
• Kilicoglu H, Demner-Fushman D. Coreference Resolution for Structured Drug Product Labels Proceedings of BioNLP 2014. pp. 44-53.

  Abstract | pub8919.pdf

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• Kilicoglu H, Fiszman M, Demner-Fushman D. Interpreting Consumer Health Questions: The Role of Anaphora and Ellipsis. Proceedings of BioNLP 2013. Pages 54-62.

  Abstract | pub7057.pdf

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• Logan RA, Tse T. A Multidiscipline Conceptual Framework for Consumer Health Informatics Stud Health Technol Inform. 2007;129(Pt 2):1169-73

  Abstract | pub2007030.pdf | PMID:  17911899

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• Lu C, Payne A, Demner-Fushman D. Classification Types: A New Feature in the SPECIALIST Lexicon. AMIA Fall Symposium, 2019.

  Abstract | pub9987.pdf

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• Lu C, Aronson, AR, Shooshan SE, Demner-Fushman D. Spell checker for consumer language (CSpell). J Am Med Inform Assoc. 2019 Jan 21. doi: 10.1093/jamia/ocy171. [Epub ahead of print]

  Abstract | PMID:  30668712

  Abstract
• McCray AT, Gallagher ME. Principles for Digital Library Development Communications of the ACM. 2001 May; 44(5): 48-54.

  Abstract | pub2001017.pdf

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• McCray AT, Dorfman E, Ripple A, Ide NC, Jha M, Katz DG, Loane RF, Tse T. Usability Issues in Developing a Web-Based Consumer Health Site Proc AMIA Symp. 2000:556-60.

  Abstract | pub2000022.pdf | PMID:  11079945 | PMCID:  PMC2244083

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• McCray AT. Better access to information about clinical trials. Ann Intern Med. 2000 Oct 17;133(8):609-14.

  Abstract | pub2000020.pdf | PMID:  11033590

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• McCray AT, Ide NC. Design and implementation of a national clinical trials registry. J Am Med Inform Assoc. 2000 May-Jun;7(3):313-23.

  Abstract | pub2000019.pdf | PMID:  10833169 | PMCID:  PMC61435

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• McCray AT, Gallagher ME, Flannick MA. Extending the role of metadata in a digital library system. In: Proceedings of the IEEE Forum on Research and Technology Advances in Digital Libraries, pp. 190-9, 1999.

  Abstract | A1999001.pdf

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• Mitchell JA, Fomous C, Fun J. Challenges and strategies of the Genetics Home Reference J Med Libr Assoc. 2006 Jul;94(3):336-42

  Abstract | pub2006026.pdf | PMID:  16888669 | PMCID:  PMC1525308

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• Morrison SM, Cheh M, Calvo SC, Collins H, Fun J, Greenberg K, Forman-Neall L. Genetics Home Reference, Ten Years In: Where We Are Now [Poster]. American Society of Human Genetics, November 9, 2012, San Francisco, CA.

  Abstract

  Abstract
• Morrison SM. Web Interface: Genetics Home Reference

  Abstract

  Abstract
• 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

  Abstract | URL:  https://doi.org/10.18653/v1/P17-1071

  AbstractExternal link
• 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.

  Abstract

  Abstract
• Mrabet Y, Kilicoglu H, Demner-Fushman D. Unsupervised Ranking of Knowledge Bases for Named Entity Recognition. ECAI 2016, The Hague, The Netherlands, 1248-1255.

  Abstract

  Abstract
• Ripple AM, Mork JG, Humphreys BL, Knecht LS. A retrospective cohort study of structured abstracts in MEDLINE, 1992-2006. J Med Libr Assoc. 2011 Apr;99(2):160-3. doi: 10.3163/1536-5050.99.2.009.

  Abstract | PMID:  21464855 | PMCID:  PMC3066587

  Abstract
• Ripple AM, Tse T, Zarin D. ClinicalTrials.gov scope expanded NLM Tech Bull. 2005 Jul-Aug;(345):e6.

  Abstract | URL:  http://www.nlm.nih.gov/pubs/techbull/ja05/ja05_clinical_trials.html

  AbstractExternal link
• Roberts K, Masterton K, Kilicoglu H, Fiszman M, Demner-Fushman D. Annotating Question Decomposition on Complex Medical Questions. LREC 2014.

  Abstract | pub7076.pdf

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