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  • Mork JG, Aronson A, Demner-Fushman D. 12 years on - Is the NLM medical text indexer still useful and relevant? J Biomed Semantics. 2017 Feb 23;8(1):8. doi: 10.1186/s13326-017-0113-5.
  • Leroy G, Miller T, Rosemblat G, Browne A. A Balanced Approach to Health Information Evaluation: A Vocabulary-based Naive Bayes Classifier and Readability Formulas JASIST, 59(9):1409-1419, 2008
  • Jimeno-Yepes A, Wilkowski B, Mork J, van Lenten E, Demner-Fushman D, Aronson AR. A bottom-up approach to MEDLINE indexing recommendations. AMIA Annu Symp Proc. 2011;2011:1583-92. Epub 2011 Oct 22.
  • Miller CM, Rindflesch TC, Fiszman M, Hristovski D, Shin D, Rosemblat G, Zhang H, Strohl KP. A closed literature-based discovery technique finds a mechanistic link between hypogonadism and diminished sleep quality in aging men. Sleep. 2012 Feb 1;35(2):279-85. doi: 10.5665/sleep.1640.
  • Kilicoglu H, Rosemblat G, Cairelli M, Rindflesch TC. A Compositional Interpretation of Biomedical Event Factuality. Proc of the Second Workshop on Extra-Propositional Aspects of Meaning in Computational Semantics (ExProM 2015).
  • Sharp M, Bodenreider O, Wacholder N. A Framework for Characterizing Drug Information Sources AMIA Annu Symp Proc. 2008 Nov 6:662-6
  • Fiszman M, Shin D, Sneiderman CA, Jin H, Rindflesch TC. A Knowledge Intensive Approach to Mapping Clinical Narrative to LOINC. AMIA Annu Symp Proc. 2010 Nov 13;2010:227-31.
  • Workman TE, Rosemblat G, Fiszman M, Rindflesch TC. A literature-based assessment of concept pairs as a measure of semantic relatedness. AMIA Annu Symp Proc. 2013 Nov 16;2013:1512-21. eCollection 2013.
  • Lu C, Humphrey SM, Browne AC. A method for verifying a vector-based text classification system AMIA Annu Symp Proc. 2008 Nov 6:1030.
  • Rosemblat G, Shin D, Kilicoglu H, Sneiderman C, Rindflesch TC. A methodology for extending domain coverage in SemRep. J Biomed Inform. 2013 Dec;46(6):1099-107. doi: 10.1016/j.jbi.2013.08.005. Epub 2013 Aug 21.
  • Bashyam V, Divita G, Bennett DB, Browne AC, Taira RK. A normalized lexical lookup approach to identifying UMLS concepts in free text. Stud Health Technol Inform. 2007;129(Pt 1):545-9.
  • Jimeno-Yepes A, Mork J, Demner-Fushman D, Aronson AR. A one-size-fits-all indexing method does not exist: automatic selection based on meta-learning. JCSE, vol. 6, no. 2, pp.151-160, 2012.
  • Rosemblat G, Graham L. A Pragmatic Approach to Summary Extraction in Clinical Trials Proc HLT-NAACL 06, pages 124-125, New York City, June 2006
  • Névéol A, Shooshan SE, Humphrey SM, Mork JG, Aronson AR. A recent advance in the automatic indexing of the biomedical literature. J Biomed Inform. 2009 Oct;42(5):814-23. doi: 10.1016/j.jbi.2008.12.007. Epub 2008 Dec 30.
  • Osborne R, Aronson A, Cohen K. A repository of semantic types in the MIMIC II database clinical notes. BioNLP 2014. pp. 93-97.
  • Friedlin FJ, McDonald C. A Software Tool for Removing Patient Identifying Information from Clinical Documents J Am Med Inform Assoc. 2008 Sep-Oct;15(5):601-10. Epub 2008 Jun 25
  • Liu H, Aronson AR, Friedman C. A Study of Abbreviations in MEDLINE Abstracts AMIA Annu Symp. 2002 ;():464-8.
  • Leroy G, Rindflesch TC, Libbus B, Kilicoglu H, Chen H. A Syntactic Parser with Semantic Filtering for Biomedical Text. Proceedings of Pacific Symposium on Biocomputing.
  • Lu C, Tormey D, McCreedy L, Browne AC. A Systematic Approach for Automatically Generating Derivational Variants in Lexical Tools Based on the SPECIALIST Lexicon. IEEE IT Professional Magazine, May/June, 2012, p. 36-42.
  • Lu C, McCreedy L, Tormey D, Browne AC. A Systematic Approach for Automatically Generating Derivational Variants in Lexical Tools Based on theSPECIALIST Lexicon IEEE IT Professional Magazine, May/June, 2012;36-42.
  • Harpaz R, Odgers D, Gaskin G, DuMouchel W, Winnenburg R, Bodenreider O, Ripple AM, Szarfman A, Sorbello A, Horvitz E, White RW, Shah NH. A time-indexed reference standard of adverse drug reactions. Sci Data. 2014 Nov 11;1:140043. doi: 10.1038/sdata.2014.43.
  • Fiszman M, Rindflesch TC, Kilicoglu H. Abstraction Summarization for Managing the Biomedical Research Literature Proceedings of the HLT-NAACL Workshop on Computational Lexical Semantics. 2004;:76-83.
  • Keselman A, Rosemblat G, Kilicoglu H, Fiszman M, Jin H, Shin D, Rindflesch TC. Adapting Semantic Natural Language Processing Technology to Address Information Overload in Influenza Epidemic Management Journal of the American Society for Information Science and Technology (JASIST), 61(12):2531-2543, 2010
  • Resnick MP, Ripple AM, Auston I, Rindflesch TC. An Ontology for Public Health to Support Enhanced Information Retrieval AMIA Annu Symp Proc. 2010
  • Sahoo SS, Bodenreider O, Rutter JL, Skinner KJ, Sheth AP. An Ontology-driven Semantic Mash-up of Gene and Biological pathway information: Application to the domain of nicotine dependence J Biomed Inform. 2008 Oct;41(5):752-65. Epub 2008 Feb 29
  • Aronson AR, Lang FM. An overview of MetaMap: historical perspective and recent advances. J Am Med Inform Assoc. 2010 May-Jun;17(3):229-36. doi: 10.1136/jamia.2009.002733.
  • Aronson AR. API: Semantic Knowledge Representation
  • Kim GR, Aronson AR, Mork JG, Cohen BA, Lehmann CU. Application of a Medical Text Indexer to an Online Dermatology Atlas. MedInfo. 2004 Sept.;2004.
  • Hanauer DA, Saeed M, Zheng K, Mei Q, Shedden K, Aronson AR, Ramakrishnan N. Applying MetaMap to Medline for identifying novel associations in a large clinical dataset: a feasibility analysis. J Am Med Inform Assoc. 2014 Sep-Oct;21(5):925-37. doi: 10.1136/amiajnl-2014-002767. Epub 2014 Jun 13.
  • Rindflesch TC, Bean CA, Sneiderman CA. Argument Identification for Arterial Branching Predications Asserted in Cardiac Catheterization Reports Proc AMIA Symp. 2000:704-8.
  • Masseroli M, Kilicoglu H, Lang F-M, Rindflesch TC. Argument-predicate Distance as a Filter for Enhancing Precision in Extracting Predications on the Genetic Etiology of Disease. BMC Bioinformatics. 2006 Jun 8;7:291.
  • Ruch P, Tbahriti I, Bobeill J, Aronson AR. Argumentative Feedback: A Linguistically-motivated Term Expansion for Information Retrieval Proc COLING/ACL 2006, 675-82
  • Kilicoglu H, Fiszman M, Rosemblat G, Marimpietri S, Rindflesch TC. Arguments of Nominals in Semantic Interpretation of Biomedical Text BioNLM Workshop Proc, Assoc. for Computational Linguistics 2010
  • Keselman A, Tse T, Crowell J, Browne AC, Ngo L, Zeng Q. Assessing Consumer Health Vocabulary Familiarity: An Exploratory Study J Med Internet Res. 2007 Mar 14;9(1):e5
  • Kilicoglu H, Rosemblat G, Rindflesch TC. Assigning factuality values to semantic relations extracted from biomedical research literature. PLoS One. 2017 Jul 5;12(7):e0179926. doi: 10.1371/journal.pone.0179926. eCollection 2017.
  • Jimeno-Yepes A, Mork J, Demner-Fushman D, Aronson AR. Automatic algorithm selection for MeSH Heading indexing based on meta-learning. International Symposium on Languages in Biology and Medicine, Singapore, December, 2011.
  • Bangalore AK, Divita G, Humphrey SM, Browne AC, Thorn KE. Automatic Categorization of Google Search Results for Medical Queries using JDI Medinfo 2007: Proc. of the 11th World Congress on Health (Medical) Informatics
  • Zhang M, Del Fiol G, Grout RW, Jonnalagadda S, Medlin R, Mishra R, Weir C, Liu H, Mostafa J, Fiszman M. Automatic identification of comparative effectiveness research from medline citations to support clinicians' treatment information needs. Stud Health Technol Inform. 2013;192:846-50.
  • Humphrey SM, Rindflesch TC, Aronson AR. Automatic Indexing by Discipline and High-Level Categories: Methodology and Potential Applications Advances in classification research. Proc. of the 11th ASIST SIG/CR Classification Research Workshop. 2001.
  • Névéol A, Mork JG, Aronson AR. Automatic indexing of specialized documents: using generic vs. domain-specific document representations. Proc 2007 Workshop BioNL'07, 183-92.
  • Humphrey S, Rindflesch TC, Aronson AR. Automatic Journal Descriptor Indexing Extended to Indexing by UMLS Semantic Type Using the Cosine Document Similarity Measure. Proc. of the 11th SIG/CR Classification Research Workshop. 2000;103-16.
  • Kim W, Aronson AR, Wilbur WJ. Automatic MeSH Term Assignment and Quality Assessment Proc AMIA Symp. 2001:319-23.
  • Kilicoglu H, Rosemblat G, Malicki M, Ter Riet G. Automatic recognition of self-acknowledged limitations in clinical research literature. J Am Med Inform Assoc. 2018 Jul 1;25(7):855-861. doi: 10.1093/jamia/ocy038.
  • Fiszman M, Demner-Fushman D, Kilicoglu H, Rindflesch TC. Automatic summarization of MEDLINE citations for evidence-based medical treatment: a topic-oriented evaluation. J Biomed Inform. 2009 Oct;42(5):801-13. doi: 10.1016/j.jbi.2008.10.002. Epub 2008 Nov 5.
  • Roberts K, Kilicoglu H, Fiszman M, Demner-Fushman D. Automatically classifying question types for consumer health questions. AMIA Annu Symp Proc. 2014 Nov 14;2014:1018-27. eCollection 2014.
  • Mishra R, Del Fiol G, Kilicoglu H, Jonnalagadda S, Fiszman M. Automatically extracting clinically useful sentences from UpToDate to support clinicians' information needs. AMIA Annu Symp Proc. 2013 Nov 16;2013:987-92. eCollection 2013.
  • Jonnalagadda SR, Del Fiol G, Medlin R, Weir C, Fiszman M, Mostafa J, Liu H. Automatically extracting sentences from Medline citations to support clinicians' information needs. J Am Med Inform Assoc. 2013 Sep-Oct;20(5):995-1000. doi: 10.1136/amiajnl-2012-001347. Epub 2012 Oct 25.
  • Kayaalp M. Bayesian Methods for Diagnosing Physiological Conditions of Human Subjects from Multivariate Time Series Biosensor Data Physiological Data Modeling Contest, the Twenty-First International Conference on Machine Learning (ICML), 2004 July.
  • Névéol A, Zeng K, Bodenreider O. Besides precision & recall: exploring alternative approaches to evaluating an automatic indexing tool for MEDLINE. AMIA Annu Symp Proc. 2006:589-93.
  • Kim H, Goryachev S, Rosemblat G, Browne A, Keselman A, Zeng-Treitler Q. Beyond Surface Characteristics: A New Health Text-specific Readability Measurement AMIA Annu Symp Proc. 2007 Oct 11:418-22
  • Zweigenbaum P, Demner-Fushman D. Bioinformatics: Tools and Applications. Springer 2009.
  • He Y, Kayaalp M. Biological Entity Recognition with Conditional Random Fields AMIA Annu Symp Proc. 2008 Nov 6:293-7
  • Hristovski D, Dinevski D, Kastrin A, Rindflesch TC. Biomedical question answering using semantic relations. BMC Bioinformatics. 2015 Jan 16;16:6. doi: 10.1186/s12859-014-0365-3.
  • Kilicoglu H. Biomedical text mining for research rigor and integrity: tasks, challenges, directions. Brief Bioinform. 2017 Jun 13. doi: 10.1093/bib/bbx057.
  • Simpson MS, Demner-Fushman D. Biomedical Text Mining: A Survey of Recent Progress. In Charu C. Aggarwal and ChengXiang Zhai, Editors. Mining Text Data. (Springer) 2011.
  • Workman TE, Fiszman M, Hurdle JF, Rindflesch TC. Biomedical text summarization to support genetic database curation: using Semantic MEDLINE to create a secondary database of genetic information. J Med Libr Assoc. 2010 Oct;98(4):273-81. doi: 10.3163/1536-5050.98.4.003.
  • Divita G, Rosemblat G, Browne AC. Building a medical Spanish lexicon. AMIA Annu Symp Proc. 2007 Oct 11:941.
  • Zeng-Treitler Q, Kim H, Rosemblat G, Kesselman A. Can multilingual machine translation help make medical record content more comprehensible to patients? Stud Health Technol Inform. 2010;160(Pt 1):73-7.
  • Morid MA, Fiszman M, Raja K, Jonnalagadda SR, Del Fiol G. Classification of clinically useful sentences in clinical evidence resources. J Biomed Inform. 2016 Apr;60:14-22. doi: 10.1016/j.jbi.2016.01.003. Epub 2016 Jan 13.
  • Logan RA. Clinical, Classroom or Personal Education: Attitudes About Health Literacy J Med Libr Assoc. 2007 Apr;95(2):127-37, e48
  • Liu F, Fontelo P, Fiszman M. Clinically-Weighted Terms in the Evaluation of MeSH Translations: BabelMeSH in Portuguese as a Model. AMIA Annu Symp Proc; 2008 Nov 8-12; Washington DC. p. 1027.
  • Zhang, H, Fiszman M, Shin D, Wilkowski B, Rindflesch TC. Clustering cliques for graph-based summarization of the biomedical research literature. BMC Bioinformatics 14:182.
  • Jimeno-Yepes A, McInnes BT, Aronson AR. Collocation analysis for UMLS knowledge-based word sense disambiguation. BMC Bioinformatics. 2011 Jun 9;12 Suppl 3:S4. doi: 10.1186/1471-2105-12-S3-S4.
  • Fung KW, Bodenreider O, Aronson AR, Hole WT, Srinivasan S. Combining Lexical and Semantic Methods of Inter-terminology Mapping Using the UMLS. Stud Health Technol Inform. 2007;129(Pt 1):605-9.
  • Yepes AJ, Prieur-Gaston E, Névéol A. Combining MEDLINE and publisher data to create parallel corpora for the automatic translation of biomedical text. BMC Bioinformatics. 2013 Apr 30;14:146. doi: 10.1186/1471-2105-14-146.
  • 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.
  • Demner-Fushman D, Humphrey SM, Ide NC, Loane RF, Mork J, Ruch P, Ruiz ME, Smith LH, Wilbur WJ, Aronson AR. Combining Resources to Find Answers to Biomedical Questions Proc TREC 2007, 205-14
  • Hristovski D, Kastrin A, Peterlin B, Rindflesch TC. Combining Semantic Relations and DNA Microarray Data for Novel Hypotheses Generation Lecture Notes in Bioinformatics. Springer
  • Névéol A, Mork JG, Aronson AR. Comment on 'MeSH-up: effective MeSH text classification for improved document retrieval'. Bioinformatics. 2009 Oct 15;25(20):2770-1; author reply 2772. doi: 10.1093/bioinformatics/btp483. Epub 2009 Aug 11.
  • Pathak J, Peters L, Chute CG, Bodenreider O. Comparing and evaluating terminology services application programming interfaces: RxNav, UMLSKS and LexBIG. J Am Med Inform Assoc. 2010 Nov-Dec;17(6):714-9. doi: 10.1136/jamia.2009.001149.
  • Mortensen J, Bodenreider O. Comparing Pharmacologic Classes in NDF-RT and SNOMED CT. Proc SMBM 2010:119-124.
  • Yepes AJ, Mork JG, Demner-Fushman D, Aronson AR. Comparison and combination of several MeSH indexing approaches. AMIA Annu Symp Proc. 2013 Nov 16;2013:709-18. eCollection 2013.
  • Kilicoglu H, Rosemblat G, Fiszman M, Rindflesch TC. Constructing a semantic predication gold standard from the biomedical literature. BMC Bioinformatics. 2011 Dec 20;12:486. doi: 10.1186/1471-2105-12-486.
  • Cameron D, Kavuluru R, Rindflesch TC, Sheth AP, Thirunarayan K, Bodenreider O. Context-driven automatic subgraph creation for literature-based discovery. J Biomed Inform. 2015 Apr;54:141-57. doi: 10.1016/j.jbi.2015.01.014. Epub 2015 Feb 7.
  • Lu C, Browne AC. Converting Unicode Lexicon and Lexical Tools for ASII NLP Applications AMIA Annu Symp Proc 2011:1870.
  • Richesson RL, Fung K, Bodenreider O. Coverage of rare disease names in cinical coding systems and ontologies and implications for electronic health records-based research [Poster]. Proc 5th Int'l Conf Conference on Biomedical Ontology.
  • Khatipov E, Madden M, Chiang P, Chuang P, Nguyen D, D'Souza I, Winnenburg R, Bodenreider O, Skapik J, McClure R, Emrick S. Creating, maintaining and publishing value sets in the VSAC [Poster]. AMIA Annu Symp Proc, 2014: p. 1459.
  • Rosemblat G, Graham L. Cross-Language Search in a Monolingual Health Information System: Flexible Designs and Lexical Processes Proc ISKO, pages 173-182, Vienna, Austria, July 2006.
  • Kilicoglu H. Dataset: Sortal Anaphora Dataset
  • Kayaalp M, Browne AC, Dodd Z, Sagan P, McDonald CJ. De-identification of Address, Date, and Alphanumeric Identifiers in Narrative Clinical Reports. AMIA Annu Symp Proc. 2014 Nov 14;2014:767-76. eCollection 2014.
  • Zhang H, Fiszman M, Shin D, Miller CM, Rosemblat G, Rindflesch TC. Degree centrality for semantic abstraction summarization of therapeutic studies. J Biomed Inform. 2011 Oct;44(5):830-8. doi: 10.1016/j.jbi.2011.05.001. Epub 2011 May 8.
  • Winnenburg R, Bodenreider O. Desiderata for an authoritative representation of MeSH in RDF. AMIA Annu Symp Proc 2014:1218-1227.
  • Bodenreider O, Burgun A. Desiderata for an Ontology of Diseases for the Annotation of Biological Datasets Proc ICBO 2009:39-42
  • Bernhardt PJ, Humphrey SM, Rindflesch TC. Determining Prominent Subdomains in Medicine. AMIA Annu Symp Proc. 2005:46-50.
  • Weeber M, Mork JG, Aronson AR. Developing a Test Collection for Biomedical Word Sense Disambiguation Proc AMIA Symp. 2001:746-50.
  • Lu C, Humphrey SM, Rogers W, Browne AC. Development of a semantic type based WSD tool [Abstract]. AMIA Annu Symp Proc 2009:943.
  • Slaughter LA, Rindflesch TC. Development of a Test Collection of Manually Extracted Semantic Relationships in Health Consumer Texts MedInfo. 2004 Sept.;2004: 1865.
  • Lu C, Browne AC. Development of Sub-Term Mapping Tools (STMT) AMIA 2012 Annual Symposium, Chicago, IL, November 3-7, 2012
  • Lu C, Browne AC. Development of sub-term mapping tools (STMT) [Poster]. AMIA 2012 Annual Symposium, Chicago, IL, November 3-7, 2012, p. 1845 (AMIA, 2012 Distinguished Poster Award) Poster.
  • Lu C, Divita G, Browne AC. Development of Visual Tagging Tool AMIA Annu Symp Proc 2010:1156.
  • Workman E, Weir, C, Rindflesch TC. Differentiating Sense through Semantic Interaction Data. AMIA Annu Symp Proc. 2017 Feb 10;2016:1238-1247. eCollection 2016.
  • Sarkar IN, Rindflesch TC. Discovering Protein Similarity Using Natural Language Processing Proc AMIA Symp. 2002:677-81.
  • Divita G, Browne AC, Loanne R. dTagger: A POS Tagger AMIA Annu Symp Proc. 2006:200-3
  • Rindflesch TC, Tanabe L, Weinstein JN, Hunter L. EDGAR: extraction of drugs, genes and relations from the biomedical literature. Pac Symp Biocomput. 2000:517-28.
  • Aronson AR. Effective Mapping of Biomedical Text to the UMLS Metathesaurus: The MetaMap Program Proc AMIA Symp. 2001:17-21.
  • Leroy G, Rindflesch TC. Effects of Information and Machine Learning Algorithms on Word Sense Disambiguation with Small Datasets Int J Med Inform. 2005 Aug;74(7-8):573-85
  • Lu C, Tormey D, McCreedy L, Browne AC. Enhanced LexSynonym Acquisition for Effective UMLS Concept Mapping. Stud Health Technol Inform. 2017;245:501-505.
  • 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
  • Névéol A, Mork JG, Aronson AR, Darmoni SJ. Evaluation of French and English MeSH indexing systems with a parallel corpus. AMIA Annu Symp Proc. 2005:565-9.
  • Cohen T, Widdows D, Rindflesch TC. Expansion-by-analogy: A vector symbolic approach to semantic search. AAAI-Fall 2014 Symposium on Quantum Informatics for Cognitive, Social, and Semantic Processes.
  • 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. eCollection 2014.
  • Jimeno-Yepes A, McInnes BT, Aronson AR. Exploiting MeSH indexing in MEDLINE to generate a data set for word sense disambiguation. BMC Bioinformatics. 2011 Jun 2;12:223. doi: 10.1186/1471-2105-12-223.
  • Hristovski D, Friedman C, Rindflesch TC. Exploiting Semantic Relations for Literature-Based Discovery AMIA Annu Symp Proc. 2006:349-53
  • Srinivasan P, Rindflesch T. Exploring Text Mining from MEDLINE Proc AMIA Symp. 2002:722-6.
  • Kang YS, Kayaalp M. Extracting laboratory test information from biomedical text. J Pathol Inform. 2013 Aug 31;4:23. doi: 10.4103/2153-3539.117450. eCollection 2013.
  • Rindflesch TC, Rajan J, Hunter L. Extracting Molecular Binding Relationships from Biomedical Text Proc. of the 6th Applied Natural Language Processing Conference. 2000;: 188-95.
  • Mork JG, Bodenreider O, Demner-Fushman D, Dogan RI, Lang FM, Lu Z, Névéol A, Peters L, Shooshan SE, Aronson AR. Extracting Rx information from clinical narrative. J Am Med Inform Assoc. 2010 Sep-Oct;17(5):536-9. doi: 10.1136/jamia.2010.003970.
  • Ahlers C, Fiszman M, Demner-Fushman D, Lang F, Rindflesch TC. Extracting Semantic Predications from MEDLINE Citations for Pharmacogenomics Pacific Symposium on Biocomputing 2007 12:209-220
  • Weeber M, Vos R. Extracting the Lowest-Frequency Words: Pitfalls and Possibilities Computational Linguistics. 2000;26(3):301-17.
  • Rosemblat G, Graham L, Tse T. Extractive Summarization in Clinical Trials Protocol Summaries: A Case Study Proc IICAI-2007, pp. 1824-1837
  • Jimeno Yepes AJ, Plaza L, Carrillo-de-Albornoz J, Mork JG, Aronson A. Feature engineering for MEDLINE citation categorization with MeSH. BMC Bioinformatics. 2015 Apr 8;16:113. doi: 10.1186/s12859-015-0539-7.
  • Srinivasan S, Rindflesch TC, Hole WT, Aronson AR, Mork JG. Finding UMLS Metathesaurus Concepts in MEDLINE. Proc AMIA Symp. 2002:727-31.
  • Névéol A, Shooshan SE, Mork JG, Aronson AR. Fine-grained indexing of the biomedical literature: MeSH subheading attachment for a MEDLINE indexing tool. AMIA Annu Symp Proc. 2007 Oct 11:553-7.
  • Workman TE, Fiszman M, Rindflesch TC, Nahl D. Framing Serendipitous Information Seeking Behavior for Facilitating Literature-Based Discovery: A Proposed Model. Journal of the American Society for Information Science and Technology 2013, in press.
  • Sahoo SS, Zeng K, Bodenreider O, Sheth A. From 'Glycosyltransferase' to 'Congenital Muscular Dystrophy': Integrating Knowledge from NCBI Entrez Gene and the Gene Ontology Stud Health Technol Inform. 2007;129(Pt 2):1260-4
  • Aronson AR, Bodenreider O, Demner-Fushman D, Fung KW, Lee VK, Mork JG, Névéol A, Peters L, Rogers WJ. From indexing the biomedical literature to coding clinical text: experience with MTI and machine learning approaches. Proc 2007 Workshop BioNL'07, June 2007, pp. 105-112, Prague, Czech Republic.
  • Aronson AR, Demner-Fushman D, Humphrey SM, Lin J, Liu H, Ruch P, Ruiz ME, Smith LH, Tanabe LK, Wilbur WJ. Fusion of Knowledge-intensive and Statistical Approaches for Retrieving and Annotating Textual Genomics Documents Proc TREC 2005, 36-45
  • Mitchell JA, Aronson AR, Mork JG, Folk LC, Humphrey SM, Ward JM. Gene Indexing: Characterization and Analysis of NLM's GeneRIFs. AMIA Annu Symp Proc. 2003:460-4.
  • 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.
  • Weeber M, Vos R, Klein H, De Jong-Van Den Berg LT, Aronson AR, Molema G. Generating Hypotheses by Discovering Implicit Associations in the Literature: A Case Report of a Search for New Potential Therapeutic Uses for Thalidomide J Am Med Inform Assoc. 2003 May-Jun;10(3):252-9. Epub 2003 Jan 28.
  • Lu C, Tormey D, McDreedy L, Browne AC. Generating SD-Rules in the SPECISLIST Lexical Tools - Optimization for suffix derivation rule set [Poster]. BIOSTEC 2016), Vol(5): HEALTHINF, Rome, Italy, February 21-23, 2016, p. 353-358 (9th International Conference on Health Informatics, HEALTHINF/BIOSTEC, 2016 Best Poster Award
  • Lu C, Tormey D, MCreedy L, Browne AC. Generating the MEDLINE N-Gram Set [Poster]. AMIA 2015 Annual Symposium, San Francisco, CA, November 14-18, 2015, p. 1569.
  • Jimeno-Yepes AJ, Sticco JC, Mork JG, Aronson AR. GeneRIF indexing: sentence selection based on machine learning. BMC Bioinformatics. 2013 May 31;14:171. doi: 10.1186/1471-2105-14-171.
  • Wilkowski B, Fiszman M, Miller CM, Hristovski D, Arabandi S, Rosemblat G, Rindflesch TC. Graph-based methods for discovery browsing with semantic predications. AMIA Annu Symp Proc. 2011;2011:1514-23. Epub 2011 Oct 22.
  • Cairelli M, Rindflesch TC. Hierarchical Summarization of Concepts for Visual Discovery Browsing - a Pilot Study [abstract and demo]. Procedings of the IEEE VisWeek Workshop on Visual Analytics in Healthcare, October 23, 2011, Providence, RI, 37-40.
  • Logan RA, Park J, Shin JH. How Two Korean Newspapers Covered a Public Health Crisis Science Communication. 25:4:365-389 (June 2004)
  • Kayaalp M. ICU Outcome Predictions using Physiologic Trends in the First Two Days. Computing in Cardiology (39)977–980.
  • Bernhardt PJ, Rindflesch TC, Kilicoglu H, Tringali M. Identifying Anatomical Concepts in Biomedical Text for Automatic Selection of Images Medinfo. 2004 Sept.;2004: 1521.
  • Zhang S, Bodenreider O. Identifying Mismatches in Alignments of Large Anatomical Ontologies AMIA Annu Symp Proc. 2007 Oct 11:851-5
  • Shang N, Xu H, Rindflesch TC, Cohen T. Identifying plausible adverse drug reactions using knowledge extracted from the literature. J Biomed Inform. 2014 Dec;52:293-310. doi: 10.1016/j.jbi.2014.07.011. Epub 2014 Jul 19.
  • Cairelli M, Rindflesch TC. Identifying Potential Biomarkers for Mild Traumatic Brain Injury by Mining Semantic Relations from MEDLINE Citations [Poster[. 2011 Trauma Spectrum Conference, Bethesda, MD, December 9, 2011.
  • Jimeno Yepes AJ, Mork JG, Aronson A. Identifying Publication Types Using Machine Learning. BioASQ Workshop 2013.
  • Chapman WW, Fiszman M, Dowling JN, Chapman BE, Rindflesch TC. Identifying Respiratory Findings in Emergency Department Reports for Biosurveillance using MetaMap Medinfo. 2004 Sept.;2004: 487-491.
  • Fiszman M, Rosemblat G, AhlersCB, Rindflesch TC. Identifying Risk Factors for Metabolic Syndrome in Biomedical Text AMIA Annu Symp Proc. 2007 Oct 11:249-53
  • Lu C, Tormey D, McDreedy L, Browne AC. Implementing comprehensive derivational features in Llexical tools using a systematical approach [Poster]. AMIA 2013 Annual Symposium, Washington, DC, November 16-20, 2013, p. 904
  • Jimeno-Yepes A, Aronson AR. Improving an automatically extracted corpus for UMLS Metathesaurus word sense disambiguation. BioSEPLN 2010, Sept. 2010.
  • 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.
  • Kilicoglu H. Inferring Implicit Causal Relationships in Biomedical Literature. Proc 15th Workshop on Biomedical Natural Language Processing. Pages 46-55. 2016.
  • Rindflesch TC, Blake CL, Fiszman M, Kilicoglu H, Rosemblat G, Schneider J, Zeiss CJ. Informatics Support for Basic Research in Biomedicine. ILAR J. 2017 Jul 1;58(1):80-89. doi: 10.1093/ilar/ilx004.
  • Fiszman M, Rindflesch TC, Kilicoglu H. Integrating a Hypernymic Proposition Interpreter into a Semantic Processor for Biomedical Texts AMIA Annu Symp Proc. 2003:239-43.
  • Maver A, Hristovski D, Rindflesch TC, Peterlin B. Integration of data from omic studies with the literature-based discovery towards identification of novel treatments for neovascularization in diabetic retinopathy. Biomed Res Int. 2013;2013:848952. doi: 10.1155/2013/848952. Epub 2013 Nov 24.
  • He Y, Kayaalp M. Interpretation of Data and Identification of Information are Sine Qua Non for Modern Digital Information Services AMIA Annu Symp Proc. 2006:946
  • Fiszman M, Demner-Fushman D, Lang FM, Goetz P, Rindflesch TC. Interpreting Comparative Constructons in Biomedical Text Proc 2007 Workshop BioNL'07, June 2007, pp. 137-144, Prague, Czech Republic
  • Fiszman M, Rindflesch TC, Kilicoglu H. Interpreting Hypernymic Propositions in an Online Medical Encyclopedia AMIA Annu Symp Proc. 2003:840.
  • Burgun A, Bodenreider O. Issues in Integrating Epidemiology and Research Information in Oncology: Experience with ICD-O3 and the NCI Thesaurus AMIA Annu Symp Proc. 2007 Oct 11:85-9
  • Humphrey SM, Lu C, Rogers W, Browne AC. Journal descriptor indexing tool for categorizing text according to discipline or semantic type. AMIA Annu Symp Proc. 2006:960.
  • Jimeno-Yepes A, Aronson AR. Knowledge-based and knowledge-lean methods combined in unsupervised word sense disambiguation. Proc 2nd ACM SIGHIT International Health Informatics (IHI) Symposium 2012, 733-736.
  • Jimeno-Yepes A, Aronson AR. Knowledge-based biomedical word sense disambiguation: comparison of approaches. BMC Bioinformatics. 2010 Nov 22;11:569. doi: 10.1186/1471-2105-11-569.
  • Sneiderman CA, Demner-Fushman D, Fiszman M, Ide NC, Rindflesch TC. Knowledge-Based Methods to Help Clinicians Find Answers in MEDLINE. J Am Med Inform Assoc. 2007 Nov-Dec;14(6):772-80. Epub 2007 Aug 21.
  • Aronson AR, Demner-Fushman D, Humphrey SM, Ide NC, Kim W, Liu H, Loane RF, Mork JG, Smith LH, Tanabe LK, Wilbur WJ, Xie N. Knowledge-intensive and statistical approaches to the retrieval and annotation of genomics MEDLINE citations. The Thirteenth Text Retrieval Conference (TREC 2004). 2004:503-11.
  • Browne AC, Divita Guy, Aronson AR, McCray AT. Language and Vocabulary Tools AMIA Annu Symp Proc. 2003:798.
  • Zhang S, Bodenreider O. Law and Order: Assessing and Enforcing Compliance with Ontological Modeling Principles in the Foundational Model of Anatomy Comput Biol Med. 2006 Jul-Aug;36(7-8):674-93. Epub 2005 Sep 6.
  • Zhang S, Mork P, Bodenreider O. Lessons Learned from Aligning two Representations of Anatomy Proc of the First International Workshop on Formal Biomedical Knowledge Representation (KR-MED 2004); 2004. p. 102-108.
  • Zhang S, Bodenreider O. Lessons Learned from Cross-Validating Alignments Between Large Anatomical Ontologies Stud Health Technol Inform. 2007;129(Pt 1):822-6
  • Hurdle JF, Botkin J, Rindflesch TC. Leveraging Semantic Knowledge in IRB Databases to Improve Translation Science AMIA Annu Symp Proc. 2007 Oct 11:349-53
  • Blake C, Rindflesch TC. Leveraging syntax to better capture the semantics of elliptical coordinated compound noun phrases. J Biomed Inform. 2017 Aug;72:120-131. doi: 10.1016/j.jbi.2017.07.001. Epub 2017 Jul 4.
  • Kastrin A, Rindflesch TC, Hristovski D. Link prediction in a MeSH co-occurrence network: preliminary results. Stud Health Technol Inform. 2014;205:579-83.
  • Kastrin A, Rindflesch TC, Hristovski D. Link prediction on a network of co-occurring MeSH terms: Towards literature-based discovery. Methods of Information in Medicine 55(4):340-6.
  • Kastrin A, Rindflesch TC, Hristovski D. Link prediction on the Semantic MEDLINE Network. Proceedings of the 17th International conference on Discovery Science.
  • Cohen T, Widdows D, Schvaneveldt RW, Rindflesch TC. Logical Leaps and Quantum Connectives: Forging Paths through Predication Space AAAI-Fall 2010 Symposium on Quantum Informatics for Cognitive, Social, and Semantic Processes
  • Zhang GQ, Zhu W, Sun M, Tao S, Bodenreider O, Cui L. MaPLE: A MapReduce Pipeline for Lattice-based Evaluation and Its Application to SNOMED CT. Proc IEEE Int Conf Big Data. 2014 Oct;2014:754-759.
  • Sneiderman C, Rosemblat G, Bray B, Fiszman M, Rindflesch TC. Matching Clinical Observations in Published Cardiology Case Reports to LOINC [Abstract]. AMIA Annu Symp Proc; 2009 Nov 14-18; San Francisco. p. 1036.
  • Balkanyi L, Schulz S, Cornet R, Bodenreider O. Medical concept representation: the years beyond 2000 [Poster]. Stud Health Technol Inform. 2013;192:1011.
  • Rindflesch TC, Pakhomov SV, Fiszman M, Kilicoglu H, Sanchez VR. Medical facts to support inferencing in natural language processing. AMIA Annu Symp Proc. 2005:634-8.
  • Jimeno-Yepes A, Mork JG, Wilkowski B, Demner-Fushman D, Aronson AR. MEDLINE MeSH indexing: lessons learned from machine learning and future directions. Proc IHI 2012, 737-742.
  • Smith L, Rindflesch TC, Wilbure WJ. MedPost: A Part of Speech Tagger for BioMedical Text Bioinformatics. 2004 Sep 22;20(14):2320-1. Epub 2004 Apr 8
  • Smith L, Rindflesch TC, Wilbure WJ. MedTag: A Collection of Biomedical Annotations Bioinformatics. 2004 Sep 22;20(14):2320-1.
  • Jimeno-Yepes AJ, Plaza L, Mork JG, Aronson AR, Díaz A. MeSH indexing based on automatically generated summaries. BMC Bioinformatics. 2013 Jun 26;14:208. doi: 10.1186/1471-2105-14-208.
  • Jimeno-Yepes A, Wilkowski B, Mork JG, Demner-Fushman D, Aronson AR. MeSH indexing: machine learning and lessons learned. ACM SIGHIT International Health Informatics Symposium, Miami, FL, USA, 2012.
  • Cho D, Mork JG, Aronson A, Demner-Fushman D, Schmidt S, Ozga D, Pash J, Kilbourne J. MeSH on demand: an easy way to identify relevant MeSH terms and related articles from text [Poster]. National Cancer Institute (NCI) Symposium "RNA Biology 2015".
  • Mork J, Peters L, Jimeno-Yepes A, Aronson AR, Bodenreider O. MetaMap in the CALBC Workshop II. CALBC Workshop II, March 2011.
  • Demner-Fushman D, Rogers W, Aronson A. MetaMap Lite: an evaluation of a new Java implementation of MetaMap. J Am Med Inform Assoc. 2017 Jul 1;24(4):841-844. doi: 10.1093/jamia/ocw177.
  • Bhupatiraju R, Fung K, Bodenreider O. MetaMapLite in Excel: Biomedical named-entity recognition for non-technical users. Stud Health Technol Inform (Proc Medinfo): 1252.
  • Aronson AR, Mork JG, Neveol A, Shooshan SE, Demner-Fushman D. Methodology for Creating UMLS Content Views Appropriate for Biomedical Natural Language Processing AMIA Annu Symp Proc. 2008 Nov 6:21-5
  • Kayaalp M, Aronson AR, Humphrey SM, Ide NC, Tanabe LK, Smith LH, Demner-Fushman D, Loane RF, Mork JG, Bodenreider O. Methods for accurate retrieval of MEDLINE citations in functional genomics. The Twelfth Text Retrieval Conference (TREC 2003). 2003:441-50.
  • Zhang R, Adam TJ, Simon G, Cairelli MJ, Rindflesch T, Pakhomov S, Melton GB. Mining Biomedical Literature to Explore Interactions between Cancer Drugs and Dietary Supplements. AMIA Jt Summits Transl Sci Proc. 2015 Mar 23;2015:69-73. eCollection 2015.
  • Demner-Fushman D, Mork JG, Aronson AR. Mining MEDLINE for problems associated with vitamin D. AMIA Annu Symp Proc. 2013 Nov 16;2013:300-8. eCollection 2013.
  • 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.
  • Kayaalp M. Modes of De-identification. AMIA Annu Symp Proc. 2018 Apr 16;2017:1044-1050. eCollection 2017.
  • Névéol A, Shooshan SE, Humphrey SM, Rindflesch TC, Aronson AR. Multiple approaches to fine-grained indexing of the biomedical literature. Pac Symp Biocomput. 2007:292-303.
  • Lu C, Tormey D, McDreedy L, Browne AC. Multiword frequency analysis based on MEDLINE N - gram set [Poster]. AMIA 2016 Annual Symposium, Chicago, IL, November 12-16, 2016.
  • Neveol A, Deserno TM, Darmoni SJ, Guld MO, Aronson AR. Natural Language Processing Versus Content-BasedImage Analysis for Medical Document Retrieval J Am Soc Inf Sci Technol. 2008 Sep 18;60(1):123-134
  • Friedman C, Rindflesch TC, Corn M. Natural language processing: state of the art and prospects for significant progress, a workshop sponsored by the National Library of Medicine. J Biomed Inform. 2013 Oct;46(5):765-73. doi: 10.1016/j.jbi.2013.06.004. Epub 2013 Jun 25.
  • Le T, Rance B, Bodenreider O. Network visualization of UMLS source vocabularies using semantic groups. AMIA Annu Symp Proc, 2013: p. 90
  • Cairelli MJ, Fiszman M, Zhang H, Rindflesch TC. Networks of neuroinjury semantic predications to identify biomarkers for mild traumatic brain injury. J Biomed Semantics. 2015 May 18;6:25. doi: 10.1186/s13326-015-0022-4. eCollection 2015.
  • Mork JG, Bodenreider O, Demner-Fushman D, Doagan RI, Lang F-M, Lu Z, Névéol A, Peters L, Shooshan SE, Aronson AR. NLM's I2B2 tool system description. Third i2b2 Workshop on Natural Language Processing Challenges for Clinical Records, November, San Francisco, 2009
  • Libbus B, Rindflesch TC. NLP-Based Information Extraction for Managing the Molecular Biology Literature Proc AMIA Symp. 2002:445-9.
  • Kayaalp M. Patient Privacy in the Era of Big Data. Balkan Med J. 2018 Jan 20;35(1):8-17. doi: 10.4274/balkanmedj.2017.0966. Epub 2017 Sep 13.
  • Ripple AM, Mork JG, Schmidt SC, Thomson H, Knecht LS. Performance Comparison of MEDLINE Structured Abstract to Unstructured Abstracts [Poster]. 2014 NIH Research Festival.
  • Huser, V, Kayaalp M, Dodd Z, Cimino J. Piloting a deceased subject integrated data repository and protecting privacy of relatives. AMIA Annu Symp Proc. 2014 Nov 14;2014:719-28. eCollection 2014.
  • Cohen T, Schvaneveldt R, Rindflesch TC. Predication-based semantic indexing: permutations as a means to encode predications in semantic space. AMIA Annu Symp Proc. 2009 Nov 14;2009:114-8.
  • Cohen T, Widdows D, Stephan C, Zinner R, Kim J, Rindflesch TC, Davies P. Predicting high-throughput screening results with scalable literature-based discovery methods. CPT Pharmacometrics Syst Pharmacol. 2014 Oct 8;3:e140. doi: 10.1038/psp.2014.37.
  • Logan RA, Shin JH, Park J. Prevailing Impressions of Social Actors in Korean News Coverage of a Public Health Crisis Science Communication. 25:4:399-418 (June 2004)
  • Jimeno-Yepes A, Aronson AR. Query expansion for UMLS Metathesaurus disambiguation based on automatic corpus extraction. ICMLA 2010, Dec 2010.
  • Wei W, Demner-Fushman D, Wang S, Jiang X, Ohno-Machado L. Ranking Medical Subject Headings using a factor graph model. AMIA Jt Summits Transl Sci Proc. 2015 Mar 23;2015:56-63. eCollection 2015.
  • Mork JG, Demner-Fushman D, Schmidt SC, Aronson A. Recent Enhancements to the NLM Medical Text Indexer. BioASQ 2014.
  • Bodenreider O, Peters L, Nguyen T. RxClass – Navigating between Drug Classes and RxNorm Drugs (Demo). Prc. ICBO 2014
  • Nguyen T, Peters L, Bodenreider O. RxClass - Navigating between drug classes and RxNorm drugs [Poster]. AMIA Annu Symp Proc, 2014: p. 1529.
  • Jimeno-Yepes A, Aronson AR. Self-training and co-training in biomedical word sense disambiguation. BioNLP 2011 Workshop, June 2011, 182-183.
  • Sneiderman C, Demner-Fushman D, Fiszman M, Rindflesch TC. Semantic Characteristics of MEDLINE Citations Useful for Therapeutic Decision-making AMIA Annu Symp Proc. 2005:1117.
  • Rindflesch TC, Fiszman M, Bisharah L. Semantic Interpretation for the Biomedical Research Literature In Hsinchun C, Fuller S, Friedman C, Hersh w (eds.) Medical Informatics: Knowledge Management and Data Mining in Biomedicine. Springer: New York, pp. 399-422, 2005.
  • Cairelli MJ, Miller CM, Fiszman M, Workman TE, Rindflesch TC. Semantic MEDLINE for discovery browsing: using semantic predications and the literature-based discovery paradigm to elucidate a mechanism for the obesity paradox. AMIA Annu Symp Proc. 2013 Nov 16;2013:164-73. eCollection 2013.
  • Kilicoglu H, Fiszman M, Rodriguez A, Shin D, Ripple AM, Rindflesch TC. Semantic MEDLINE: A Web Application for Managing the Results of PubMed Searches Proc. Third Int'l Symposium for Semantic Mining in Biomedicine, 69-76
  • Rindflesch TC, Kilicoglu H, Fiszman M, Rosemblat G, Shin D. Semantic MEDLINE: An advanced information management application for biomedicine. Information Services and Use, 2011, 31(1): 15-21.
  • Rindflesch TC, Aronson AR. Semantic Processing for Enhanced Access to Biomedical Knowledge Real World Semantic Web Applications, IOS Press. 2002;:157-72.
  • Sneiderman C, Demner-Fushman D, Fiszman M, Rosemblat G, Lang FM, Norwood D, Rindflesch TC. Semantic Processing to Enhance Retrieval of Diagnosis Citations from Medline AMIA Annu Symp Proc. 2006:1104
  • Culbertson A, Fiszman M, Shin D, Rindflesch TC. Semantic processing to identify adverse drug event information from black box warnings. AMIA Annu Symp Proc. 2014 Nov 14;2014:442-8. eCollection 2014.
  • Fiszman M, Ortiz E, Bray BE, Rindflesch TC. Semantic Processing to Support Clinical Guideline Development AMIA Annu Symp Proc. 2008 Nov 6:187-91
  • Rindflesch TC, Libbus B, Hristovski D, Aronson AR, Kilicoglu H. Semantic Relations Asserting the Etiology of Genetic Diseases AMIA Annu Symp Proc. 2003:554-8.
  • Hristovski D, Kastrin A, Peterlin P, Rindflesch TC. Semantic relations for interpreting DNA microarray data. AMIA Annu Symp Proc. 2009 Nov 14;2009:255-9.
  • Slaughter LA, Soergel D, Rindflesch TC. Semantic Representation of Consumer Questions and Physician Answers Int J Med Inform. 2006 Jul;75(7):513-29. Epub 2005 Aug 24
  • Gay CW, Kayaalp M, Aronson AR. Semi-Automatic Indexing of Full Text Biomedical Articles AMIA Annu Symp Proc. 2005:271-5
  • Kilicoglu H, Shin D, Fiszman M, Rosemblat G, Rindflesch TC. SemMedDB: a PubMed-scale repository of biomedical semantic predications. Bioinformatics. 2012 Dec 1;28(23):3158-60. doi: 10.1093/bioinformatics/bts591. Epub 2012 Oct 8.
  • Kilicoglu H. Software: Bio-SCoRes
  • Kayaalp M, Dodd Z, Browne AC, Sagan, P, McDonald CJ. Software: NLM-Scrubber
  • Kilicoglu H, Rosemblat G, Fiszman M, Rindflesch TC. Sortal anaphora resolution to enhance relation extraction from biomedical literature. BMC Bioinformatics. 2016 Apr 14;17:163. doi: 10.1186/s12859-016-1009-6.
  • Workman TE, Fiszman M, Cairelli MJ, Nahl D, Rindflesch TC. Spark, an application based on Serendipitous Knowledge Discovery. J Biomed Inform. 2016 Apr;60:23-37. doi: 10.1016/j.jbi.2015.12.014. Epub 2015 Dec 28.
  • Zeng K, Bodenreider O, Kilbourne J, Nelson SJ. Standards, Security and Usability: Experience with MyMedicationList [Abstract]. Proc. AMIA Spring Congress 2008
  • Tringali M, Rindflesch TC, Kilicoglu H, Fiszman M, Bodenreider O. Strategies for Mapping Concepts in Gastrointestinal Endoscopy Reports to the UMLS Metathesaurus Medinfo. 2004 Sept.;2004: 1885.
  • Plaza L, Jimeno-Yepes A, Diaz A, Aronson AR. Studying the correlation between different word sense disambiguation methods and summarization effectiveness in biomedical texts. BMC Bioinformatics. 2011 Aug 26;12:355. doi: 10.1186/1471-2105-12-355.
  • Fiszman M, Rindflesch TC, Kilicoglu H. Summarization of an Online Medical Encyclopedia MedInfo. 2004 Sept.;2004: 506-510.
  • Fiszman M, Rindflesch TC, Kilicoglu H. Summarizing Drug Information in Medline Citations AMIA Annu Symp Proc. 2006; 254-8
  • Rosemblat G, Logan R, Tse T, Graham L. Text Features and Readability: Expert Evaluation of Consumer Health Text Mednet 2006. October 14-16, 2006. Toronto, Canada
  • Workman TE, Fiszman M, Hurdle JF. Text summarization as a decision support aid. BMC Med Inform Decis Mak. 2012 May 23;12:41. doi: 10.1186/1472-6947-12-41.
  • Mishra R, Bian J, Fiszman M, Weir CR, Mostafa J, Fiol GD. Text summarization in the biomedical domain: a systematic review of recent research. J Biomed Inform. 2014 Dec;52:457-67. doi: 10.1016/j.jbi.2014.06.009. Epub 2014 Jul 10.
  • Weeber M, Klein H, Aronson AR, Mork JG, de Jong-van den Berg LT, Vos R. Text-Based Discovery in Biomedicine: The Architecture of the DAD-System AMIA Annu Symp Proc. 2000 ;():903-7.
  • Tharakaraman K, Bodenreider O, Landsman D, Spouge JL, Marino-Ramirez. The Biological Function of Some Human Transcription Factor Binding Motifs Varies with Position Relative to the Transcription Start Site Nucleic Acids Res. 2008 May;36(8):2777-86. Epub 2008 Mar 26
  • Browne AC, Kayaalp M, Dodd Z, Sagan, P, McDonald CJ. The Challenges of Creating a Gold Standard for De-identification Research. AMIA Annu Symp Proc. 2014 Nov 14;2014:353-8. eCollection 2014.
  • Rosemblat G, Logan R. The Consumers' Perspective: Text Features and Readability of Consumer Health Text Mednet 2007: Germany. 12 Oct 2007
  • Keselman A, Massengale L, Ngo L, Browne A, Zeng Q. The Effect of User Factors on Consumer Familiarity with Health Terms: Using Gender as a Proxy for Background Knowledge about Gender-Specific Illnesses ISBMDA 2006: 472-481
  • Aronson AR, Lang FM. The Evolution of MetaMap, a Concept Search Program for Biomedical Text AMIA Annu Symp Proc. 2009 Nov:22
  • Golbreich C, Zhang S, Bodenreider O. The Foundational Model of Anatomy in OWL: Experience and Perspectives Web Semant. 2006;4(3):181-195
  • Leroy G, Fiszman M, Rindflesch TC. The Impact of Directionality in Predications on Text Mining Hawaii International Conference on System Sciences (HICSS-41), January 2008
  • Smith LH, Rindflesch TC, Wilbur WJ. The Importance of the Lexicon in Tagging Biological Text Natural Language Engineering 2005.
  • Rindflesch TC, Fiszman M. The Interaction of Domain Knowledge and Linguistic Structure in Natural Language Processing: Interpreting Hypernymic Propositions in Biomedical Text Journal of Biomedical Informatics. 2003;36(6):462-77.
  • McCray AT, Browne AC, Bodenreider O. The Lexical Properties of the Gene Ontology (GO) Proc AMIA Symp. 2002;:504-8.
  • Mork JG, Aronson AR. The Medical Text Indexer (MTI) system for indexing biomedical literature. book chapter submitted to monograph Indexing Specialities: Medicine. Edited by L. Pilar Wyman. Medford, NJ: Information Today, Inc., in association with the American Society of Indexers, Phoenix, AZ. 2010.
  • Aronson AR, Mork JG, Gay CW, Humphrey SM, Rogers W. The NLM Indexing Initiative's Medical Text Indexer. Stud Health Technol Inform. 2004;107(Pt 1):268-72.
  • Aronson AR, Bodenreider O, Chang HF, Humphrey SM, Mork JG, Nelson SJ, Rindflesch TC, Wilbur WJ. The NLM Indexing Initiative. Proc AMIA Symp. 2000:17-21.
  • Mork JG, Jimeno Yepes A, Aronson A. The NLM Medical Text Indexer System for Indexing Biomedical Literature. BioASQ 2013.
  • Kayaalp M, Browne AC, Callaghan FM, Dodd Z, Divita G, Ozturk S, McDonald CJ. The pattern of name tokens in narrative clinical text and a comparison of five systems for redacting them. J Am Med Inform Assoc. 2014 May-Jun;21(3):423-31. doi: 10.1136/amiajnl-2013-001689. Epub 2013 Sep 11.
  • Kashyap V. The UMLS Semantic Network and the Semantic Web. AMIA Annu Symp Proc. 2003:351-5.
  • Kilicoglu H, Demner-Fushman D, Rindflesch TC, Wilczynski NL, Haynes RB. Toward Automatic Recognition of High Quality Clinical Evidence. AMIA Annu Symp Proc. 2008 Nov 6:368
  • Rosemblat G, Fiszman, M, Shin D, Kilicoglu H. Towards a characterization of apparent contradictions in the biomedical literature using context analysis. Journal of Biomedical Informatics. 2019. In Press. https://doi.org/10.1016/j.jbi.2019.103275.
  • Kilicoglu H, Demner-Fushman D, Rindflesch TC, Wilczynski NL, Haynes RB. Towards Automatic Recognition of Scientifically Rigorous Clinical Research Evidence J Am Med Inform Assoc. 2009 Jan-Feb;16(1):25-31. Epub 2008 Oct 24.
  • Brennan PF, Rindflesch TC. Towards Linking Patients and Clinical Information: Detecting UMLS Concepts in E-mail J Biomed Inform. 2003 Aug-Oct;36(4-5):334-41
  • Kashyap V, Ramakrishan C, Rindflesch TC. Towards Semi-Automatic Generation of Biomedical Ontologies AMIA Annu Symp Proc. 2003 Nov;:886.
  • Demner-Fushman D, Mork JG, Shooshan SE, Aronson AR. UMLS content views appropriate for NLP processing of the biomedical literature vs. clinical text. J Biomed Inform. 2010 Aug;43(4):587-94. doi: 10.1016/j.jbi.2010.02.005. Epub 2010 Feb 10.
  • Rosemblat G, Tse T. User Study of a Spanish-language ClinicalTrials.gov Prototype System AMIA Annu Symp Proc. 2006:659-63
  • Vizenor L, Bodenreider O. Using Dependence Relations in MeSH as a Framework for the Analysis of Disease Information in Medline Proc SMBM-2006, 2006:76-83
  • Ruch P, Geissbuhler A, Gobeill J, Lisacek F, Tbahriti I, Veuthey A, Aronson AR. Using Discourse Analysis to Improve Text Categorization in MEDLINE Stud Health Technol Inform. 2007;129(Pt 1):710-5
  • Lu C, Tormey D, McDreedy L, Browne AC. Using element words to generate (multi)words for the SPECIALIST Lexicon [Poster]. AMIA 2014 Annual Symposium, Washington, DC, November 15-19, 2014, p. 1499. Poster
  • Lu C, Browne AC, Allen C, Divita G. Using Lexical tools to convert Unicode characters to ASCII AMIA Annu Symp Proc. 2008 Nov 6:1031.
  • Hristovski D, Kastrin A, Dinevski D, Burgun A, Ziberna L, Rindflesch TC. Using Literature-Based Discovery to Explain Adverse Drug Effects. J Med Syst. 2016 Aug;40(8):185. doi: 10.1007/s10916-016-0544-z. Epub 2016 Jun 18.
  • Hristovski D, Rindflesch TC, Peterlin B. Using literature-based discovery to identify novel therapeutic approaches. Cardiovasc Hematol Agents Med Chem. 2013 Mar;11(1):14-24.
  • Libbus B, Kilicoglu H, Rindflesch TC, Mork JG, Aronson AR. Using Natural Languge Processing, Locus Link, and the Gene Ontology to Compare OMIM to MEDLINE Proceedings of the HLT-NAACL Workshop on Linking the Biological Literature, Ontologies and Databases: Tools for Users. 2004;:69-76.
  • 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. J Biomed Inform. 2014 Jun;49:134-47. doi: 10.1016/j.jbi.2014.01.004. Epub 2014 Jan 19.
  • Zhang G-Q, Bodenreider O. Using SPARQL to Test for Lattices: Application to Quality Assurance in Biomedical Ontologies In: Patel-Schneider PF, Pan Y, Hitzler P, Mika P, Zhang L, Pan JZ, et al., editors. Proceedings of the 9th International Semantic Web Conference (ISWC 2010), Shanghai, China, November 7-11, 2010. Berlin, Heidelberg: Springer; 2010. p. 273-288.
  • Leroy G, Rindflesch TC. Using Symbolic Knowledge in the UMLS to Disambiguate Words in Small Datasets with a Naive Bayes Classifier Medinfo. 2004 Sept.;2004: 381-385.
  • Jimeno Yepes A, Mork JG, Aronson A. Using the argumentative structure of scientific literature to improve information access [Poster]. BioNLP 2013.
  • Ahlers CB, Hristovski D, Kilicoglu H, Rindflesch TC. Using the Literature-based Discovery Paradigm to Investigate Drug Mechanisms AMIA Annu Symp Proc. 2007 Oct 11:6-10
  • Ozturk S, Kayaalp M, McDonald CJ. Visualization of patient prescription history data in emergency care. AMIA Annu Symp Proc. 2014 Nov 14;2014:963-8. eCollection 2014.
  • Mork JG, Demner-Fushman D, Schmidt SC, Aronson A. Vocabulary Density Method for Personalized Indexing of MEDLINE Journals [Poster]. 2014 AMIA Symposium.