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  • Lederberg J, McCray AT. 'Ome Sweet 'Omics - A Genealogical Treasury of Words Genealogical Treasury of Words. Scientist. 2001;15(7):8.
  • Lin J, Demner-Fushman D. "Bag of words" is not enough for strength of evidence classification AMIA Annu Symp Proc. 2005:1031.
  • 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.
  • 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.
  • Felts RL, Bennett A, Shi D, Freed E, Lifson J, Lowekamp B, Yoo TS, Bliss D, Subramaniam S. 3D Imaging of HIV transmission and entry using electron tomography and ion-abrasion scanning electron microscopy. Three Dimensional Electron Microscopy: Technical Advances and Recent Breakthroughs in 3DEM. Gordon Research Conference; 2008 Jun 15-20; Lucca (Barga), Italy.
  • 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
  • Antani S, Long LR, Thoma GR. A Biomedical Information System for Combined Content-Based Retrieval of Spine X-ray Images and Associated Text Information 3rd Indian Conference on Computer Vision, Graphics, and Image Processing. 2002 Dec.
  • Locatis C, Gaines C, Liu W, Gill MJ, Carney J, Foster J, McCall V, Woods M. A Blended Training Approach Using Videoconferencing for Distance Education. J Med Libr Assoc. 2006 Oct;94(4):464-8.
  • 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.
  • Rahman MM, Antani SK, Thoma GR. A Classification-Driven Similarity Matching Framework For Retrieval of Biomedical Images. 11th ACM International Conference on Multimedia Information Retrieval (MIR 2010). 2010:147-154.
  • Xue Z, Bryant B, Long LR, Sari-Sarraf H, Thoma GR, Wachtel M. A Client-Server Tool for Automatic Fast GPU-based Detection of Squamous Epithelium Tissue Regions in Histology Images [Poster]. RSNA 2014. Chicago, USA, Nov 30-Dec 5, 2014
  • 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.
  • Karargyris A, Candemir S, Jaeger S, Xue Z, Antani SK, Thoma GR. A Combined Approach for Lung Boundary Segmentation of Chest X-Ray Images [Poster]. NIH Intramural Research Festival, Bethesda MD, November 6-8, 2013.
  • 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).
  • McCray AT, Bodenreider O. A Conceptual Framework for the Biomedical Domain The Semantics of Relationships: An Interdisciplinary Perspective. Boston: Kluwer Academic Publishers. 2002;:181-198.
  • 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
  • You D, Antani SK, Demner-Fushman D, Thoma GR. A Contour-based Shape Descriptor For Biomedical Image Classification and Retrieval. Proceedings of SPIE 2014, Vol. 9021, Document Recognition and Retrieval XXI. February 2014;9021.
  • Demner-Fushman D. A dataset of 200 structured product labels annotated for adverse drug reactions. Sci Data. 2018 Jan 30;5:180001. doi: 10.1038/sdata.2018.1.
  • Lau JJ, Gayen S, Ben Abacha A, Demner-Fushman D. A dataset of clinically generated visual questions and answers about radiology images. Sci Data. 2018 Nov 20;5:180251. doi: 10.1038/sdata.2018.251.
  • Demner-Fushman D, Antani S, Kalpathy-Cramer J, Müller H. A decade of community-wide efforts in advancing medical image understanding and retrieval. Comput Med Imaging Graph. 2015 Jan;39:1-2. doi: 10.1016/j.compmedimag.2014.12.002.
  • Mao S, Kim J, Thoma G. A Dynamic Feature Generation System for Automated Metadata Extraction in Preservation of Digital Materials Proc. International Workshop on Document Image Analysis for Libraries (DIAL2004). 2004 Jan;: 225-32.
  • Winnenburg R, Bodenreider O. A framework for assessing the consistency of drug classes across sources. J Biomed Semantics. 2014 Jul 9;5:30. doi: 10.1186/2041-1480-5-30. eCollection 2014.
  • Sharp M, Bodenreider O, Wacholder N. A Framework for Characterizing Drug Information Sources AMIA Annu Symp Proc. 2008 Nov 6:662-6
  • Bodenreider O, Burgun A. A framework for comparing phenotype annotations of orthologous genes. Stud Health Technol Inform. 2010;160(Pt 2):1309-13.
  • Jaeger S. A geomedical approach to Chinese medicine: The origin of the yin-yang symbol. Recent Advances in Theories and Practice of Chinese Medicine, Haixue Kuang (Ed.), ISBN: 978-953-307-903-5, InTech, 2012.
  • Bodenreider O, Peters LB. A graph-based approach to auditing RxNorm. J Biomed Inform. 2009 Jun;42(3):558-70. doi: 10.1016/j.jbi.2009.04.004. Epub 2009 Apr 24.
  • Cameron D, Bodenreider O, Yalamanchili H, Danh T, Vallabhaneni S, Thirunarayan K, Sheth AP, Rindflesch TC. A graph-based recovery and decomposition of Swanson's hypothesis using semantic predications. J Biomed Inform. 2013 Apr;46(2):238-51. doi: 10.1016/j.jbi.2012.09.004. Epub 2012 Sep 28.
  • Kim E, Huang X, Tan G, Long LR, Antani S. A Hierarchical SVG Image Abstraction Layer for Medical Imaging Medical Imaging 2010: Advanced PACS-based Imaging Informatics and Therapeutic Applications. San Diego, California. March 2010;7628
  • 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.
  • Kilicoglu H, Rogers W. A Hybrid System for Extracting Chemical-Disease Relationships from Scientific Literature. 2015. BioCreative 5 Proceedings.
  • Bryant B, Sari-Sarraf H, Long LR, Antani SK. A Kernel Support Vector Machine Trained Using Approximate Global and Exhaustive Local Sampling. Proceedings of the 4th IEEE/ACM International Conference on Big Data Computing, Applications and Technologies (BDCAT) 2017, Austin, Texas, USA, December 2017. Pp. 267-8 DOI: https://doi.org/10.1145/3148055.3149206
  • 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.
  • Rahman MM, Antani SK, Thoma GR. A learning-based similarity fusion and filtering approach for biomedical image retrieval using SVM classification and relevance feedback. IEEE Trans Inf Technol Biomed. 2011 Jul;15(4):640-6. doi: 10.1109/TITB.2011.2151258. Epub 2011 Jun 16.
  • Simpson M, Ford G, Antani S, Demner-Fushman D, Thoma GR. A Lightweight Statistics Package for Interactive Publications Poster at 20th NIH Research Festival (TECH-15), September 2007, National Institutes of Health
  • 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.
  • Krainak DM, Long LR, Thoma GR. A Method of Content-Based Retrieval for a Spinal X-Ray Image Database Proc. of SPIE Medical Imaging: PACS and Integrated Medical Systems. 2002 Feb;4685.
  • Karargyris A, Bourbakis N. A methodology for detecting blood-based abnormalities in wireless capsule endoscopy videos. BioInformatics and BioEngineering, 2008. BIBE 2008. 8th IEEE International Conference. 2008 Oct 8; pp 1-6. doi: 10.1109/BIBE.2008.4696806.
  • 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.
  • You D, Antani SK, Demner-Fushman D, Thoma GR. A MRF Model for Biomedical Image Segmentation. CBMS 2014. May 2014.
  • Borovikov E, Zavorin I. A multi-stage document processing approach To Arabic text recognition. Guide to OCR for Arabic Scripts. 2012:55-78.
  • Logan RA, Tse T. A Multidiscipline Conceptual Framework for Consumer Health Informatics Stud Health Technol Inform. 2007;129(Pt 2):1169-73
  • Rance B, Doughty E, Demner-Fushman D, Kann MG, Bodenreider O. A mutation-centric approach to identifying pharmacogenomic relations in text. J Biomed Inform. 2012 Oct;45(5):835-41. doi: 10.1016/j.jbi.2012.05.003. Epub 2012 Jun 7.
  • Xu T, Xin C, Long LR, Antani SK, Xue Z, Kim E, Huang X. A New Image Data Set and Benchmark for Cervical Dysplasia Classification Evaluation. Machine Learning in Medical Imaging: 6th International Workshop, MLMI 2015, LNCS 9352, pp. 26–35, 2015. DOI: 10.1007/978-3-319-24888-2 4.
  • 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.
  • Cheng B, Stanley RJ, Antani SK, Thoma GR. A Novel Computational Intelligence-based Approach For Medical Image Artifacts Detection Proceedings of the 2010 International Conference on Artificial Intelligence and Pattern Recognition. Orlando, FL. July 2010:113-20
  • Rajaraman S, Candemir S, Xue Z, Alderson P, Kohli M, Abuya J, Thoma GR, Antani SK. A novel stacked generalization of models for improved TB detection in chest radiographs. Proc. IEEE Engineering in Medicine and Biology Conference (EMBC 2018), Honolulu, Hawaii, 2018. pp. 718-721.
  • Rajaraman S, Candemir S, Xue Z, Alderson P, Thoma G, Antani SK. A Novel Stacked Model Ensemble for Improved TB Detection in Chest Radiographs. In Santosh KC et al. (Eds.). Medical Imaging: Artificial Intelligence, Image Recognition, and Machine Learning Techniques. (pp. 1-26). New York, NY: CRC Press, Taylor & Francis Group.
  • 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.
  • Sorbello A, Ripple AM, Bodenreider O. A pilot study to support prospective detection of emerging adverse drug events [Poster]. AMIA Annu Symp Proc 2015:1699.
  • 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
  • Bodenreider O, Coban ZH, Doganay MC, Erdem E, Kosucu H. A preliminary report on answering complex queries related to drug discovery using answer set programming. Proceedings of the 3rd International Workshop on Applications of Logic Programming to the (Semantic) Web and Web Services (ALPSWS2008), 2008: p. 85-90 (electronic proceedings: http://ceur-ws.org/Vol-434/).
  • Tulpule B, Hernes DL, Srinivasan Y, Mitra S, Sriraja Y, Nutter BS, Phillips B, Long RL, Ferris DG. A Probabilistic Approach to Segmentation and Classification of Neoplasia in Uterine Cervix Images Using Color and Geometric Features SPIE Medical Imaging, February 2005; San Diego, CA; vol. 5748:995-1003
  • 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.
  • Long LR, Antani SK, Thoma GR. A Prototype Content-Based Image Retrieval System for Spine X-Rays Proc. 16th IEEE Symposium on Computer-Based Medical Systems. 2003 June;: 156-62.
  • Demner-Fushman D, Seckman C, Fisher C, Hauser SE, Clayton J, Thoma GR. A prototype system to support evidence-based practice AMIA Annu Symp Proc. 2008 Nov 6:151-5.
  • Cohen T, Roberts K, Gururaj AE, Chen X, Pournejati S, Alter G, Hersh WR, Demner-Fushman D, Ohno-Machado L, Lu H. A publicly available benchmark for biomedical dataset retrieval: the reference standard for the 2016 bioCADDIE dataset retrieval challenge. Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax061.
  • Rahman MM, Antani SK, Thoma GR. A Query Expansion Framework in Image Retrieval Domain Based on Local and Global Analysis. Inf Process Manag. 2011 Sep 1;47(5):676-691.
  • Stanley RJ, Long LR. A Radius of Curvature Approach to Cervical Spine Vertebra Image Analysis Proc. 38th Annual Rocky Mountain Bioengineering Symposium, 37. 2001 Apr;: 385-90.
  • 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.
  • 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.
  • Candemir S, Antani SK. A review on lung boundary detection in chest X-rays. Int J Comput Assist Radiol Surg. 2019 Feb 7. doi: 10.1007/s11548-019-01917-1.
  • You D, Simpson M, Antani SK, Demner-Fushman D, Thoma GR. A robust pointer segmentation in biomedical images toward building a visual ontology for biomedical article retrieval. Proc. SPIE 8658, Document Recognition and Retrieval XX, 86580Q (February 4, 2013); doi:10.1117/12.2005934.
  • Bodenreider O. A Semantic Navigation Tool for the UMLS AMIA Annu Symp Proc. 2000;: 971.
  • Zhang X, Zou J, Le DX, Thoma GR. A Semi-supervised Learning Method to Classify Grant Support Zone in Web-based Medical Articles Proc SPIE Electronic Imaging Science and Technology, Document Recognition and Retrieval. January 2009;7247:7247 OW(1-8)
  • KC S, Alam M, Roy P, Wendling L, Antani SK, Thoma GR. A simple and efficient arrowhead detection in biomedical images. International J Pattern Recognition and Artificial Intelligence (IJPRAI), 30(5), 1657002, 2016, DOI: 10.1142/S0218001416570020.
  • Abhyankar S, Demner-Fushman D. A simple method to extract key maternal data from neonatal clinical notes. AMIA Annu Symp Proc. 2013 Nov 16;2013:2-9. eCollection 2013.
  • Walker FL, Thoma GR. A SOAP-Based Tool for User Feedback and Analysis Proc. InfoToday. 2003 ;: 313-322.
  • Walker FL, Thoma GR. A SOAP-Enabled System for an Online Library Service Proc. InfoToday 2002, Medford NJ: Information Today. 2002 May;:320-9.
  • Xu X, Lee DJ, Antani S, Long LR. A Spine X-ray Image Retrieval System using Partial Shape Matching IEEE Trans Inf Technol Biomed. 2008 Jan;12(1):100-8.
  • Zhang X, Zou J, Le DX, Thoma GR. A Stacked Sequential Learning Method For Investigator Name Recognition From Web-based Medical Articles 17th Document Recognition and Retrieval Conference (SPIE-DR&R). San Jose, CA. January 2010;7534:753404-7
  • Zhang X, Zou J, Le DX, Thoma GR. A structural SVM approach for reference parsing. BMC Bioinformatics. 2011 Jun 9;12 Suppl 3:S7. doi: 10.1186/1471-2105-12-S3-S7.
  • Liu H, Aronson AR, Friedman C. A Study of Abbreviations in MEDLINE Abstracts AMIA Annu Symp. 2002 ;():464-8.
  • Antani S, Kasturi R, Jain R. A Survey on the Use of Pattern Recognition Methods for Abstraction Indexing and Retrieval of Images and Video Pattern Recognition Journal. 2002;35(4): 945-965.
  • 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.
  • Xue Z, Jaeger S, Karargyris A, Candemir S, Antani SK, Long LR, Thoma GR, McDonald CJ. A System for Automated Screening for Tuberculosis using Digital Chest X-rays for Resources-Constrained Regions [Poster]. NIH Intramural Research Festival, Bethesda MD, November 6-8, 2013.
  • 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.
  • Hauser SE, Demner-Fushman D, Ford G, Thoma GR. A Testbed System for Mobile Point-Of-Care Information Delivery Proc. 17th IEEE Symposium on Computer-Based Medical Systems. 2004 June;: 147-52.
  • Zeng Q, Kin E, Crowell J, Tse T. A Text Corpora-Based Estimation of the Familiarity of Health Terminology ISBMD, Aveiro, Portugal, 10-11 November 2005:184-92.
  • 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.
  • Jeronimo J, Schiffman M, Long LR, Neve L, Antani S. A Tool for Collection of Region Based Data from Uterine Cervix Images for Correlation of Visual and Clinical Variables Related to Cervical Neoplasia Proc. 17th IEEE Symposium on Computer-Based Medical Systems: IEEE Computer Society. 2004 June.;:558-62.
  • Sahoo SS, Nguyen V, Bodenreider O, Parikh P, Minning T, Sheth AP. A unified framework for managing provenance information in translational research. BMC Bioinformatics. 2011 Nov 29;12:461. doi: 10.1186/1471-2105-12-461.
  • Xue Z, Long LR, Antani SK, Neve L, Zhu Y, Thoma GR. A unified set of analysis tools for uterine cervix image segmentation. Comput Med Imaging Graph. 2010 Dec;34(8):593-604. doi: 10.1016/j.compmedimag.2010.04.002. Epub 2010 May 26.
  • Alexander GL, Hauser S, Steely K, Ford G, Demner-Fushman D. A Usability Study of the PubMed on Tap User Interface for PDAs Medinfo. 2004 Sept.;2004: 1411-1415.
  • Rahman MM, Antani SK, Demner-Fushman D, Thoma GR. A visual concept-based interactive biomedical image retrieval using entropy and spatial information. Proc. SPIE. 9418, Medical Imaging 2015: PACS and Imaging Informatics: Next Generation and Innovations, 94180U. (March 17, 2015) doi: 10.1117/12.2081456.
  • Crowell J, Zeng QT, Tse T. A Web Application to Support Consumer Health Vocabulary Development AMIA Annu Symp Proc. 2005:932
  • Xue Z, Long R, Antani SK, Thoma GR. A Web-accessible Content-based Cervicographic Image Retrieval System Proc SPIE Medical Imaging 2008. April 2008;6919:691907-1-9
  • Walker FL, Thoma GR. A Web-Based Paradigm for File Migration Proc. of IS and T's Archiving Conference. 2004 April.
  • 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.
  • Burgun A, Bodenreider O. Accessing and Integrating Data and Knowledge for Biomedical Research Yearb Med Inform. 2008:91-101
  • Rosemblat G, Tse T, Gemoets D. Adapting A Monolingual Consumer Health System for Cross-Language Information Retrieval Advances in Knowledge Organization, Proceedings of the Eighth International ISKO Conference. 2004 July;9:315-321.
  • 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
  • Callaghan F, Demner-Fushman D, Abhyankar S, McDonald CJ. Addressing errors in a retrospective observational ICU database [poster]. AMIA 2011 Fall Symposium.
  • Zweigenbaum P, Demner-Fushman D. Advanced Literature-Mining Tools. In Edwards D, Stajich J, and Hansen D. (Editors). Bioinformatics: Tools and Applications. Springer 2009.
  • Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H, Doherty D, Forsberg K, Gao Y, Kashyap V, Kinoshita J, Luciano J, Marshall MS, Oqbuji C, Rees J, Stephens S, Wong GT, Wu E, Zaccaqnini D, Hongsermeier T, Neumann E, Herman I, Cheung KH. Advancing Translational Research with the Semantic Web BMC Bioinformatics. 2007 May 9;8 Suppl 3:S2
  • Castle PE, Jeronimo J, Schiffman M, Herroro R, Rodriguez AC, Bratti MC, Hildesheim A, Wacholder S, Long LR, Neve L, Pfeiffer R, Burk RD. Age-related changes of the cervix influence human papillomavirus type distribution Cancer Res. 2006 Jan 15;66(2):1218-24.
  • McCray AT, Burgun A, Bodenreider O. Aggregating UMLS Semantic Types for Reducing Conceptual Complexity Medinfo. 2001 ;10(Pt 1):216-20.
  • Cheng W, Pearson G. Algorithm Developed To Make More Reliable Links To Better Photographic Views of Nursing Homes For Prototype "Nursing Home Screener" Web Site. Poster Section III at NIH Research Festival (TECH-3). National Institutes of Health October 2008. Bethesda, MD. October 2008.
  • Almubarak H, Guo P, Stanley RJ, Long LR, Antani SK, Thoma GR. Algorithm Enhancements for Improvement of Localized Classification of Uterine Cervical Cancer Digital Histology Images. in Handbook of Research on Emerging Perspectives on Healthcare Information Systems and Informatics,. IGI Global (Hershey, PA).
  • Parascandola J. Alice Catherine Evans (1881-1975) J Public Health Policy. 2001 ;22(1):105-11.
  • Bodenreider O, Burgun A. Aligning Knowledge Sources in the UMLS: Methods, Quantitative Results, and Applications Medinfo. 2004 Sept.;2004:327-331.
  • Winnenburg R, Rodriguez L, Callaghan F, Sorbello A, Szarfman A, Bodenreider O. Aligning Pharmacologic Classes Between MeSH and ATC. 4th International Conference on Biomedical Ontology · ICBO 2013
  • Zhang S, Bodenreider O. Aligning Representations of Anatomy Using Lexical and Structural Methods AMIA Annu Symp Proc. 2003 Nov;:753-757.
  • 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.
  • Zhang S, Bodenreider O. Alignment of Multiple Ontologies of Anatomy: Deriving Indirect Mappings from Direct Mappings to a Reference AMIA Annu Symp Proc 2005:864-868
  • Schulz S, Beisswanger, van den Hoek L, Bodenreider O, van Mulligen EM. Alignment of the UMLS Semantic Network with BioTop: Methodology and Assessment Bioinformatics 2009;25(12):i69-i76
  • Peters L, Nguyen T, Bodenreider O. An application programming interface for NDF-RT AMIA Annu Symp Proc 2011:1922
  • Peters L, Kapusnik-Uner JE, Nguyen T, Bodenreider O. An approximate matching method for clinical drug names. AMIA Annu Symp Proc. 2011;2011:1117-26. Epub 2011 Oct 22.
  • Bopf M, Coleman T, Long LR, Antani S, Thoma GR, Jeronimo J, Schiffman M. An Architecture for Streamlining the Implementation of Biomedical Text/Image Databases on the Web Proc. 17th IEEE Symposium on Computer-Based Medical Systems. 2004 June.;: 563-69.
  • 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.
  • 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.
  • Cantor MN, SI N, Hartel F, Bodenreider O, Lussier YA. An Evaluation of Hybrid Methods for Matching Biomedical Terminologies: Mapping the Gene Ontology to the UMLS Stud Health Technol Inform. 2003;:62-67.
  • Pearson G, Gill MJ. An Evaluation of Motion JPEG 2000 for Video Archiving. Proc. Archiving 2005. Washington, D.C. April 2005:237-43.
  • Sahoo S, Bodenreider O, Zeng K, Sheth AP. An Experiment in Integrationg Large Biomedical Knowledge Resources with RDF: Application to Associating Genotype and Phenotype Information Proc Workshop on Health Care and Life Sciences Data Integration for the Semantic Web at WWW2007 (electronic proceedings: http://www2007.org/workshops/paper_149.pdf)
  • Stanley RJ, De S, Demner-Fushman D, Antani SK, Thoma GR. An image feature-based approach to automatically find images for application to clinical decision support. Comput Med Imaging Graph. 2011 Jul;35(5):365-72. doi: 10.1016/j.compmedimag.2010.11.008. Epub 2010 Dec 8.
  • Jaeger S. An information-theoretic neural model based on concepts in Chinese medicine. 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW).
  • Rahman MM, You D, Simpson M. An interactive image retrieval framework for biomedical articles based on visual region-of-interest (ROI) identification and classification [Abstract]. The 2nd IEEE Conference on Healthcare Informatics, Imaging, and Systems Biology Analyzing Big Data for Healthcare and Biomedical Sciences (HISB 2012). La Jolla, CA. September 2012.
  • Rahman MM, Antani SK, Demner-Fushman D, Thoma GR. An Interactive Region-Of-interest (ROI)- Based Image Retrieval Approach of Biomedical Articles in a Local Concept- Based Feature Space [Poster]. NIH Intramural Research Festival, Bethesda MD, November 6-8, 2013.
  • Bodenreider O. An Object-Oriented Model for Representing Semantic Locality in the UMLS Medinfo. 2001 ;10(Pt 1):161-5.
  • Hu L, Bell D, Antani SK, Xue Z, Yu K, Horning MP, Gachuhi N, Wilson B, Jaiswal MS, Befano B, Long LR, Herrero R, Einstein MH, Burk RD, Demarco M, Gage JC, Wentzensen N, Schiffman M. An Observational Study of Deep Learning and Automated Evaluation of Cervical Images for Cancer Screening. J Natl Cancer Inst. 2019 Jan 10. doi: 10.1093/jnci/djy225
  • Xue Z, Antani SK, Long LR, Thoma GR. An online segmentation tool for cervicographic image analysis. ACM International Health Informatics Symposium, IHI 2010, Arlington, VA, USA, November 11 - 12, 2010, Proceedings; 01/2010.
  • Resnick MP, Ripple AM, Auston I, Rindflesch TC. An Ontology for Public Health to Support Enhanced Information Retrieval AMIA Annu Symp Proc. 2010
  • Bergun A, Bodenreider O. An ontology of chemical entities helps identify dependence relations among Gene Ontology terms Proc SMBM-2005
  • Wang H, Azuaje F, Bodenreider O. An Ontology-Driven Clustering Method for Supporting Gene Expression Analysis CBMS’2005. 2005:389-394.
  • 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.
  • Van Der Volgen J, Harris BR, Demner-Fushman D. Analysis of Consumer Health Questions for Development of Question-Answering Technology [Poster]. Proceedings of One HEALTH: Information in an Interdependent World, the 2013 Annual Meeting and Exhibition of the Medical Library Association (MLA), 2013.
  • Callaghan F, Jackson MT, Demner-Fushman D, Abhyankar S, McDonald C. Analysis of data that has been extracted from free-text using natural language processing: a likelihood model for misclassification with an application to medical informatics. International Conference on Advances in Interdisciplinary Statistics and Combinatorics (AISC2012), Greensboro, NC, October 2012
  • Zamora G, Sari-Sarraf H, Mitra S, Long R. Analysis of the Feasibility of Using Active Shape Models for Segmentation of Gray Scale Images Proc. of SPIE Medical Imaging: Image Processing. 2002 Feb;4684:1370-81.
  • Mougin FL, Bodenreider O, Burgun A. Analyzing polysemous concepts from a clinical perspective: application to auditing concept categorization in the UMLS. J Biomed Inform. 2009 Jun;42(3):440-51. doi: 10.1016/j.jbi.2009.03.008. Epub 2009 Mar 18.
  • You D, Simpson M, Antani SK, Demner-Fushman D, Thoma GR. Annotating image ROIs with text descriptions for multimodal biomedical document retrieval. Proc. SPIE 8658, Document Recognition and Retrieval XX, 86580Q (February 4, 2013); doi:10.1117/12.2005934; http://dx.doi.org/10.1117/12.2005934.
  • Roberts K, Demner-Fushman D. Annotating Logical Forms for EHR Questions. Proceedings of the Language Resources and Evaluation Conference, LREC,23-28 May 2016, Portorož.
  • 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.
  • Roberts K, Masterton K, Kilicoglu H, Fiszman M, Demner-Fushman D. Annotating Question Decomposition on Complex Medical Questions. LREC 2014.
  • Roberts K, Masterton K, Fiszman M, Kilicoglu H, Demner-Fushman D. Annotating Question Types for Consumer Health Questions. LREC 2014, BioTxtM workshop.
  • Demner-Fushman D, Simpson M, Antani S, Thoma GR. Annotation and retrieval of clinically relevant images. Int J Med Inform. 2009 Dec;78(12):e59-67. doi: 10.1016/j.ijmedinf.2009.05.003. Epub 2009 Jul 9.
  • 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
  • Demner-Fushman D, Lin J. Answer Extraction, Semantic Clustering, and Extractive Summarization for Clinical Question Answering Proc COLING/ACL 2006. July 2006, Sydney, Australia
  • Demner-Fushman D, Lin J. Answering Clinical Questions with Knowledge-based and Statistical Techniques Computational Linguistics. 2007 Jan;33(1):63-103
  • Cherukuri M, Stanley RJ, Long R, Antani S, Thoma G. Anterior Osteophyte Discrimination in Lumbar Vertebrae Using Size-Invariant Features Comput Med Imaging Graph. 2004 Jan-Mar;28(1-2):99-108.
  • Bodenreider O. API: NDF-RT
  • Bodenreider O. API: Prescribable
  • 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.
  • Gandhi T, Kasturi R, Antani S. Application of Planar Motion Segmentation for Scene Text Extraction Proc. of the 15th IEEE International Conference of Pattern Recognition. 2000 Sept.;1:1831-4.
  • Guan Y, Li M, Jaeger S, Lure F, Raptopoulos V, Lu P, Folio LR, Candemir S, Antani SK, Siegelman J, Li J, Wu T, Thoma GR, Qu S. Applying Artificial Intelligence and Radiomics for Computer Aided Diagnosis and Risk Assessment in Chest Radiographs. 2nd Conference on Machine Intelligence in Medical Imaging (CMIMI) of the Society for Imaging Informatics in Medicine (SIIM), Poster, 2017.
  • 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.
  • Antani SK, Long RL, Thoma GR. Applying Vertebral Boundary Semantics to CBIR of Digitized Spine X-Ray Images Proc SPIE Electronic Imaging Science and Technology, Conference on Storage and Retrieval Methods and Applications for Multimedia. 2005;5682:98-107.
  • Mougin F, Bodenreider O. Approaches to Eliminating Cycles in the UMLS Metathesaurus: Naive vs. Formal AMIA Annu Symp Proc. 2005:550-4
  • 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.
  • Lasko TA, Hauser SE. Approximate String Matching Algorithms for Limited-Vocabulary OCR Output Correction Proc. SPIE, Document Recognition and Retrieval VIII. 2001 Jan;4307:232-40.
  • Misra D, Mao S, Rees J, Thoma GR. Archiving a Historic Medico-legal Collection: Automation and Workflow Customization Proc IS&T Archiving 2007. Arlington, Virginia, May 2007; 157-61
  • Amini S, Kilicoglu H, Hooft L, ter Riet G. Are we expressing uncertainty of our claims enough? Towards automatic detection of overstatement of claims [Poster]. 2015. World Conference on Research Integrity (WCRI).
  • 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
  • KC S, Naved A, Roy PP, Wendling L, Antani SK, Thoma GR. Arrowhead detection in biomedical images. Proceedings IS&T Electronic Imaging, Document Recognition and Retrieval XXIII, 2016, pp. 1-7.
  • Burgun A, Bodenreider O. Aspects of the Taxonomic Relation in the Biomedical Domain FOIS. 2001;: 222-233
  • 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.
  • 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
  • Gemoets D, Rosemblat G, Tse T, Logan R. Assessing Readability of Consumer Health Information: An Exploratory Study Medinfo. 2004 Sept.;2004:869-73.
  • Bodenreider O, Burgun A, Rindflesch TC. Assessing the Consistency of a Biomedical Terminology Through Lexical Knowledge Int J Med Inf. 2002 Dec 4;67(1-3):85-95.
  • Rajaraman S, Sornapudi S, Kohli M, Antani SK. Assessment of an ensemble of machine learning models toward abnormality detection in chest radiographs. Proc. IEEE Engineering in Medicine and Biology Conference (EMBC), Berlin, Germany, 23 – 27 July 2019. pp. 3689 – 3692.
  • Ganesan P, Rajaraman S, Long LR, Ghoraani B, Antani SK. Assessment of Data Augmentation Strategies Toward Performance Improvement of Abnormality Classification in Chest Radiographs. Proc. IEEE Engineering in Medicine and Biology Conference (EMBC), Berlin, Germany, 23 – 27 July 2019. pp. 841 – 844.
  • Siegel ER, Wood FB, Dutcher GA, Ruffin A, Logan RA, Scott J. Assessment of the National Library of Medicine's Health Disparities Plan: A Focus on Native American Outreach J Med Libr Assoc. 2005 Oct;93(4 Suppl):S10-20
  • 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.
  • Candemir S, Jaeger S, Antani S, Bagci U, Folio LR, Xu Z, Thoma G. Atlas-based rib-bone detection in chest X-rays. Comput Med Imaging Graph. 2016 Jul;51:32-9. doi: 10.1016/j.compmedimag.2016.04.002. Epub 2016 Apr 13.
  • Vizenor LT, Bodenreider O, McCray AT. Auditing associative relations across two knowledge sources. J Biomed Inform. 2009 Jun;42(3):426-39. doi: 10.1016/j.jbi.2009.01.004.
  • Cui L, Bodenreider O, Shi J, Zhang GQ. Auditing SNOMED CT hierarchical relations based on lexical features of concepts in non-lattice subgraphs. Biomed Inform. 2018 Feb;78:177-184. doi: 10.1016/j.jbi.2017.12.010. Epub 2017 Dec 20.
  • Mougin F, Bodenreider O. Auditing the NCI Thesaurus with Semantic Web Technologies AMIA Annu Symp Proc. 2008 Nov 6:500-4
  • Chen G, Cairelli MJ, Kilicoglu H, Shin D, Rindflesch TC. Augmenting microarray data with literature-based knowledge to enhance gene regulatory network inference. PLoS Comput Biol. 2014 Jun 12;10(6):e1003666. doi: 10.1371/journal.pcbi.1003666. eCollection 2014 Jun.
  • Le DX, Thoma GR. Automated Article Links Identification for Web-Based Online Medical Journals Proc. 8th World Multiconference on Systemics, Cybernetics and Informatics. 2004 Jul.;5:462-6.
  • KC S, Antani SK. Automated chest X-ray screening: Can lung region symmetry help detect pulmonary abnormalities? IEEE Transactions on Medical Imaging. doi: https://doi.org/10.1109/TMI.2017.2775636.
  • Santosh KC, Antani SK. Automated chest x-ray screening: Can lung region symmetry help detect pulmonary abnormalities? doi: 10.1109/TMI.2017.2775636 vol. 37, no. 5, 1168-1177.
  • Kim I, Thoma GR. Automated Classification of Author’s Sentiments in Citation Using Machine Learning Techniques: A Preliminary Study. Proc. the 2015 IEEE Conf. Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2015), Niagara Falls, Canada, Aug. 12-15, 2015.
  • Zhang, K, Demner-Fushman D. Automated classification of eligibility criteria in clinical trials to facilitate patient-trial matching for specific patient populations. J Am Med Inform Assoc. 2017 Jul 1;24(4):781-787. doi: 10.1093/jamia/ocw176.
  • Kim I, Le DX, Thoma GR. Automated Cleanup Processing for Extracting Bibliographic Data from Biomedical Online Journals In: Callaos N, Lesso W, editors. SCI 2005. Proc. 9th World Multiconference on Systemics, Cybernetics and Informatics; 2005 Jul 10-13; Vol. 4; Orlando (FL): International Institute of Informatics and Systemics; c2005. 401-5
  • Thoma GR, Ford G. Automated Data Entry System: Performance Issues Proc. SPIE: Document Recognition and Retrieval IX. 2002 Jan;4670: 181-90.
  • Le DX, Thoma GR. Automated Document Labeling for Web-Based Online Medical Journals Proc. 7th World Multiconference on Systemics, Cybernetics and Informatics. 2003 July;II: 411-15.
  • Kim I, Le DX, Thoma GR. Automated identification of biomedical article type using support vector machines. Proc. 18th SPIE Document Recognition and Retrieval, 7874:787403 (1-9), San Francisco, January 2011.
  • Kim I, Thoma GR. Automated Identification of Potential Conflict-of-Interest in Biomedical Articles Using Hybrid Deep Neural Network. Proc. 14th Int’l Conf. Machine Learning and Data Mining (MLDM 2018), LNAI 10934, pp. 99-112, Newark, NJ, July 2018.
  • Kim I, Thoma GR. Automated Identification of Potential Conflict-of-Interest in Biomedical Articles Using Hybrid Deep Neural Network. Proc. 14th Int’l Conf. Machine Learning and Data Mining (MLDM 2018), LNAI 10934, pp. 99-112, Newark, NJ, July 2018.
  • Kim J, Le DX, Thoma GR. Automated Labeling Algorithms for Biomedical Document Images Proc. 7th World Multiconference on Systemics, Cybernetics and Informatics. 2003 July;V: 352-57.
  • Kim J, Le DX, Thoma GR. Automated Labeling for Biomedical Journals Published in Foreign Languages Proc. 8th World Multiconference on Systemics, Cybernetics and Informatics. 2004 Jul.;:444-9.
  • Kim J, Le DX, Thoma GR. Automated Labeling in Document Images Proc. SPIE, Document Recognition and Retrieval VIII. 2001 Jan;4307:111-22.
  • Kim J, Le DX, Thoma GR. Automated Labeling of Bibliographic Data Extracted from Biomedical Online Journals Proc. SPIE Electronic Imaging. 2003 Jan;5010: 47-56.
  • Kim J, Le DX, Thoma GR. Automated Labeling Of Biomedical Online Journal Articles In: Callaos N, Lesso W, editors. SCI 2005. Proc 9th World Multiconference on Systemics, Cybernetics and Informatics; 2005 Jul 10-13; Vol. 4; Orlando (FL): International Institute of Informatics and Systemics; c2005. 406-11
  • Le DX, Tran LQ, Chow J, Kim J, Hauser SE, Moon CW, Thoma GR. Automated Medical Citation Records Creation for Web-Based Online Journals Proc. 14th IEEE Symposium on Computer-Based Medical Systems: IEEE Computer Society. 2001.
  • Thoma GR, Mao S, Misra D. Automated Metadata Extraction to Preserve the Digital Contents of Biomedical Collections Proc VIIP 2005. September 2005. Benidorm, Spain; 214-19
  • Kim I, Le DX, Thoma GR. Automated method for extracting "citation sentences" from online biomedical articles using SVM-based text summarization technique. Proc. the 2014 IEEE Int'l Conf. on Systems, Man, and Cybernetics (SMC 2014), pp. 2006-2011, San Diego, October, 2014
  • Lure F, Jaeger S, Antani SK. Automated Systems for microscopic and radiographic tuberculosis screening. Electronic Journal of Emerging Infectious Diseases, Vol. 2, No. 1, pp. 5-9, February 2017. [In Chinese]
  • Hauser SE, Le DX, Thoma GR. Automated Zone Correction in Bitmapped Document Images SPIE: Document Recognition and Retrieval VII. 2000 Jan;3976: 248-58.
  • 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
  • Rodriguez LM, Fushman DD. Automatic Classification of Structured Product Labels for Pregnancy Risk Drug Categories, a Machine Learning Approach. AMIA Annu Symp Proc. 2015 Nov 5;2015:1093-102. eCollection 2015.
  • Greenspan H, Gordon S, Zimmerman G, Lotenberg S, Jeronimo J, Antani S, Long LR. Automatic Detection of Anatomical Landmarks In Uterine Cervix Images IEEE Trans Med Imaging. 2009 Mar;28(3):454-68
  • Bodenreider O, Mougin F, Burgun A. Automatic Determination of Anti-coagulation Status with NDF-RT Proceedings of the 13th ISMB'2010 SIG meeting Bio-ontologies 2010:140-143
  • Lotenberg S, Gordon S, Long LR, Antani SK, Jeronimo J, Greenspan H. Automatic Evaluation of Uterine Cervix Segmentations Proc. SPIE Medical Imaging 2007. Vol. 6515: 65151J-1-12.
  • Roberts K, Rodriguez L, Shooshan SE, Demner-Fushman D. Automatic Extraction and Post-coordination of Spatial Relations in Consumer Language. AMIA Annu Symp Proc. 2015 Nov 5;2015:1083-92. eCollection 2015.
  • Kim J, Le DX, Thoma GR. Automatic Extraction of Bibliographic Information from Biomedical Online Journal Articles Using a String Matching Algorithm Proc IEEE CBMS, June 2006, Salt Lake City, Utah; 905-10
  • Xue Z, Long LR, Antani SK, Thoma GR. Automatic Extraction of Mosaic Patterns In Uterine Cervix Images 23rd IEEE International Symposium on Computer-Based Medical Systems (CBMS) 2010. Perth, Australia. October 2010:273-8.
  • Candemir S, Jaeger S, Lin W, Xue Z, Antani SK, Thoma GR. Automatic heart localization and radiographic index computation in chest x-rays. Proc. SPIE. 9785, Medical Imaging 2016: Computer-Aided Diagnosis, 978517. DOI: 10.1117/12.2217209.
  • Folio, L, Sigelman, J, Wang, Y, Lu, P, Antani SK, Jaeger S. Automatic Identification and Classification of Tuberculosis Findings on Chest Radiographs for Global Surveillance Programs [Abstract]. Annual Meeting of the American Roentgen Ray Society (ARRS)
  • 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.
  • You D, Antani SK, Demner-Fushman D, Rahman MM, Govindaraju V, Thoma GR. Automatic identification of ROI in figure images toward improving hybrid (text and image) biomedical document retrieval. Proceedings of SPIE Electronic Imaging Science and Technology, Document Retrieval and Recognition XVIII. San Francisco, CA. January 2011;7874:78740K.
  • 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.
  • Yao J, Antani S, Long LR, Thoma GR, Zhang Z. Automatic Medical Image Annotation and Retrieval Using SECC Proc CBMS 2006, June 2006, Salt Lake City, Utah; 105-10
  • Kim W, Aronson AR, Wilbur WJ. Automatic MeSH Term Assignment and Quality Assessment Proc AMIA Symp. 2001:319-23.
  • Mougin F, Burgun A, Bodenreider O, Chabalier J, Loreal O, Le Beux P. Automatic Methods for Integrating Biomedical Data Sources in a Mediator-Based System Proc DILS 2008. Berlin Heidelberg New York: Springer; 2008. p. 61-76
  • Xue Z, Antani SK, Long LR, Thoma GR. Automatic multi-label annotation of abdominal CT images using CBIR. Proc. SPIE 10138, Medical Imaging 2017: Imaging Informatics for Healthcare, Research, and Applications, 1013807 (March 13, 2017); doi:10.1117/12.2254368.
  • KC S, Vajda S, Antani SK, Thoma GR. Automatic Pulmonary Abnormality Screening using Thoracic Edge Map. IEEE, 28th International Symposium on Computer-Based Medical Systems (CBMS), pp. 360-361, 2015.
  • 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.
  • Jaeger S, Karargyris A, Antani SK, Thoma GR. Automatic Screening For Lung Diseases In Chest Radiographs: a Global Health Initiative [Poster].. NIH Research Festival. October 2012.
  • Jaeger S, Karargyris A, Candemir S, Siegelman J, Folio L, Antani S, Thoma G. Automatic screening for tuberculosis in chest radiographs: a survey. Quant Imaging Med Surg. 2013 Apr;3(2):89-99. doi: 10.3978/j.issn.2223-4292.2013.04.03.
  • Apostolova E, Channin DS, Demner-Fushman D, Furst J, Lytinen S, Raicu D. Automatic segmentation of clinical texts. 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Minneapolis, MN, 2009, pp. 5905-5908. doi: 10.1109/IEMBS.2009.5334831
  • Cheng B, Antani SK, Stanley J, Demner-Fushman D, Thoma GR. Automatic segmentation of subfigure image panels for multimodal biomedical document retrieval. Proceeding of: Document Recognition and Retrieval XVIII - DRR 2011, 18th Document Recognition and Retrieval Conference, part of the IS&T-SPIE Electronic Imaging Symposium, San Jose, CA, USA, January 24-29, 2011, Proceedings.
  • 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.
  • Mao S, Kanungo T. Automatic Training of Page Segmentation Algorithms: An Optimization Approach International Conference on Pattern Recognition. 2000 Sept.;:531-534.
  • 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.
  • Antani SK. Automatic x-ray screening for tuberculosis. SPIE Newsroom. October 2015. DOI: 10.1117/2.1201509.006128
  • Demner-Fushman D, Karpinski J, Thoma GR. Automatically building a repository to support evidence-based practice. Proceedings of the 2nd Workshop on Building and evaluating resources for biomedical text mining (BioTxtM 2010), 7th Language Resources and Evaluation Conference (LREC 2010). Valetta, Malta. May 2010.
  • 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.
  • Le DX, Thoma GR. Automatically Creating Biomedical Bibliographic Records from Printed Volumes of Old Indexes In: Callaos N, Lesso W, editors. SCI 2005. Proc 9th World Multiconference on Systemics, Cybernetics and Informatics; 2005 Jul 10-13; Vol. 3, Computer Science and Engineering. Orlando (FL): International Institute of Informatics and Systemics; c2005. 267-74
  • KC S, Candemir S, Jaeger S, Folio L, Karargyris A, Antani SK, Thoma GR. Automatically detecting rotation in chest radiographs using principal rib-orientation measure for quality control. Int. J. Patt. Recogn. Artif. Intell, Vol 29 No. 2. DOI: 10.1142/S021800141.5570013
  • 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.
  • Demner-Fushman D, Antani S, Thoma GR. Automatically Finding Images for Clinical Decision Support Proc of IEEE DM-Med 2007. Omaha, NE, October 2007, pp. 139-144
  • Demner-Fushman D, Few B, Hauser SE, Thoma GR. Automatically Identifying Health Outcome Information in MEDLINE Records J Am Med Inform Assoc. 2006 Jan-Feb;13(1):52-60. Epub 2005 Oct 12.
  • Rahman MM, Antani SK, Thoma GR. Bag of Keypoints-Based Biomedical Image Search With Affine Covariant Region Detection and Correlation-Enhanced Similarity Matching. 23rd IEEE International Symposium on Computer-Based Medical Systems (CBMS ) 2010. Perth, Australia. October 2010:261-6.
  • Zhu Y, Huang X, Wang W, Lopresti D, Long LR, Antani SA, Xue Z, Thoma GR. Balancing the Role of Priors in Multi-Observer Segmentation Evaluation J Signal Process Syst. 2008 May 28;55(1-3):185-207
  • Mao S, Thoma G. Bayesian Learning of 2D Document Layout Models for Automated Preservation Metadata Extraction Proc. of the Fourth IASTED International Conference on Visualization, Imaging, and Image Processing (VIIP). 2004 Sept.;:329-34.
  • 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.
  • McCray AT. Better access to information about clinical trials. Ann Intern Med. 2000 Oct 17;133(8):609-14.
  • 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
  • Bodenreider O, Stevens R. Bio-ontologies: Current Trends and Future Directions Brief Bioinform. 2006 Sep;7(3):256-74. Epub 2006 Aug 9
  • Kilicoglu H, Demner-Fushman D. Bio-SCoRes: A Smorgasbord Architecture for Coreference Resolution in Biomedical Text. PLoS One. 2016 Mar 2;11(3):e0148538. doi: 10.1371/journal.pone.0148538. eCollection 2016.
  • 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
  • You D, Antani S, Demner-Fushman D, Rahman MM, Govindarju V, Thoma GR. Biomedical Article Retrieval Using Multimodal Features and Image Annotations In Region-based CBIR. Document Recognition and Retrieval XVII. Edited by Likforman-Sulem, Laurence; Agam, Gady. Proceedings of the SPIE. San Jose, CA. January 2010;7534:75340V-75340V-12.
  • Rahman MM, Antani SK, Demner-Fushman D, Thoma GR. Biomedical image representation approach using visualness and spatial information in a concept feature space for interactive region-of-interest-based retrieval. J Med Imaging (Bellingham). 2015 Oct;2(4):046502. doi: 10.1117/1.JMI.2.4.046502. Epub 2015 Dec 30.
  • Rahman MM, Antani SK, Thoma GR. Biomedical Image Retrieval In a Fuzzy Feature Space With Affine Region Detection and Vector Quantization of a Scale-Invariant Descriptor. 6th International Symposium on Visual Computing (ISVC) 2010. Las Vegas, NV. November 2010.
  • Roberts K, Boland MR, Pruinelli L, Dcruz J, Berry A, Georgsson M, Hazen R, Sarmiento RF, Backonja U, Yu K-H, Jiang Y, Brennan PF. Biomedical informatics advancing the national health agenda: the AMIA 2015 year-in-review in clinical and consumer informatics. J Am Med Inform Assoc. 2017 Apr 1;24(e1):e185-e190. doi: 10.1093/jamia/ocw103.
  • Long LR, Antani S, Lee DJ, Krainak DM, Thoma GR. Biomedical Information from a National Collection of Spine X-Rays: Film to Content-Based Retrieval Proc. of SPIE Medical Imaging: PACS and Integrated Medical Information Systems. 2003 Feb;5033: 70-84.
  • Cohen KB, Demner-Fushman D. Biomedical Natural Language Processing John Benjamins Publishing Company, 2014. DOI: 10.1075/nlp.11
  • Bodenreider O, Mitchell JA, McCray AT. Biomedical Ontologies Pacific Symposium on Biocomputing: World Scientific. 2003;:562-564.
  • Bodenreider O. Biomedical Ontologies in Action: Role in Knowledge Management, Data Integration and Decision Support. Geissbuhler A, Kulikowski C, editors. IMIA Yearbook of Medical Informatics 2008. Methods Inf Med, 2008. 47(Suppl 1): p. 67-79.
  • 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.
  • Xue Z, Antani SK, Long LR, Demner-Fushman D, Thoma GR. Body Segment Classification for Visible Human Cross Section Slices. IEEE 27th International Symposium on Computer-Based Medical Systems (CBMS), New York, NY, May 2014: pp. 199-204
  • Antani S, Long LR, Thoma GR. Bridging the Gap: Enabling CBIR in Medical Applications Proc IEEE CBMS. Jyvaskyla, Finland. June 2008:4-6
  • Pearson G, Moon CW. Bridging Two Biomedical Journal Databases with XML - A Case Study. Proc. 14th IEEE Symposium on Computer-Based Medical Systems: IEEE Computer Society. 2001 Jul;:309-14.
  • Bodenreider O, Peters L, Nguyen T. Browser and application programming interfaces for drug information sources. AMIA Annu Symp Proc, 2011: p. 2129.
  • 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.
  • Karargyris A, Koulaouzidis A. Capsule-odometer: a concept to improve accurate lesion localisation. World J Gastroenterol. 2013 Sep 21;19(35):5943-6. doi: 10.3748/wjg.v19.i35.5943.
  • Chang Y, Antani S, Lee DJ, Gledhill K, Long LR, Christensen P. CBIR of Spine X-ray Images on Inter-vertebral Disc Space and Shape Profiles Proc IEEE CBMS. Jyvaskyla, Finland. June 2008:224-9.
  • Lee DJ, Antani S, Chang Y, Long LR, Christensen P, Jeronimo J. CBIR of Spine X-ray Images On Inter-vertebral Disc Space and Shape Profiles Using Feature Ranking and Voting Consensus. Data & Knowledge Engineering, Special Issue on Knowledge Discovery in Medicine. 2009.
  • 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.
  • Mitchell JA, Fomous C, Fun J. Challenges and strategies of the Genetics Home Reference J Med Libr Assoc. 2006 Jul;94(3):336-42
  • Srinivasan Y, Nutter BS, Mitra SD, Yang S, Phillips B, Long LR. Challenges in Automated Detection of Cervical Intraepithelial Neoplasia Proc SPIE Medical Imaging 2007. Vol. 6514: 65140F-1-11
  • 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.
  • Williams R, Tse T, Zarin D. Characterizing sponsor-imposed restrictions on disclosing results of clinical trials. Presented at: Sixth International Congress on Peer Review and Biomedical Publication; September 2009; Vancouver, BC, Canada.
  • Bodenreider O, Burgun A. Characterizing the Definitions of Anatomical Concepts in WordNet and Specialized Sources Proc. of the First Global WordNet Conference. 2002;:223-230.
  • Parascandola J. Chaulmoogra Oil and the Treatment of Leprosy Pharm Hist. 2003 ;45(2):47-57.
  • Xue Z, You D, Candemir S, Jaeger S, Antani SK, Long LR, Thoma GR. Chest X-ray Image View Classification The 28th IEEE International Symposium on Computer-Based Medical Systems
  • Jaeger S. Chest X-ray Screening System: Segmentation Module – v3
  • Zohora FT, Antani SK, Santosh KC. Circle-like foreign element detection in chest x-rays using normalized cross-correlation and unsupervised clustering. Proc. SPIE 10574, Medical Imaging 2018: Image Processing, 105741V (2 March 2018); doi: 10.1117/12.2293739; doi.org/10.1117/12.2293739.
  • Bodenreider O. Circular hierarchical relationships in the UMLS: etiology, diagnosis, treatment, complications and prevention. Proc AMIA Symp. 2001:57-61.
  • Zarin D, Tse T. Clarification about ClinicalTrials.gov [Letter]. IRB. 2013 May-Jun;35(3):19.
  • 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.
  • 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.
  • Xue Z, Antani SK, Long LR, Demner-Fushman D, Thoma GR. Classification of CT Figures in Biomedical Articles Based on Body Segments. 2013 IEEE International Conference on Healthcare Informatics (ICHI), pp.264,268, 9-11 Sept. 2013. doi: 10.1109/ICHI.2013.17.
  • Xue Z, You D, Antani SK, Long LR, Demner-Fushman D, Thoma GR. Classification of Visual Signs in Abdominal CT Image Figures in Biomedical Literature. Proc. SPIE. 9039. Medical Imaging 2014: PACS and Imaging Informatics: Next Generation and Innovations. 90390T.
  • 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.
  • Bergun A, Bodenreider O, Mougin F. Classifying diseases with respect to anatomy: a study in SNOMED CT AMIA Annu Symp Proc. 2005:91-5
  • Lussier YA, Bodenreider O. Clinical Ontologies for Discovery Applications In: Baker CJO, Cheung K-H, editors. Semantic Web: Revolutionizing knowledge discovery in the life sciences. New York: Springer; 2007. p. 101-119.
  • Del Fiol G, Workman TE, Gorman PN. Clinical questions raised by clinicians at the point of care: a systematic review. JAMA Intern Med. 2014 May;174(5):710-8. doi: 10.1001/jamainternmed.2014.368.
  • Tse T, Zarin DA. Clinical Trial Registration and Results Reporting: ClinicalTrials.gov and FDAAA FDLI Update. 2009 Jan/Feb;1:18-22
  • 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.
  • Williams R, Tse T. ClinicalTrials.gov: A public database of clinical research. Presented at: American Public Health Association 137th Annual Meeting and Expo; November 2009; Philadelphia, PA.
  • McCray AT. Clinicaltrials.gov: Linking Patients to Medical Research Cancer Informatics: Essential Technologies for Clinical Trials. New York: Springer Verlag. 2002;:302-307.
  • 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.
  • Liang Z, Powell A, Ersoy I, Poostchi M, Silamut K, Palaniappan K, Guo P, Hossain M, Antani SK, Maude R, Huang J, Jaeger S, Thoma GR. CNN-Based Image Analysis for Malaria Diagnosis. IEEE International Conference on Bioinformatics & Biomedicine (BIBM), Shenzhen, China, 2016.
  • 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.
  • Guo P, Stanley RJ, Cole JG, Hagerty JR, Stoecker WV. Color Feature-based Pillbox Image Color Recognition. Published 2017 in VISIGRAPP DOI:10.5220/0006136001880194.
  • Karargyris A, Siegelman J, Tzortzis D, Jaeger S, Candemir S, Xue Z, KC S, Vajda S, Antani SK, Folio L, Thoma GR. Combination of texture and shape features to detect pulmonary abnormalities in digital chest X-rays. Int J Comput Assist Radiol Surg. 2016 Jan;11(1):99-106. doi: 10.1007/s11548-015-1242-x. Epub 2015 Jun 20.
  • Zhang X, Zou J, Le DX, Thoma GR. Combining Discriminative SVM models for the Improved Recognition of Investigator Names in Medical Articles. Proceedings of SPIE Volume 8658, Document Recognition and Retrieval XX, IS&T/SPIE Electronic Imaging 2013.
  • Zou J, Le DX, Thoma GR. Combining DOM Tree and Geometric Layout Analysis for Online Medical Journal Article Segmentation Proc JCDL, June 2006, Chapel Hill, NC; 119-28
  • 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.
  • Demner-Fushman D, Antani SK, Simpson M, Thoma GR. Combining Medical Domain Ontological Knowledge and Low-level Image Features for Multimedia Indexing Procf OntoImage 2008, part of LREC 2008. Marrakech, Morrocco. May 2008:CDROM Proceedings
  • 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.
  • Fiszman M, Bray B, Shin D, Kilicoglu H, Bennett GC, Bodenreider O, Rindflesch TC. Combining relevance assignment with quality of the evidence to support guideline development. Stud Health Technol Inform. 2010;160(Pt 1):709-13.
  • 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
  • Mao S, Mansukhani P, Thoma GR. Combining Static Classifiers and Class Syntax Models for Logical Entity Recognition in Scanned Historical Documents Proc IEEE CVPR, Minneapolis, Minnesota, June 2007, pp. 1-8.
  • Abhyankar S, Demner-Fushman D, Callaghan FM, McDonald CJ. Combining structured and unstructured data to identify a cohort of ICU patients who received dialysis. J Am Med Inform Assoc. 2014 Sep-Oct;21(5):801-7. doi: 10.1136/amiajnl-2013-001915. Epub 2014 Jan 2.
  • Kim J, Le DX, Thoma GR. Combining SVM Classifiers to Identify Investigator Name Zones in Biomedical Articles. IS&T/SPIE’s 22nd Annual Symposium on Electronic Imaging. San Francisco, CA, January 2012; 8297.
  • Bodenreider O. Comment les Usagers Accedent a l'Information Medicale Aux USA: l'Exemple de MEDLINEplus [How Consumers Access Health Information in the USA: The MEDLINEplus Example] Innovation et Technologie en Biologie et Medecine. 2000;21(5):286-90.
  • 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.
  • Xue Z, Antani SK, Long LR, Thoma GR. Comparative Performance Analysis of Cervix ROI Extraction and Specular Reflection Removal Algorithms for Uterine Cervix Image Analysis Proc SPIE Medical Imaging 2007. Vol. 6512: 65124I-1-9
  • 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.
  • Zhang S, Bodenreider O. Comparing Associative Relationships Among Equivalent Concepts Across Ontologies MedInfo. 2004 Sept.;2004: 459-463.
  • Rajaraman S, Antani SK, Candemir S, Xue Z, Abuya J, Kohli M, Alderson P, Thoma GR. Comparing deep learning models for population screening using chest radiography. Proc. SPIE 10575, Medical Imaging 2018: Computer-Aided Diagnosis, 105751E (27 February 2018).
  • Mougin F, Burgun A, Bodenreider O. Comparing Drug-class Membership in ATC and NDF-RT Proc IHI 2012 2012:437-443
  • Mortensen J, Bodenreider O. Comparing Pharmacologic Classes in NDF-RT and SNOMED CT. Proc SMBM 2010:119-124.
  • Bodenreider O. Comparing SNOMED CT and the NCI Thesaurus through Semantic Web Technologies Proc. KR-MED 2008
  • Burgun A, Bodenreider O. Comparing Terms, Concepts and Semantic Classes in WordNet and the Unified Medical Language System Proc. of the NAACL'2001 Workshop; WordNet and Other Lexical Resources: Applications, Extensions and Customizations. 2001;:77-82.
  • Karargyris A, Folio L, Siegelman J, Callaghan FM, Candemir S, Xue Z, Lu P-X, Wang Y, Antani SK, Thoma GR, Jaeger S. Comparing the Performance of Man and Machine for TB Screening in Chest Radiographs [Poster]. NIH Intramural Research Festival, Bethesda MD, November 6-8, 2013.
  • Bodenreider O, Zhang S. Comparing the Representation of Anatomy in the FMA and SNOMED CT AMIA Annu Symp Proc. 2006:46-50
  • Zheng S, Mork P, Bodenreider O, Bernstein PA. Comparing Two Approaches for Aligning Representations of Anatomy Artif Intell Med. 2007 Mar;39(3):227-36. Epub 2007 Jan 23
  • Mougin F, Bodenreider O. Comparing Two Approaches to Eliminating Cycles in Terminological Systems Proc RFIA 2006
  • 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.
  • Fung K, Kapusnik-Uner J, Cunningham J, Higby-Baker S, Bodenreider O. Comparison of three commercial knowledge bases for detection of drug-drug interactions in clinical decision support. J Am Med Inform Assoc. 2017 Jul 1;24(4):806-812. doi: 10.1093/jamia/ocx010.
  • Thamizhvani TR, Lakshmanan S, Rajaraman S. Computer Aided Diagnosis of Skin Tumours from Dermal Images. Hemanth D., Smys S. (eds) Computational Vision and Bio Inspired Computing. Lecture Notes in Computational Vision and Biomechanics, vol 28. Springer, Cham
  • Long LR, Thoma GR. Computer-Assisted Retrieval of Biomedical Image Features from Spine X-Rays: Progress and Prospects Proceeding of the 14th IEEE Symposium on Computer-Based Medical Systems (CBMS). 2001 Jul;:46-50.
  • Kilicoglu H, Peng Z, Tafreshi S, Tran T, Rosemblat G, Schneider J. Confirm or Refute?: A Comparative Study on Citation Sentiment Classification in Clinical Research Publications. J Biomed Inform. 2019 Feb 9:103123. doi: 10.1016/j.jbi.2019.103123.
  • 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.
  • Gordon S, Zimmerman G, Long LR, Antani S, Jeronimo J, Greenspan H. Content Analysis of Uterine Cervix Images: Initial Steps Towards Content Based Indexing and Retrieval of Cervigrams Proc of SPIE Vol. 6144 61444U-7
  • De Herrera A, Long LR, Antani SK. Content-Based fMRI Brain Maps Retrieval. International Conference on Brain and Health Informatics, Omaha, NE, USA, October 13-16, 2016.
  • Long LR, Antani SK, Thoma GR, Deserno TM. Content-based Image Retrieval For Advancing Medical Diagnostics, Treatment, and Education New Technologies for Advancing Healthcare and Clinical Practices. June 2011:1-17.
  • Antani S, Long R, Thoma GR. Content-Based Image Retrieval for Large Biomedical Image Archives Medinfo. 2004 Sept.;2004: 829-833.
  • Deserno TM, Antani S, Long LR. Content-based image retrieval for scientific literature access. Methods Inf Med. 2009;48(4):371-80. doi: 10.3414/ME0561. Epub 2009 Jul 20.
  • Long LR, Antani SK, Deserno TM, Thoma GR. Content-based Image Retrieval in Medicine: Retrospective Assessment, State of the Art, and Future Directions Int J Healthc Inf Syst Inform. 2009 Jan 1;4(1):1-16
  • Deserno TM, Long LR, Greenspan H. Content-based Image Retrieval: Major Challenges for Biomedical Applications Intl Journal of Healthcare Information Systems and Informatics. January 2009;4(1):i-iii
  • De Herrera A, Long LR, Antani SK. Content–based fMRI activation maps retrieval [Poster]. BIH 2016: Brain Informatics and Health pp 173-180, October 13-16, 2016.
  • 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.
  • Demner-Fushman D, Seckman C, Fisher C, Thoma GR. Continual development of a personalized decision support system. Stud Health Technol Inform. 2013;192:175-9.
  • Lu C, Browne AC. Converting Unicode Lexicon and Lexical Tools for ASII NLP Applications AMIA Annu Symp Proc 2011:1870.
  • Almubarak HA, Stanley RJ, Long LR, Antani SK, Thoma GR, Zuna R, Frazier SR. Convolutional Neural Network Based Localized Classification of Uterine Cervical Cancer Digital Histology Images. Procedia Computer Science, Volume 114, 2017, Pages 281-287, ISSN 1877-0509, https://doi.org/10.1016/j.procs.2017.09.044.
  • Kilicoglu H, Demner-Fushman D. Coreference Resolution for Structured Drug Product Labels Proceedings of BioNLP 2014. pp. 44-53.
  • Hauser SE, Schlaifer J, Sabir TF, Demner-Fushman D, Thoma GR. Correcting OCR Text by Association with Historic Datasets Proc. SPIE Electronic Imaging. 2003 Jan;5010: 84-93.
  • Winnenburg R, Bodenreider O. Coverage of human phenotypes in SNOMED CT [Poster]. SNOMED CT Implementation Showcase, 2014.
  • Winnenburg R, Bodenreider O. Coverage of phenotypes in standard terminologies. Joint Bio-Ontologies and BioLINK ISMB'2014 SIG session "Phenotype Day" 2014:41-44. 
  • 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.
  • Fung KW, Richesson R, Bodenreider O. Coverage of rare disease names in standard terminologies and implications for patients, providers, and research. AMIA Annu Symp Proc. 2014 Nov 14;2014:564-72. eCollection 2014.
  • Buchanan BG, Chapman W, Cooper GF, Hanbury P, Kayaalp M, Ramachandran M, Saul M. Creating a Software Tool for the Clinical Researcher -- the IPS System Proc AMIA Symp. 2002: : 1210.
  • 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.
  • Xu X, Lee DJ, Antani S, Long LR. Curve Matching for Spine X-ray Image Retrieval Using Dynamic Programming Proc. 8th World Multiconference on Systemics, Cybernetics and Informatics. 2004 Jul.;12:172-6.
  • Tezmol A, Sari-Sarraf H, Mitra S, Long R, Gururajan A. Customized Hough Transform for Robust Segmentation of Cervical Vertebrae from X-Ray Images SSIAI. 2002;: 224-228.
  • Mougin F, Burgun A, Bodenreider O. Data Integration Through Data Elements: Mapping Data Elements to Terminological Resources BMC Bioinformatics. 2006 Nov 24;7 Suppl 3:S6.
  • Thoma GR, Razi A, Seamans J, Strupp-Adams A, Edwards L, Gao J, Ledoux MT. Dataset: AnatQuest
  • Demner-Fushman D, Kilicoglu H. Dataset: CHQA Named Entity Dataset
  • Demner-Fushman D, Roberts K. Dataset: Question Decomposition Data
  • Demner-Fushman D, Roberts K. Dataset: Question Type Data
  • Kilicoglu H. Dataset: Sortal Anaphora Dataset
  • Kilicoglu H. Dataset: Structured Drug Product Label (SPL) Coreference Dataset
  • Botti G, Bodenreider O, Burgun A, Le Beux P, Fieschi M. De la Classification à la Connaissance des Maladies: Une Réflexion à Partir de la Classification Internationale des Maladies [From Classification to Knowledge About Diseases: Thoughts about the International Classification of Diseases] Innovation et Technologie en Biologie et Médecine. 2000;21(5):291-97.
  • 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.
  • Roberts K, Kilicoglu H, Fiszman M, Demner-Fushman D. Decomposing consumer health questions. BioNLP 2014.
  • Candemir S, Rajaraman S, Thoma GR, Antani SK. Deep Learning for Grading Cardiomegaly Severity in Chest X-rays: An Investigation. Proc. IEEE Life Sciences Conference (LSC 2018), Montreal, Quebec, Canada, 28 – 30 October 2018. pp. 109-113.
  • Sornapudi S, Stanley RJ, Stoecker WV, Almubarak H, Long LR, Antani SK, Thoma GR, Zuna R, Frazier SR. Deep Learning Nuclei Detection in Digitized Histology Images by Superpixels. J Pathol Inform. 2018 Mar 5;9:5. doi: 10.4103/jpi.jpi_74_17. eCollection 2018.
  • 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 Nov 14;2014:1218-27. eCollection 2014.
  • 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
  • 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.
  • Demner-Fushman D, Antani SK, Simpson M, Thoma GR. Design and Development of a Multimodal Biomedical Information Retrieval System JCSE. June 2012;6(2):168-177.
  • Lee D, Antani SK, Xu X, Long LR. Design and Evaluation of a Curve Matching-based Spine X-ray Image Retrieval System SPIE Medical Imaging, February 2005; San Diego, CA; vol. 5748:365-373
  • 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.
  • Zeng K, Bodenreider O, Nelson SJ. Design and Implementation of a Personal Medication Record - MyMedicationList AMIA Annu Symp Proc. 2008 Nov 6:844-8
  • Thoma GR, Mao S, Misra D, Rees J. Design of a Digital Library for Early 20th Century Medico-legal Documents Proc ECDL 2006. Eds: Gonzalo J et al. Berlin: Springer-Verlag; LNCS 4172: 147-57
  • Mitchell JA, Fun J, McCray AT. Design of Genetics Home Reference: A New NLM Consumer Health Resource Journal of the American Medical Informatics Association. 2004 Nov.;11(6):439-447.
  • Mao S, Misra D, Seamans J, Thoma GR. Design Strategies for a Prototype Electronic Preservation System for Biomedical Documents IS&T Archiving 2005 Conference, April 2005; 48-53.
  • Gillen JE, Tse T, Ide NC, McCray AT. Design, Implementation and Management of a Web-based Data Entry System for ClinicalTrials.gov Medinfo. 2004 Sept.;2004:1466-70.
  • Moallem G, Sari-Sarraf H, Poostchi Mohammadabadi M, Maude R, Silamut K, Antani SK, Jaeger S. Detecting and segmenting overlapping red blood cells in microscopic images of thin blood smears. SPIE Medical Imaging, 2018.
  • Moallem G, Poostchi M, Yu H, Palaniappan N, Silamut K, Maude RJ, Hossain Md Amir, Jaeger S, Antani SK, Thoma GR. Detecting and Segmenting White Blood Cells in Microscopy Images of Thin Blood Smears [Poster]. Annual Meeting of the American Society of Tropical Medicine & Hygiene (ASTMH), Poster, 2017
  • Jaeger S. Detecting Disease in Radiographs with Intuitive Confidence. ScientificWorldJournal. 2015;2015:946793. doi: 10.1155/2015/946793. Epub 2015 Oct 1.
  • Jaeger S, Juarez-Espinosa O, Candemir S, Poostchi Mohammadabadi M, Yang F, Kim L, Ding M, Folio L, Antani SK, Gabrielian A, Hurt D, Rosenthal A, Thoma GR. Detecting drug-resistant tuberculosis in chest radiographs International Journal of Computer Assisted Radiology and Surgery https://doi.org/10.1007/s11548-018-1857-9
  • Jaeger S, Juarez-Espinosa OH, Candemir S, Poostchi M, Yang F, Kim L, Ding M, Folio LR, Antani SK, Gabrielian A, Hurt D, Rosenthal A, Thoma G. Detecting drug-resistant tuberculosis in chest radiographs. Int J Comput Assist Radiol Surg. 2018 Dec;13(12):1915-1925. doi: 10.1007/s11548-018-1857-9. Epub 2018 Oct 3.
  • You D, Antani SK, Demner-Fushman D, Govindaraju V, Thoma GR. Detecting Figure-Panel Labels In Medical Journal Articles Using MRF. Proceedings of 11th International Conference on Document Analysis and Recognition (ICDAR 2011). Beijing, China. September 2011:967-971.
  • Jaeger S, Karargyris A, Antani SK, Thoma GR. Detecting tuberculosis in radiographs using combined lung masks. 34th Int. Conf. of the IEEE Engineering in Medicine & Biology Society (EMBC). San Diego, CA. August 2012:4978-4981. doi: 10.1109/EMBC.2012.6347110.
  • Bernhardt PJ, Humphrey SM, Rindflesch TC. Determining Prominent Subdomains in Medicine. AMIA Annu Symp Proc. 2005:46-50.
  • Antani SK, Natarajan M, Long JL, Long RL, Thoma GR. Developing a Comprehensive System for Content-based Image Retrieval of Image and Text from a National Survey SPIE Medical Imaging, February 2005; San Diego, CA; vol. 5748:152-161.
  • Weeber M, Mork JG, Aronson AR. Developing a Test Collection for Biomedical Word Sense Disambiguation Proc AMIA Symp. 2001:746-50.
  • Ammenwerth E, Wolff AC, Knaup P, Ulmer H, Skonetzki S, Van Bemmel JH, McCray AT, Haux R, Kulikowski C. Developing and Evaluating Criteria to Help Reviewers of Biomedical Informatics Manuscripts: A Case Report J Am Med Inform Assoc. 2003 June.
  • Lu CJ, Bangalore A, Tse T. Developing Web Browser Recording Tools Using Server-Side Programming Technology. Proc. of WebNet 2000, World conference on WWW and Internet: Association for the Advancement of Computing in Education. 2000;:372-7.
  • 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.
  • Misra D, Hall RH, Payne SM, Thoma GR. Digital preservation and knowledge discovery based on documents from an international health science program. Proc. 12th ACM/IEEE-CS JCDL, pg 23-26 (2012). doi: 10.1145/2232817.2232823.
  • Jeronimo J, Long R, Neve L, Bopf M, Antani K, Schiffman M. Digital Tools for Collecting Data from Cervigrams for Research and Training in Colposcopy J Low Genit Tract Dis. 2006 Jan;10(1):16-25.
  • Sarkar IN, Rindflesch TC. Discovering Protein Similarity Using Natural Language Processing Proc AMIA Symp. 2002:677-81.
  • Bodenreider O. Disease Ontologies In: Dubitzky W, Wolkenhauer O, Cho K-H, Yokota H, editors. Encyclopedia of Systems Biology: Springer; 2013. p. 578-581.
  • Peters L, Nguyen T, Bodenreider O. Displaying drug classes in RxNav [Poster]. AMIA Annu Symp Proc, 2013: p. 1134.
  • He L, Long LR, Antani S, Thoma GR. Distribution Fitting-based Pixel Labeling For Histology Image Segmentation Proceedings of SPIE Medical Imaging 2011. February 2011
  • Mao S, Rosenfeld A, Kanungo T. Document Structure Analysis Algorithms: A Literature Survey Proc. SPIE Electronic Imaging. 2003 Jan;5010:197-207.
  • You D, Antani SK, Demner-Fushman D, Thoma GR. Does Figure-Text Improve Biomedical Article Retrieval? A Pilot Study. CBMS 2014. May 2014.
  • You D, Antani SK, Demner-Fushman D, Thoma GR. Does figure-text improve biomedical image retrieval [Poster]. NIH Intramural Research Festival, Bethesda MD, November 6-8, 2013.
  • Nguyen V, Bodenreider O, Sheth AP. Don't Like RDF Reification? Making Statements about Statements Using Singleton Property. Proc Int World Wide Web Conf. 2014 Apr 11;2014:759-770.
  • Kamalakannan S, Gururajan A, Sari-Sarraf H, Long LR, Antani SK. Double-edge detection of radiographic lumbar vertebrae images using pressurized open DGVF snakes. IEEE Trans Biomed Eng. 2010 Jun;57(6):1325-34. doi: 10.1109/TBME.2010.2040082. Epub 2010 Feb 17.
  • 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.
  • KC S, Vajda S, Antani S, Thoma GR. Edge map analysis in chest X-rays for automatic pulmonary abnormality screening. Int J Comput Assist Radiol Surg. 2016 Sep;11(9):1637-46. doi: 10.1007/s11548-016-1359-6. Epub 2016 Mar 19.
  • 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
  • Chen S, Misra D, Thoma GR. Efficient Automatic OCR Word Validation Using Word Partial Format Derivation and Language Model Document Recognition and Retrieval XVII. Proceedings of the SPIE. San Jose, CA. January 2010;7534:75340O-75340O-8
  • 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.
  • Mao S, Kanungo T. Empirical Performance Evaluation Methodology and its Application to Page Segmentation Algorithms IEEE Transactions on Pattern Analysis and Machine Intelligence. 2001 Mar;23(3): 242-256.
  • Mao S, Kanungo T. Empirical Performance Evaluation of Page Segmentation Algorithms SPIE conference on Document Recognition and Retrieval. 2000 Jan.;:303-314.
  • Peters L, Mortensen J, Nguyen T, Bodenreider O. Enabling complex queries to drug information sources through functional composition. Stud Health Technol Inform. 2013;192:692-6.
  • Lu C, Tormey D, McCreedy L, Browne AC. Enhanced LexSynonym Acquisition for Effective UMLS Concept Mapping. Stud Health Technol Inform. 2017;245:501-505.
  • Guo P, Almubarak H, Banerjee K, Stanley RJ, Long LR, Antani SK, Thoma GR, Zuna R, Frazier S, Moss R, Stoecker W. Enhancements in localized classification for uterine cervical cancer digital histology image assessment. J Pathol Inform. 2016 Dec 30;7:51. doi: 10.4103/2153-3539.197193. eCollection 2016.
  • Beaudoin DE, Rocha RA, Tse T. Enhancing Access to Patient Education Information: A Pilot Usability Study AMIA Annu Symp Proc. 2005:892
  • Vizenor L, Bodenreider O, Peters L, McCray AT. Enhancing Biomedical Ontologies through Alignment of Semantic Relationships: Exploratory Approaches AMIA Annu Symp Proc. 2006:804-8.
  • 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
  • Yao S, Yu H, AliAkbarpour H, Seetharaman G, Palaniappan K. EpiX: A 3D Measurement Tool for Heritage, Archeology, and Aerial Photogrammetry Heritage Preservation, pp. 47-66, 2018.
  • Roberts K, Cahan A, Demner-Fushman D. Error Propagation in EHRs via Copy/Paste: An Analysis of Relative Dates [Poster]. Proceedings of the American Medical Informatics Association Fall Symposium (AMIA), Washington, D.C., Nov 15-19, 2014.
  • 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
  • Zamora G, Sari-Sarraf H, Mitra S, Long LR. Estimation of Orientation and Position of Cervical Vertebrae for Segmentation with Active Shape Models Proc. SPIE Medical Imaging: Image Processing. 2001 Feb;4322:378-87.
  • Logan RA. Evaluating Consumer Informatics: Learning from Health Campaign Research Medinfo. 2004;2004:1147-51.
  • Peters LB, Bahr N, Bodenreider O. Evaluating drug-drug interaction information in NDF-RT and DrugBank. J Biomed Semantics. 2015 May 11;6:19. doi: 10.1186/s13326-015-0018-0. eCollection 2015.
  • Shou J, Antani S, Long LR, Thoma GR. Evaluating Partial Shape Queries for Pathology-Based Retrieval of Verterbra Proc. 8th World Multiconference on Systemics, Cybernetics and Informatics. 2004 Jul.;12:155-60.
  • Winnenburg R, Bodenreider O. Evaluating the consistency of inferred drug-class membership relations in NDF-RT. Proc 17th ISMB'2014 SIG meeting "Bio-Ontologies" 2014
  • Simpson M, Demner-Fushman D, Thoma GR. Evaluating the Importance of Image-related Text for Ad-hoc and Case-based Biomedical Article Retrieval. AMIA Annu Symp Proc. 2010 Nov 13;2010:752-6.
  • McCray AT, Bodenreider O, Malley JD, Browne AC. Evaluating UMLS Strings for Natural Language Processing AMIA Annu Symp Proc. 2001;():448-52.
  • Karargyris A, Rondonotti E, Mandelli G, Koulaouzidis A. Evaluation of 4 three-dimensional representation algorithms in capsule endoscopy images. World J Gastroenterol. 2013 Nov 28;19(44):8028-33. doi: 10.3748/wjg.v19.i44.8028.
  • Edinger T, Demner-Fushman D, Cohen AM, Bedrick S, Hersh W. Evaluation of Clinical Text Segmentation to Facilitate Cohort Retrieval. AMIA Annu Symp Proc. 2018 Apr 16;2017:660-669. eCollection 2017.
  • 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.
  • Jeronimo J, Wentzensen N, Long R, Schiffman M, Dunst ST, Allen RA, Walker JL, Gold MA, Zuna RE, Sherman ME, Wacholder S, Wang SS. Evaluation of Linear Array Human Papillomavirus Genotyping Using Automatic Optical Imaging Software J Clin Microbiol. 2008 Aug;46(8):2759-65. Epub 2008 Jun 11
  • Huang X, Lin J, Demner-Fushman D. Evaluation of PICO as a knowledge representation for clinical questions AMIA Annu Symp Proc. 2006:359-63.
  • Antani S, Long LR, Lee DJ, Thoma GR. Evaluation of Shape Indexing Methods for Content-Based Retrieval of X-Ray Images Proceedings of IS&T/SPIE Electronic Imaging Science and Technology, Storage and Retrieval for Media Databases. 2003 Jan; 5021: 405-16.
  • Gordon S, Lotenberg S, Long LR, Antani SK, Jeronimo J, Greenspan H. Evaluation of uterine cervix segmentations using ground truth from multiple experts. Comput Med Imaging Graph. 2009 Apr;33(3):205-16. doi: 10.1016/j.compmedimag.2008.12.002. Epub 2009 Feb 13.
  • Bodenreider O, Burgun A, Mitchell JA. Evaluation of WordNet as a Source of Lay Knowledge for Molecular Biology and Genetic Diseases: A Feasibility Study Stud Health Technol Inform. 2003;95:379-84.
  • Scarton LA, Wang L, Kilicoglu H, Jahries M, Del Fiol M. Expanding vocabularies for complementary and alternative medicine therapies. Int J Med Inform. 2019 Jan;121:64-74. doi: 10.1016/j.ijmedinf.2018.11.009. Epub 2018 Nov 22.
  • 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 S, Bodenreider O. Experience in Aligning Anatomical Ontologies Int J Semant Web Inf Syst. 2007;3(2):1-26
  • Zeng K, Bodenreider O. Experience in Integrating Large RDF-based Biomedical Knowledge Resources with Oracle [Abstract]. Proc 8th International Oracle Life Sciences User Group Meeting 2007:(electronic proceedings: http://www.olsug.org/wiki/images/d/d1/Kelly_Zheng.pdf)
  • Zhang S, Bodenreider O, Golbreich C. Experience in Reasoning with the Foundational Model of Anatomy in OWL DL Pac Symp Biocomput. 2006:200-11
  • Bodenreider O. Experiences in Visualizing and Navigating Biomedical Ontologies and Knowledge Bases Proc. of the ISMB'SIG meeting; Bio-ontologies. 2002;:29-32.
  • 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
  • Erdogan H, Erdem E, Bodenreider O. Exploiting UMLS semantics for checking semantic consistency among UMLS concepts. Stud Health Technol Inform. 2010;160(Pt 1):749-53.
  • Deserno TM, Antani SK, Long LR. Exploring Access to Scientific Literature Using Content-Based Image Retrieval Proc SPIE Medical Imaging 2007. Vol. 6516: 65160L-1-8.
  • Bodenreider O, Pakhomov S. Exploring Adjectival Modification in Biomedical Discourse Across Two Genres Proc. of the ACL, 2003 Workshop, Natural Language Processing in Biomedicine. 2003;:105-112.
  • Winnenburg R, Sorbello A, Bodenreider O. Exploring adverse drug events at the class level. J Biomed Semantics. 2015 May 1;6:18. doi: 10.1186/s13326-015-0017-1. eCollection 2015.
  • Zeng QT, Tse T. Exploring and Developing Consumer Health Vocabularies J Am Med Inform Assoc. 2006 Jan-Feb;13(1):24-9. Epub 2005 Oct 12
  • Rance B, Demner-Fushman D, Rindflesch TC, Bodenreider O. Exploring Automatic Approaches to Extracting Pharmacogenomic Information from the Biomedical Literature Proceedings of the 2011 PSB Workshop on Mining the Pharmacogenomics Literature 2011
  • Tse T, Soergel D. Exploring Medical Expressions Used by Consumers and the Media: An Emerging View of Consumer Health Vocabularies AMIA Annu Symp Proc. 2003:674-8
  • Winnenburg R, Bodenreider O. Exploring pharmacoepidemiologic groupings of drugs from a clinical perspective. Stud Health Technol Inform. 2013;192:827-31.
  • Bodenreider O, McCray AT. Exploring Semantic Groups Through Visual Approaches J Biomed Inform. 2003 Dec;36(6):414-432.
  • Srinivasan P, Rindflesch T. Exploring Text Mining from MEDLINE Proc AMIA Symp. 2002:722-6.
  • Antani SK, Demner-Fushman D, Li J, Srinivasan BV, Thoma GR. Exploring Use of Images in Clinical Articles for Decision Support in Evidence-Based Medicine Proc. SPIE-IS/T Electronic Imaging. San Jose, CA. January 2008;6815:68150Q(1-10)
  • Graham L, Tse T, Keselman A. Exploring User Navigation during Online Health Information Seeking AMIA Annu Symp Proc. 2006:299-303
  • Fu GE, Bolton NQ, Rosinach LI, Furlong V, Nguyen AP, Sheth O, Bodenreider O, Dumontier M. Exposing provenance metadata using different RDF models. Proceedings of the International Conference on Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2015), 2015: p. (electronic proceedings: http://www.swat4ls.org/wp-content/uploads/2015/10/SWAT4LS_2015_paper_11.pdf).
  • Locatis C, Gaines C, Liu W, Gill MJ. Extending a Blended Education Programme to Native American High School Students in Alaska. J Vis Commun Med. 2009 Jan;32(1):8-13.
  • Rosemblat G, Resnick MP, Auston I, Shin D, Sneiderman C, Fizsman M, Rindflesch TC. Extending SemRep to the Public Health Domain. J Am Soc Inf Sci Technol. 2013 Oct;64(10):1963-1974.
  • Dhombres F, Winnenburg R, Case JT, Bodenreider O. Extending the coverage of phenotypes in SNOMED CT through post-coordination. Stud Health Technol Inform. 2015;216:795-9.
  • 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.
  • Zou J, Le DX, Thoma GR. Extracting a Sparsely-Located Named Entity from Online HTML Medical Articles Using Support Vector Machine Proc SPIE-IS/T Electronic Imaging. San Jose, CA. January 2008;6815:6815OP(1-10)
  • 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.
  • Rodriguez L, Demner-Fushman D. Extracting Diseases Co-occurring with Past Medical History of Lyme Disease. AMIA 2018 Informatics Summit
  • Fung KW, Jao CS, Demner-Fushman D. Extracting drug indication information from structured product labels using natural language processing. J Am Med Inform Assoc. 2013 May 1;20(3):482-8. doi: 10.1136/amiajnl-2012-001291. Epub 2013 Mar 9.
  • 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
  • Demner-Fushman D, Abhyankar S, Callaghan FM, McDonald CJ. Extracting sources of admission and discharge destinations from discharge summaries [Poster]. AMIA 2011 Fall Symposium.
  • Weeber M, Vos R. Extracting the Lowest-Frequency Words: Pitfalls and Possibilities Computational Linguistics. 2000;26(3):301-17.
  • Chachra S, Xue Z, Antani SK, Demner-Fushman D, Thoma GR. Extraction and Labeling High-resolution Images from PDF Documents. Proc. SPIE 9021, Document Recognition and Retrieval XXI, 90210Q (December 27, 2013). doi:10.1117/12.2042336.
  • Xue Z, Long LR, Jaeger S, Folio L, Thoma GR. Extraction of Aortic Knuckle Contour in Chest Radiographs Using Deep Learning. EMBC 2018.
  • Xue Z, You D, Chachra S, Antani SK, Long LR, Demner-Fushman D, Thoma GR. Extraction of endoscopic images for biomedical figure classification. Proc. SPIE. 9418, Medical Imaging 2015: PACS and Imaging Informatics: Next Generation and Innovations, 94180P. (March 17, 2015) doi: 10.1117/12.2081033.
  • Crandall D, Antani S, Kasturi R. Extraction of Special Effects Caption Text Events from Digital Video International Journal of Document Analysis and Recognition. 2003;5(2-3):138-57.
  • Rosemblat G, Graham L, Tse T. Extractive Summarization in Clinical Trials Protocol Summaries: A Case Study Proc IICAI-2007, pp. 1824-1837
  • Drake-Perez M, Smirniotopoulos J. Extraparenchymal Lesions in Adults. Neuroimaging Clin N Am. 2016 Nov;26(4):621-646. doi: 10.1016/j.nic.2016.06.009.
  • Borovikov E, Vajda S, Gill MJ. Face Match for Family Reunification: Real-World Face Image Retrieval International Journal of Computer Vision and Image Processing. DOI: 10.4018/IJCVIP.2017040102.
  • Borovikov E, Vajda S, Lingappa G, Antani SK, Thoma GR. Face matching for post-disaster family reunification. IEEE International Conference on Healthcare Informatics. Philadelphia, PA, USA. September 2013.
  • Misra D, Gill MJ. FaceMatch: A System for Dynamic Search and Retrieval of Faces. Proc. Archiving 2018. Washington DC. pp. 53-57. DOI: 10.2352/issn.2168-3204.2018.1.0.12.
  • Borovikov E, Bonifant MC, Lingappa G, Gill MJ, Thoma GR. FaceMatch: a visual search system for family reunification during disasters [Poster]. NIH Research Festival, September 2016
  • Borovikov E, Vajda S. FaceMatch: real-world face image retrieval. In: Santosh K., Hangarge M., Bevilacqua V., Negi A. (eds) Recent Trends in Image Processing and Pattern Recognition. RTIP2R 2016. Communications in Computer and Information Science, vol 709. Springer, Singapore. 405-419.
  • Borovikov E. FaceMatch: visual search for pictures of missing persons during a disaster event. NIH Research Festival. October 2012.
  • Borovikov E, Vajda S, Lingappa G, Candemir S, Antani SK, Gill MJ, Thoma GR. FaceMatch: visual search of missing persons during a disaster event [Poster]. NIH Intramural Research Festival, Bethesda MD, November 6-8, 2013.
  • Divita G, Tse T, Roth L. Failure Analysis of MetaMap Transfer (MMTx) Medinfo. 2004 Sept.;2004:763-7.
  • Bryant B, Sari-Sarraf H, Wachtel M, Long LR, Antani SK. Fast GPU-based segmentation of H&E stained squamous epithelium from multi-gigapixel tiled virtual slides [Poster]. Proc. SPIE 8676, Medical Imaging 2013: Digital Pathology, 86760X (March 29, 2013); doi:10.1117/12.2007800
  • Locatis C, Fontelo P, Ackerman MJ, Sneiderman C. Feasibility Studies in IP Videoconferencing, Streaming, and Wireless Communication. AMIA Annu Symp Proc [Proceedings of the American Medical Informatics Association Annual Symposium]; 2002 Nov 9-13; San Antonio, Texas. p. 1090.
  • Bekhuis T, Tseytlin E, Mitchell KJ, Demner-Fushman D. Feature engineering and a proposed decision-support system for systematic reviewers of medical evidence. PLoS One. 2014 Jan 27;9(1):e86277. doi: 10.1371/journal.pone.0086277. eCollection 2014.
  • 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.
  • Long LR, Thoma GR. Feature Indexing in a Database of Digitized X-Rays Proc. of SPIE Storage and Retrieval for Media Databases. 2001 Jan;4315:393-403.
  • Vajda S, Karargyris A, Jaeger S, Santosh KC, Candemir S, Xue Z, Antani SK, Thoma GR. Feature Selection for Automatic Tuberculosis Screening in Frontal Chest Radiographs. J Med Syst. 2018 Jun 29;42(8):146. doi: 10.1007/s10916-018-0991-9.
  • Guo P, Stanley RJ, De S, Long LR, Antani SK, Thoma GR, Demner-Fushman D, Sornapudia S. Features Advances to Automatically Find Images for Application to Clinical Decision Support. Medical Research Archives. 4(7) 2016. DOI: 10.18103/mra.v4i7.761
  • You D, Apostolova E, Antani SK, Demner-Fushman D, Thoma GR. Figure content analysis for improved biomedical article retrieval. Proceedings of IS&T/SPIE Electronic Imaging, 2009, San Jose, California, United States, Document Recognition and Retrieval XVI; 72470V (2009), 1-10; doi: 10.1117/12.805976
  • Wei W, Marmor R, Singh S, Wang S, Demner-Fushman D, Kuo TT, Hsu CN, Ohno-Machado L. Finding Related Publications: Extending the Set of Terms Used to Assess Article Similarity. AMIA Jt Summits Transl Sci Proc. 2016 Jul 20;2016:225-34. eCollection 2016.
  • Demner-Fushman D, Humphrey SM, Ide NC, Loane RF, Ruch P, Ruiz ME, Smith LH, Tanabe LK, Wilbur WJ, Aronson AR. Finding Relevant Passages in Scientific Articles: Fusion of Automatic Approaches vs. an Interactive Team Effort. Proc TREC 2006, 569-76.
  • Srinivasan S, Rindflesch TC, Hole WT, Aronson AR, Mork JG. Finding UMLS Metathesaurus Concepts in MEDLINE. Proc AMIA Symp. 2002:727-31.
  • Rodriguez L, Demner-Fushman D. Finding Understudied Disorders Potentially Associated with Maternal Morbidity and Mortality. AJP Rep. 2019 Jan;9(1):e36-e43. doi: 10.1055/s-0039-1683363. Epub 2019 Mar 4.
  • 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.
  • Rance B, Le T, Bodenreider O. Fingerprinting Biomedical Terminologies--Automatic Classification and Visualization of Biomedical Vocabularies through UMLS Semantic Group Profiles. Stud Health Technol Inform. 2015;216:771-5.
  • Xue Z, Candemir S, Antani SK, Long LR, Jaeger S, Demner-Fushman D, Thoma GR. Foreign Object Detection in Chest X-rays. Proc IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2015, International Workshop on Biomedical and Health Informatics, Bethesda, Maryland, Nov. 9-12, 2015, pp: 56-61.
  • 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.
  • Zarin D, Tse T, Williams R. Frequency and nature of changes in primary outcome measures. Presented at: Sixth International Congress on Peer Review and Biomedical Publication; September 2009; Vancouver, BC, Canada.
  • 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
  • Parascandola J. From Cards to Computers: The National Library of Medicine and the Transmission of Medical Knowledge Medicina nei Secoli. 2002;:14.
  • Schulz S, Balkanyi L, Cornet R, Bodenreider O. From concept representations to ontologies: a paradigm shift in health informatics? Healthc Inform Res. 2013 Dec;19(4):235-42. doi: 10.4258/hir.2013.19.4.235. Epub 2013 Dec 31.
  • Bodenreider O, Aubry M, Burgun A. From Functional Similarity Among Gene Products to Dependence Relations Among Gene Ontology Terms Proc SOFG, 2004:53.
  • Parascandola J. From Germs to Genes: Trends in Drug Therapy, 1852-2002 Pharm Hist. 2002 ;44(1):3-11.
  • 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.
  • Mitchell JA, McCray AT, Bodenreider O. From Phenotype to Genotype: Issues in Navigating the Available Information Resources Methods Inf Med. 2003;42(5):557-63.
  • Zweigenbaum P, Demner-Fushman D, Yu H, Cohen KB. Frontiers of biomedical text mining: current progress Brief Bioinform. 2007 Sep;8(5):358-75. Epub 2007 Oct 30.
  • 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
  • Deserno TM, Antani SK, Long LR. Gaps in Content-Based Image Retrieval Proc SPIE Medical Imaging 2007. Vol. 6516: 65160J-1-11
  • Xue Z, Rajaraman S, Long LR, Antani SK, Thoma GR. Gender Detection from Spine X-ray Images Using Deep Learning. Proc. IEEE International Symposium on Computer-Based Medical Systems (CBMS), Karlstad, Sweden, 2018. pp. 54-58, DOI:10.1109/CBMS.2018.00017.
  • Wang H, Azuaje F, Bodenreider O, Dopazo J. Gene Expression Correlation and Gene Ontology-Based Similarity: An Assessment of Quantitative Relationships Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB'2004) 2004:25-31.
  • 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.
  • Azuaje FJ, Bodenreider O, Wang H, Dopazo J. Gene Ontology-Driven Similarity for Gene Expression Correlation Analysis Proceedings of the second conference on Standards and Ontologies for Functional Genomics (SOFG 2) 2004:47.
  • Sehgal AK, Srinivasan P, Bodenreider O. Gene Terms and English Words: An Ambiguous Mix Proc of the SIGIR 2004 Workshop on Search and Discovery in Bioinformatics 2004.
  • Villegas M, Müller R, De Herrera A, Schaer R, Bromuri S, Gilbert A, Piras L, Wang J, Yan F, Ramisa A, Dellandrea E, Gaizauskas R, Mikolajczyk K, Puigcerver J, Toselli A, Sánchez J, Vidal E. General Overview of ImageCLEF at the CLEF 2016 Labs. CLEF Proceedings, Springer, 2016
  • 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.
  • Mao S, Kim J, Le DX, Thoma GR. Generating Robust Features for Style-Independent Labeling of Bibliographic Fields in Medical Journal Articles Proc. 7th World Multiconference on Systemics, Cybernetics and Informatics.2003 July;III:53-6.
  • 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
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  • Cantor MN, Sarkar INK, Bodenreider O, Lussier YA. GenesTrace: Phenomic Knowledge Discovery Via Structured Terminologies Pac Symp Biocomput. 2005:103-14.
  • Sarkar IN, Cantor MN, Bodenreider O, Lussier YA. GenesTraceTM: Biological Knowledge Discovery via Structured Terminology MedInfo.
  • 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.
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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
  • Antani SK, Deserno TM, Long LR, Thoma GR. Geographically Distributed Complementary Content-Based Image Retrieval Systems for Biomedical Image Informatics Stud Health Technol Inform. 2007;129(Pt 1):493-7
  • Tsaparas P, Marino-Ramirez L, Bodenreider O. Global Similarity and Local Divergence in Human and Mouse Gene Co-expression Networks BMC Evol Biol. 2006 Sep 12;6:70
  • Candemir S, Jaeger S, Palaniappan K, Antani SK, Thoma GR. Graph Cut Based Automatic Lung Boundary Detection in Chest Radiographs. 1st Annual IEEE Healthcare Innovation Conference of the IEEE EMBS Houston, Texas USA, 7 - 9 November, 2012.
  • de Herrera G, Long LR, Antani SK. Graph Representation for Content–based fMRI Activation Map Retrieval. Proceedings of 1st Life Sciences Conference, Sydney, Australia, December 2017 pp. 129-32 DOI: https://doi.org/10.1109/LSC.2017.8268160.
  • 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.
  • Bodenreider O, Mitchell JA. Graphical Visualization and Navigation of Genetic Disease Information AMIA Annu Symp Proc. 2003:792.
  • Le DX, Straughan SR, Thoma GR. Greek Alphabet Recognition Technique for Biomedical Documents Proc. 6th World Multiconference on Systemics, Cybernetics and Informatics, eds: Callaos N, et al. 2002 July;III: 86-91.
  • Ford G, Thoma GR. Ground Truth Data for Document Image Analysis Proceedings of 2003 Symposium on Document Image Understanding and Technology. 2003 April 9-11;: 199-205.
  • Sorbello A, Ripple AM, Tonning J, Munoz M, Hasan R, Ly T, Francis H, Bodenreider O. Harnessing scientific literature reports for pharmacovigilance. Prototype software analytical tool development and usability testing. Appl Clin Inform. 2017 Mar 22;8(1):291-305. doi: 10.4338/ACI-2016-11-RA-0188.
  • Soergel D, Tse T, Slaughter L. Helping Healthcare Consumers Understand: An "Interpretive Layer" for Finding and Making Sense of Medical Information Medinfo. 2004 Sept.;2004:931-5.
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  • Callaghan FM, Leishear K, Abhyankar S, Demner-Fushman D, McDonald CJ. High vitamin B12 levels are not associated with increased mortality risk for ICU patients after adjusting for liver function: a cohort study. ESPEN J. 2014 Apr 1;9(2):e76-e83.
  • He L, Long LR, Antani SK, Thoma GR. Histology image analysis for carcinoma detection and grading. Comput Methods Programs Biomed. 2012 Sep;107(3):538-56. doi: 10.1016/j.cmpb.2011.12.007. Epub 2012 Mar 20.
  • Sabir TF, Hauser SE, Thoma GR. Historical Author Affiliations Assist Verification of Automatically Generated MEDLINE Citations AMIA Annu Symp Proc. 2006:1082
  • Logan RA, Park J, Shin JH. How Two Korean Newspapers Covered a Public Health Crisis Science Communication. 25:4:365-389 (June 2004)
  • Zhang S, Bodenreider O. Hybrid Alignment Strategy for Anatomical Ontologies Results of the 2007 Ontology Alignment Contest Proc OAEI 2007:139-149
  • Kim IC, Le DX, Thoma GR. Hybrid approach combining contextual and statistical information for identifying and statistical information for identifying MEDLINE citation terms. Proc. SPIE-IS/T Electronic Imaging. San Jose, CA. January 2008;6815:68150P(1-9)
  • Kayaalp M. ICU Outcome Predictions using Physiologic Trends in the First Two Days. Computing in Cardiology (39)977–980.
  • Long LR, Thoma GR. Identification and Classification of Spine Vertebrae by Automated Methods Proc. SPIE Medical Imaging: Image Processing. 2001 Feb;:1478-89.
  • Srinivasan B, Antani S, Demner-Fushman D, Thoma GR. Identification and Segmentation of Multi-Panel Images in Biomedical Journal Articles [Poster]. Poster at 20th NIH Research Festival (BIOINFO-1), September 2007, National Institutes of Health
  • Kim IC, Le DX, Thoma GR. Identification of "comment-on sentences" in online biomedical documents using support vector machines. Proc. SPIE conference on Document Recognition and Retrieval, 6500:65000O (1-8), San Jose, January 2007.
  • Mariño-Ramírez L, Tharakaraman K, Bodenreider O, Spounge J, Landsman D. Identification of cis-regulatory Elements in Gene Co-expression Networks Using A-GLAM. Methods Mol Biol. 2009;541:1-22.
  • Kim J, Le DX, Thoma GR. Identification of Investigator Name Zones Using SVM Classifiers and Heuristic Rules. 12th international Conference on Document Analysis and Recognition (ICDAR). Washington D.C., August 2013.
  • Mougin F, Bodenreider O, Burgun A. Identifying anatomical concepts associated with ICD10 diseases. Proceedings of the 8th Conference on Terminology and Artificial Intelligence (TIA 2009), 2009: p. (electronic proceedings: http://www.irit.fr/TIA09/start_here.htm).
  • Bernhardt PJ, Rindflesch TC, Kilicoglu H, Tringali M. Identifying Anatomical Concepts in Biomedical Text for Automatic Selection of Images Medinfo. 2004 Sept.;2004: 1521.
  • Zeng QT, Tse T, Crowell J, Divita G, Roth L, Browne AC. Identifying Consumer-Friendly Display (CFD) Names for Health Concepts AMIA Annu Symp Proc. 2005:859-63
  • Long LR, Krainak DM, Thoma GR. Identifying Image Structures for Content-Based Retrieval of Digitized Spine X-Rays Proc. of SPIE Medical Imaging: Image Processing. 2002 Feb; 4684.
  • Jao CS, Fung KW, Demner-Fushman D. Identifying indications for drugs in drug package inserts. AMIA Annual Symposium Proceedings 2010. November 2010
  • Zhang S, Bodenreider O. Identifying Mismatches in Alignments of Large Anatomical Ontologies AMIA Annu Symp Proc. 2007 Oct 11:851-5
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  • 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.
  • Bodenreider O, Zweigenbaum P. Identifying Proper Names in Parallel Medical Terminologies Stud Health Technol Inform. 2000;77:443-7
  • 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
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  • Poostchi M, Silamut K, Maude RJ, Jaeger S, Thoma GR. Image analysis and machine learning for detecting malaria. Transl Res. 2018 Apr;194:36-55. doi: 10.1016/j.trsl.2017.12.004. Epub 2018 Jan 12.
  • Chamarthy P, Stanley RJ, Cizek G, Long R, Antani S, Thoma G. Image Analysis Techniques for Characterizing Disc Space Narrowing in Cervical Vertebrae Computerized Medical Imaging and Graphics. 2004; 28: 39-50.
  • Stanley RJ, Seetharaman S, Long LR, Antani S, Thoma GR, Downey E. Image Analysis Techniques for the Automated Evaluation of Subaxial Subluxation in Cervical Spine X-Ray Images Proc. 17th IEEE Symposium on Computer-Based Medical Systems: IEEE Computer Society. 2004 June.;: 204-9.
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  • Apostolova E, You D, Xue Z, Antani SK, Demner-Fushman D, Thoma GR. Image Retrieval From Scientific Publications: Text and Image Content Processing To Separate Multipanel Figures. JASIST (Journal of the American Society for Information Science and Technology), 64(5):893–908, 2013.
  • Faruque J, Antani SK, Long LR, Kim L, Thoma GR. Image similarity ranking of focal computed tomography liver lesions using a 2AFC technique. Proc. SPIE. 9787, Medical Imaging 2016: Image Perception, Observer Performance, and Technology Assessment, 97870N. DOI: 10.1117/12.2217364.
  • Xue Z, Long LR, Antani SK, Jeronimo J, Thoma GR. Image-retrieval System Aids Cervical Cancer Studies SPIE Newsroom. April 2009
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  • Kim J, Le DX, Thoma GR. Inferring Grant Support Types From Online Biomedical Articles 22nd IEEE ISCBMS. Albuquerque, NM. August 2009
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  • Doughty E, Kirk B, Kann MG, Bodenreider O. Integrating Drug-gene Associations Mined from the Literature with Drug Information Sources - A Comparison with PharmGKB Proceedings of the 2011 PSB Workshop on Mining the Pharmacogenomics Literature 2011
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  • Bodenreider O, Demner-Fushman D. Investigating drug classes in biomedical terminologies from the perspective of clinical decision support. AMIA Annu Symp Proc. 2010 Nov 13;2010:56-60.
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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.
  • Zhang S, Bodenreider O. Knowledge Augmentation for Aligning Ontologies: An Evaluation in the Biomedical Domain Proceedings of the Semantic Integration Workshop at the Second International Semantic Web Conference. 2003: 109-114.
  • Backer A, Bodenreider O, Karp P, Kelly H, Loranger S, Musen M, Sriram R, Wroe C. Knowledge Integration for Bio-Threat Response Los Alamos White Paper
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  • Kim J, Hong S, Thoma GR. Labeling Author Affiliations in Biomedical Articles Using Markov Model Classifiers. The 13th International Conference on Data Mining (DMIN2017), pp. 105-110, Las Vegas, USA, July 2017.
  • 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.
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  • 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.
  • Lord AM. Learning The "Washington Way": The United States Public Health Service and the History of Sex Education
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  • 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
  • Locatis CN, Gaines C, Liu WL, Gill MJ, Ackerman MJ. Lessons learned from ten years of distance learning outreach. J Med Libr Assoc. 2015 Apr;103(2):78-82. doi: 10.3163/1536-5050.103.2.004.
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  • Rance B, Snyder M, Lewis J, Bodenreider O. Leveraging terminological resources for mapping between rare disease information sources. Stud Health Technol Inform. 2013;192:529-33.
  • Bodenreider O. Lexical, Terminological and Ontological Resources for Biological Text Mining Ananiadou S, McNaught J, editors. Text mining for biology and biomedicine: Artech House; 2006. p. 43-66.
  • Bodenreider O, Burgun A, Rindflesch TC. Lexically-Suggested Hyponymic Relations Among Medical Terms and Their Representation in the UMLS Proc. of TIA'2001; Terminology and Artificial Intelligence. 2001;:11-21.
  • KC S, Aafaque A, Antani SK, Thoma GR. Line Segment-Based Stitched Multipanel Figure Separation for Effective Biomedical CBIR. Int. J. Patt. Recogn. Artif. Intelligence 31, 1757003 (2017) https://doi.org/10.1142/S0218001417570038.
  • 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.
  • Bodenreider O, Burgun A. Linking the Gene Ontology to other biological ontologies Proc ISMB'2005 SIG meeting on Bio-ontologies 2005:17-18
  • Seetharaman S, Stanley RJ, De S. Live Wire Segmentation Tool for Osteophyte Detection in Lumbar Spine X-Ray Images Proc IEEE ICETET 2008. Nagpur, India. July 2008:715-20
  • He L, Long LR, Antani SK, Thoma GR. Local and Global Gaussian Mixture Models For Hematoxylin and Eosin Stained Histology Image Segmentation 20th International Conference on Hybrid Intelligence Systems. Atlanta, GA. August 2010:223-8
  • Rahman MM, Antani SK, Thoma GR. Local Concept-Based Medical Image Retrieval With Correlation-Enhanced Similarity Matching Based On Global Analysis IEEE Computer Society Workshop on Mathematical Methods in Biomedical Image Analysis (MMBIA10) in conjunction with IEEE International Conference on Computer Vision and Pattern Recognition (CVPR) 2010. June 2010:87-94
  • Ding M, Antani SK, Jaeger S, Xue Z, Candemir S, Kohli M, Thoma GR. Local-Global Classifier Fusion for Screening Chest Radiographs. Proc. SPIE 10138, Medical Imaging 2017: Imaging Informatics for Healthcare, Research, and Applications, 101380A (March 13, 2017); doi:10.1117/12.2252459
  • Zou J, Antani SK, Thoma GR. Localizing and Recognizing Labels for Multi-Panel Figures in Biomedical Journals. Proceedings of International Conference on Document Analysis and Recognition, November 13, 2017
  • Xu X, Lee DJ, Antani S, Long LR. Localizing Contour Points for Indexing an X-Ray Image Retrieval System Los Alamitos, CA: IEEE Computer Society. 2003 June;: 169-74.
  • Li J, Demner-Fushman D, Thoma GR. Localizing Text and Symbols in Images from Biomedical Journal Articles Poster at 20th NIH Research Festival (BIOINFO-6), September 2007, National Institutes of Health
  • Xue Z, Jaeger S, Antani SK, Long LR, Karargyris A, Siegelman J, Folio L, Thoma GR. Localizing tuberculosis in chest radiographs with deep learning. Proc SPIE 10579, Medical Imaging 2018: Imaging Informatics for Healthcare, Research, and Applications, 105790U (6 March 2018) pp. doi: 10.1117/12.2293022
  • Xue Z, Jaeger S, Antani SK, Long LR, Karargyris A, Siegelman J, Folio LR, Thoma GR. Localizing tuberculosis in chest radiographs with deep learning. SPIE Medical Imaging 2018
  • Zou J, Le DX, Thoma GR. Locating and parsing bibliographic references in HTML medical articles. Int J Doc Anal Recognit. 2010 Jun 1;13(2):107-119.
  • 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
  • Mougin F, Bodenreider O, Burgun A. Looking for Anemia (and Other Disorders) in SNOMED CT: Comparison of Three Approaches and Practical Implications. AMIA Annu Symp Proc. 2010 Nov 13;2010:527-31.
  • Abhyankar S, Leishear K, Callaghan FM, Demner-Fushman D, McDonald CJ. Lower short- and long-term mortality associated with overweight and obesity in a large cohort study of adult intensive care unit patients. Crit Care. 2012 Dec 18;16(6):R235. doi: 10.1186/cc11903.
  • Candemir S, Antani SK, Jaeger SR, Thoma GR. Lung boundary detection in pediatric chest x-rays. Proc. SPIE. 9418, Medical Imaging 2015: PACS and Imaging Informatics: Next Generation and Innovations, 94180Q. (March 17, 2015) doi: 10.1117/12.2081060.
  • Candemir S, Jaeger S, Palaniappan K, Musco J, Singh RK, Xue Z, Karargyris A, Antani SK, Thoma GR, McDonald CJ. Lung segmentation in chest radiographs using anatomical atlases with nonrigid registration. IEEE Trans Med Imaging. 2014 Feb;33(2):577-90. doi: 10.1109/TMI.2013.2290491. Epub 2013 Nov 13.
  • Roberts K, Shooshan SE, Rodriguez L, Abhyankar S, Kilicoglu H, Demner-Fushman D. Machine Learning Methods for Detecting Risk Factors for Heart Disease in EHRs. Proc i2b2 2014 Workshop
  • Kim I, Thoma GR. Machine Learning with Selective Word Statistics for Automated Classification of Citation Subjectivity in Online Biomedical Articles. Proc. Int’l Conf. Artificial Intelligence (ICAI’17), pp. 201-207, Las Vegas, July 2017.
  • Rosemblat G, Gemoets D, Browne AC, Tse T. Machine Translation-Supported Cross Language Information Retrieval for a Consumer Health Resource AMIA Annu Symp Proc. 2003:564-8.
  • Rae A, Kim J, Le DX, Thoma GR. Main Content Detection in HTML Journal Articles. DocEng ’18: ACM Symposium on Document Engineering 2018, August 28–31, 2018, Halifax, NS, Canada. ACM, New York, NY, USA, 4 pages. https://doi.org/10.1145/3209280.3229115
  • Jaeger S. Malaria Datasets
  • Poostchi M, Ilker E, McMenamin K, Gordon E, Palaniappan N, Pierce S, Maude RJ, Bansal A, Srinivasan P, Miller L, Palaniappan K, Thoma GR, Jaeger S. Malaria parasite detection and cell counting for human and mouse using thin blood smear microscopy. J Med Imaging (Bellingham). 2018 Oct;5(4):044506. doi: 10.1117/1.JMI.5.4.044506. Epub 2018 Dec 12.
  • 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.
  • Mougin F, Burgun A, Bodenreider O. Mapping Data Elements to Terminological Resources for Integrating Biomedical Data Sourcse BMC Bioinformatics. 2006 Nov 24;7 Suppl 3:S6
  • Lomax J, McCray AT. Mapping the Gene Ontology Into the Unified Medical Language System Comparative and Functional Genomics
  • Burgun A, Bodenreider O. Mapping the UMLS Semantic Network into General Ontologies Proc AMIA Symp. 2001:81-5.
  • 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.
  • Antani S, Cheng J, Long J, Long LR, Thoma GR. Medical Validation and CBIR of Spine X-ray Images over the Internet Proc IS and T/SPIE Electronic Imaging Science and Technology 2006: Internet Imaging VII. San Jose. CA Jan 15-19, 2006, SPIE Vol. 6061 pp. 60610J (1-9).
  • Demner-Fushman D, Hauser SE, Humphrey SM, Ford GM, Jacobs JL, Thoma GR. MEDLINE as a Source of Just-in-Time Answers to Clinical Questions. AMIA Annu Symp Proc. 2006:190-4.
  • 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".
  • Ben Abacha A, Demner-Fushman D. Meta-Learning with Selective Data Augmentation for Medical Entity Recognition. International Journal of Computational Linguistics and Applications (IJCLA) 7(2): 167-182 (2016)
  • 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.
  • Moyer E, Hagenauer M, Lesko M, Francis F, Rodriguez O, Nagarajan V, Huser V, Busby B. MetaNetVar: Pipeline for applying network analysis tools for genomic variants analysis. F1000Res. 2016 Apr 13;5:674. doi: 10.12688/f1000research.8288.1. eCollection 2016.
  • 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.
  • Huser V, Kahn MG, Brown JS, Gouripeddi R. Methods for examining data quality in healthcare integrated data repositories. Pac Symp Biocomput. 2018;23:628-633.
  • Burgun A, Bodenreider O. Methods for Exploring the Semantics of the Relationships Between Co-Occurring UMLS Concepts Medinfo. 2001 ;10(Pt 1):171-5.
  • Peters L, Kapusnik-Uner JE, Bodenreider O. Methods for managing variation in clinical drug names. AMIA Annu Symp Proc. 2010 Nov 13;2010:637-41.
  • Winnenburg R, Bodenreider O. Metrics for assessing the quality of value sets in clinical quality measures. AMIA Annu Symp Proc. 2013 Nov 16;2013:1497-505. eCollection 2013.
  • Golbreich C, Zhang S, Bodenreider O. Migrating the FMA from Protege to OWL Proc of the Eighth International Protege Conference 2005:108-111.
  • Abhyankar S, Demner-Fushman D, Callaghan F, Leishear K, McDonald CJ. MIMIC-II: a database of 30,000+ patients for ICU research. NIH Intramural Research Festival, Bethesda MD, October 9-12, 2012.
  • Guan H, Antani S, Long LR, Thoma GR. Minimizing the Semantic Gap In Biomedical Content-based Image Retrieval Proc SPIE, Medical Imaging: Advanced PACS-based Imaging Informatics, and Therapeutic Applications. March 2010;7628:762807-1 ~ 762807-8
  • An L, Obradovic Z, Smith D, Bodenreider O, Megalooikonomou V. Mining Association Rules among Gene Functions in Clusters of Similar Gene Expression Maps. Workshop proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM09) -- Workshop on Data Mining in Functional Genomics 2009: p. 254-259
  • 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.
  • Cui L, Zhu W, Tao S, Case JT, Bodenreider O, Zhang GQ. Mining non-lattice subgraphs for detecting missing hierarchical relations and concepts in SNOMED CT. J Am Med Inform Assoc. 2017 Jul 1;24(4):788-798. doi: 10.1093/jamia/ocw175.
  • Tao S, Cui L, Zhu W, Sun M, Bodenreider O, Zhang GQ. Mining Relation Reversals in the Evolution of SNOMED CT Using MapReduce. AMIA Jt Summits Transl Sci Proc. 2015 Mar 23;2015:46-50. eCollection 2015.
  • 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.
  • Altemus AR. Mobile App: Native Voices: Native Peoples' Concepts of Health and Illness
  • Gill MJ, Pearson G, Neve L, Miernicki G, Antani SK, Thoma GR. Mobile App: ReUnite iOS app
  • Thoma GR. Mobile App: Turning the Pages
  • Thamizhvani TR, Lakshmanan S, Rajaraman S. Mobile application-based computer-aided diagnosis of skin tumours from dermal images. The Imaging Science Journal, 66:6, 382-391, 2018, DOI: 10.1080/13682199.2018.1492682
  • Xue Z, Rahman M, Antani SK, Long LR, Demner-Fushman D, Thoma GR. Modality Classification for Searching Figures in Biomedical Literature. Proceedings of the IEEE 29th International Symposium on Computer-Based Medical Systems, pp. 152-157, 2016. doi:10.1109/CBMS.2016.29.
  • Jacquelinet C, Bodenreider O, Burgun A. Modelling Syllepse in Medical Knowledge Bases with Application in the Domain of Organ Failure and Transplantation Proc. of OntoLex; Workshop on Ontologies and Lexical Knowledge Bases 2000.
  • Lord AM. Models of Masculinity: Sex Education, the United States Public Health Service, and the YMCA, 1919-1924 J Hist Med Allied Sci. 2003 Apr ;58(2):123-52.
  • Kayaalp M. Modes of De-identification. AMIA Annu Symp Proc. 2018 Apr 16;2017:1044-1050. eCollection 2017.
  • Zarin DA, Tse T. Moving Towards Transparency of Clinical Trials Science. 2008 Mar 7;319(5868):1340-2.
  • Xu T, Zhang H, Xin C, Kim E, Long LR, Xue Z, Antani SK, Huang Z. Multi-feature based Benchmark for Cervical Dysplasia Classification Evaluation. Pattern Recognition. ISSN 0031-3203, DOI: 10.1016/j.patcog.2016.09.027.
  • Bodenreider O. Multi-lingual features of the Unified Medical Language System. Proc. CLEF-ER 2013 workshop 2013.
  • Rahman MM, Antani S, Long LR, Demner-Fushman D, Thoma GR. Multi-Modal Query Expansion Based on Local Analysis for Medical Image Retrieval. Lecture Notes in Computer Science. First MICCAI International Workshop on Medical Content-Based Retrieval for Clinical Decision Support (MCBR-CDS 2009); part of the 12th International Conference on Medical Image Computing and Computer Assisted Interventio February 2010;5853/2010(doi: 10.1007/978-3-642-11769-5):110-9..
  • Xu T, Huang X, Kim E, Long LR, Antani SK. Multi-test cervical cancer diagnosis with missing data estimation. Proc. SPIE. 9414, Medical Imaging 2015: Computer-Aided Diagnosis, 94140X. (March 20, 2015) doi: 10.1117/12.2080871.
  • 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.
  • Huser V, DeFalco FJ, Schuemie M, Ryan PB, Shang N, Velez M, Park RW, Boyce RD, Duke J, Khare R, Utidjian L, Bailey L. Multisite Evaluation of a Data Quality Tool for Patient-Level Clinical Data Sets. EGEMS (Wash DC). 2016 Nov 30;4(1):1239. doi: 10.13063/2327-9214.1239. eCollection 2016.
  • Yang S, Guo J, King PS, Sriraja Y, Long LR. Multispectral Digital Cervigram Analyser in the Wavelet Domain for Early Detection of Cervical Cancer Proc. SPIE Medical Imaging. 2004 Feb; 5370.
  • 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.
  • Nelson SJ, Zeng K, Bodenreider O. MyMedicationList: Integrating Personal Medication Records with Resources AMIA Annu Symp Proc. 2008 Nov 6:1228
  • Kim J, Le DX, Thoma GR. Naive Bayes and SVM Classifiers For Classifying Databank Accession Number Sentences From Online Biomedical Articles IS&T/SPIE's 22nd Annual Symposium on Electronic Imaging. San Jose, CA. January 2010;7534:75340U-1 - 8
  • Kim J, Le DX, Thoma GR. Naive Bayes Classifier for Extracting Bibliographic Information From Biomedical Online Articles Proc 2008 International Conference on Data Mining. Las Vegas, Nevada, USA. July 2008;II:373-8
  • Kim J, Thoma GR. Named Entity Recognition in Affiliations of Biomedical Articles Using Statistics and HMM Classifiers. The 2016 International Conference on Data Mining (DMIN2016), Las Vegas, USA, pp. 236-241, July, 2016.
  • Ben Abacha A, Long LR, Seco de Herrera AG, Antani SK, Wang K, Demner-Fushman D. Named Entity Recognition in Functional Neuroimaging Literature. BIBM 2017
  • 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.
  • 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.
  • 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.
  • Zhang S, Bodenreider O. NLM Anatomical Ontology Alignment system: Results of the 2006 ontology alignment contest Proc OAEI 2006 2006:145-156
  • KC S, Xue Z, Antani SK, Thoma GR. NLM at ImageCLEF 2015: Biomedical Multipanel Figure Separation. Editors: Cappellato, L., Ferro, N., Jones, G., and San Juan, E., CLEF 2015 Labs and Workshops, Notebook Papers. CEUR WorkshopProceedings (CEUR-WS.org), ISSN 1613-0073, http://ceur-ws.org/ Vol-1391/.
  • Ben Abacha A, De Herrera A, Gayen S, Demner-Fushman D, Antani SK. NLM at ImageCLEF 2017 Caption Task. International Conference of the Cross-Language Evaluation Forum for European Languages 2017 Sep 11 (pp. 358-360). Springer, Cham.
  • Ben Abacha A, Gayen S, Lau JJ, Rajaraman S, Demner-Fushman D. NLM at ImageCLE