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  • Rosemblat G, Fiszman, M, Shin D, Kilicoglu H. Towards a characterization of apparent contradictions in the biomedical literature using context analysis. Journal of Biomedical Informatics. 2019. In Press. https://doi.org/10.1016/j.jbi.2019.103275.
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  • 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.
    Abstract | pub9960.pdf
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  • Divita G, Rosemblat G, Browne AC. Building a medical Spanish lexicon. AMIA Annu Symp Proc. 2007 Oct 11:941.
    Abstract | PMID:  18694041
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  • Xue Y, Zhou Q, Ye J, Long LR, Antani SK, Cornwell C, Xue Z, Huang X. Synthetic Augmentation and Feature-based Filtering for Improved Cervical Histopathology Image Classification. ArXiv, abs/1907.10655.
    Abstract | pub9956.pdf
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  • 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.
    Abstract | pub9938.pdf
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  • Ganesan P, Xue Z, Singh S, Long LR, Ghoraani B, Antani SK. Performance Evaluation of a Generative Adversarial Network for Deblurring Mobile-phone Cervical Images. Proc. IEEE Engineering in Medicine and Biology Conference (EMBC), Berlin, Germany, 23 – 27 July 2019. pp. 4487 – 4490.
    Abstract | pub9936.pdf
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  • 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.
    Abstract | pub9937.pdf
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  • Kim J, Tran L, Chew E, Antani SK. Optic Disc and Cup Segmentation for Glaucoma Characterization Using Deep Learning 2019 IEEE 32th International Symposium on Computer-Based Medical Systems (CBMS), pp 489-494, Cordoba, Spain, June 2019.
    Abstract | pub9929.pdf
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  • Rajaraman S, Jaeger S, Antani SK. Performance evaluation of deep neural ensembles toward malaria parasite detection in thin-blood smear images. PeerJ 7:e6977
    Abstract | URL:  https://doi.org/10.7717/peerj.6977
    AbstractExternal link
  • Kim I, Rajaraman S, Antani SK. Visual Interpretation of Convolutional Neural Network Predictions in Classifying Medical Image Modalities. Diagnostics (Basel). 2019 Apr 3;9(2). pii: E38. doi: 10.3390/diagnostics9020038.
    Abstract | PMID:  30987172 | URL:  https://www.mdpi.com/2075-4418/9/2/38/htm
    AbstractExternal link
  • Kim J, Tran L, Chew E, Antani SK, Thoma GR. Optic Disc Segmentation in Fundus Images Using Deep Learning. SPIE Medical Imaging 2019: Imaging Informatics for Healthcare, Research, and Applications, Vol. 10954, San Diego, USA, February 2019.
    Abstract | pub9901.pdf
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  • Rajaraman S, Candemir S, Thoma G, Antani SK. Visualizing and explaining deep learning predictions for pneumonia detection in pediatric chest radiographs. Proc. SPIE 10950, Medical Imaging 2019: Computer-Aided Diagnosis, 109500S (13 March 2019); doi: 10.1117/12.2512752.
    Abstract | pub9899.pdf
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  • 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.
    Abstract | PMID:  30753947
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  • 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.
    Abstract | PMID:  30730032
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  • Ben Abacha A, Demner-Fushman D. On the role of question summarization and information source restriction in consumer health question answering. In Proceedings of the AMIA 2019 Informatics Summit, San Francisco, CA, USA, 2019.
    Abstract | pub9917.pdf
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  • 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.
    Abstract | pub9896.pdf | PMID:  30838163
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  • Zolnoori M, Fung K, Patrick TB, Fontelo P, Kharrazi H, Faiola A, Wu YSS, Eldredge CE, Luo J, Conway M, Zhu J, Park SK, Xu K, Moayyed H, Goudarzvand S. A systematic approach for developing a corpus of patient reported adverse drug events: A case study for SSRI and SNRI medications. NCBINCBI Logo Skip to main content Skip to navigation Resources How To About NCBI Accesskeys PubMed US National Library of Medicine National Institutes of Health Search databaseSearch term 30611893[uid] Clear inputSearch Create RSSCreate alertAdvancedHelp Result Filters Format: AbstractSend to J Biomed Inform. 2019 Feb;90:103091. doi: 10.1016/j.jbi.2018.12.005. Epub 2019 Jan 4.
    Abstract | PMID:  30611893
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  • 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
    Abstract | PMID:  30629194
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  • 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.
    Abstract | PMID:  30545491
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  • Rindflesch TC, Blake CL, Cairelli MJ, Fiszman M, Zeiss CJ, Kilicoglu H. Investigating the role of interleukin-1 beta and glutamate in inflammatory bowel disease and epilepsy using discovery browsing. J Biomed Semantics. 2018 Dec 27;9(1):25. doi: 10.1186/s13326-018-0192-y.
    Abstract | PMID:  30587224 | PMCID:  PMC6307110
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  • 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.
    Abstract | PMID:  30284153 | PMCID:  PMC6223762
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  • Lu C, Demner-Fushman D. Improving Spelling Correction with Consumer Health Terminology Improving Spelling Correction with Consumer Health Terminology AMIA 2018 Annual Symposium, San Francisco, CA, November 3-7, 2018, p. 2053.
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  • 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.
    Abstract | pub9872.pdf
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  • Dhoot R, Humphrey JM, O'Meara P, Gardner A, McDonald CJ, Ogot K, Antani SK, Abuya J, Kohli M. Implementing a mobile diagnostic unit to increase access to imaging and laboratory services in western Kenya. BMJ Glob Health. 2018 Oct 8;3(5):e000947. doi: 10.1136/bmjgh-2018-000947. eCollection 2018.
    Abstract | PMID:  30364326 | PMCID:  PMC6195141
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  • 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.
    Abstract | PMID:  30840746 | PMCID:  PMC6290955
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  • Zolnoori M, Fung K, Fontelo P, Kharrazi H, Faiola A, Wu YSS, Stoffel V, Patrick T. Identifying the Underlying Factors Associated With Patients' Attitudes Toward Antidepressants: Qualitative and Quantitative Analysis of Patient Drug Reviews. JMIR Ment Health. 2018 Sep 30;5(4):e10726. doi: 10.2196/10726.
    Abstract | PMID:  30287417
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  • Fontelo P, Liu F. A review of recent publication trends from top publishing countries. Syst Rev. 2018 Sep 27;7(1):147. doi: 10.1186/s13643-018-0819-1.
    Abstract | PMID:  30261915 | PMCID:  PMC6161455
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  • Rajaraman S, Candemir S, Kim I, Thoma GR, Antani SK. Visualization and Interpretation of Convolutional Neural Network Predictions in Detecting Pneumonia in Pediatric Chest Radiographs. Appl. Sci. 2018, 8, 1715.
    Abstract | pub9855.pdf
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  • 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.
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  • Sylim P, Liu F, Marcelo A, Fontelo P. Blockchain Technology for Detecting Falsified and Substandard Drugs in Distribution: Pharmaceutical Supply Chain Intervention. JMIR Res Protoc. 2018 Sep 13;7(9):e10163. doi: 10.2196/10163.
    Abstract | PMID:  30213780
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  • Ben Abacha A, Gayen S, Lau JJ, Rajaraman S, Demner-Fushman D. NLM at ImageCLEF 2018 Visual Question Answering in the Medical Domain. CLEF2018 Working Notes. CEUR Workshop Proceedings, Avignon, France, CEUR-WS.org (September 10-14 2018).
    Abstract | pub9812.pdf
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  • 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
    Abstract | URL:  https://link.springer.com/content/pdf/10.1007%2Fs11548-018-1857-9.pdf
    AbstractExternal link
  • Beare R, Lowekamp B, Yaniv Z. Image Segmentation, Registration and Characterization in R with SimpleITK. J Stat Softw. 2018 Aug;86. pii: 8. doi: 10.18637/jss.v086.i08. Epub 2018 Sep 4.
    Abstract | PMID:  30288153 | PMCID:  PMC6168008
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  • McDonald CJ, Maglott D, Abhyankar S, Goodwin RM, Kanduru A, Lu S, Lynch P, Vreeman D, Wang Y, Wood G. US Realm, Chapter 14, Use Case – Clinical Genomics Code Systems. in HL7 Version 2.5.1 Implementation Guide: Lab Results Interface (LRI), DTSU3. HL7 International (Ann Arbor).
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  • McDonald CJ, Maglott D, Abhyankar S, Goodwin RM, Kanduru A, Lu S, Lynch P, Vreeman D, Wang Y, Wood G. US Realm, Chapter 5, Use Case – Clinical Genomics Results Reporting in HL7 Version 2.5.1 Implementation Guide: Lab Results Interface (LRI), DTSU3. HL7 International (Ann Arbor).
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  • 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.
    Abstract | PMID:  29959539
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  • Bodenreider O, Cornet R, Vreeman DJ. Recent Developments in Clinical Terminologies - SNOMED CT, LOINC, and RxNorm. Yearb Med Inform. 2018 Aug;27(1):129-139. doi: 10.1055/s-0038-1667077. Epub 2018 Aug 29.
    Abstract | PMID:  30157516
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  • Rajaraman S, Silamut K, Hossain MA, Ersoy I, Maude RJ, Jaeger S, Thoma GR, Antani SK. Understanding the learned behavior of customized convolutional neural networks toward malaria parasite detection in thin blood smear images. J Med Imaging (Bellingham). 2018 Jul;5(3):034501. doi: 10.1117/1.JMI.5.3.034501. Epub 2018 Jul 18.
    Abstract | pub9809.pdf | PMID:  30035153 | PMCID:  PMC6050500
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  • 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.
    Abstract | pub9810.pdf
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  • Xue Z, Long LR, Jaeger S, Folio L, Thoma GR. Extraction of Aortic Knuckle Contour in Chest Radiographs Using Deep Learning. EMBC 2018.
    Abstract | pub9818.pdf
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  • 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
    Abstract | pub9811.pdf
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  • 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.
    Abstract | pub9781.pdf
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  • 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.
    Abstract | PMID:  29718377 | PMCID:  PMC6016608
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  • Kim J, Candemir S, Chew E, Thoma GR. Region of Interest Detection in Fundus Images Using Deep Learning and Blood Vessel Information. The 31th IEEE International Symposium on Computer-Based Medical Systems. (IEEE CBMS 2018), pp. 357-362, Karlstad, Sweden, June 2018.
    Abstract | pub9808.pdf
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  • McDonald CJ. Logical Observation Identifiers Names and Codes for In Vitro Diagnostic Test; Guidance for Industry and Food and Drug Administration Staff. Silver Spring, Md: Center for Devices and Radiological Health, FDA, 2018.
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  • Goss FR, Lai KH, Topaz M, Acker WW, Kowalski L, Plasek JM, Blumenthal KG, Seger DL, Slight SP, Fung KW, Chang FY, Bates DW, Zhou L. A value set for documenting adverse reactions in electronic health records. J Am Med Inform Assoc. 2018 Jun 1;25(6):661-669. doi: 10.1093/jamia/ocx139.
    Abstract | PMID:  29253169
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  • Yaniv Z, Lowekamp B, Johnson HJ, Beare R. SimpleITK Image-Analysis Notebooks: a Collaborative Environment for Education and Reproducible Research. J Digit Imaging. 2018 Jun;31(3):290-303. doi: 10.1007/s10278-017-0037-8.
    Abstract | PMID:  29181613 | PMCID:  PMC5959828
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  • 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.
    Abstract | PMID:  29619277 | PMCID:  PMC5869967
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  • 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.
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  • Vreeman DJ, Abhyankar S, McDonald CJ. Re: Unit conversions between LOINC codes Published June 19, 2017 [Letter]. J Am Med Inform Assoc. 2018 May 1;25(5):614-615. doi: 10.1093/jamia/ocx087.
    Abstract | PMID:  29025119
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  • 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.
    Abstract | PMID:  29854131 | PMCID:  PMC5977655
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  • Fung K, Xue Z, Ameye F, Gutierrez AR, D'Have A. Achieving Logical Equivalence between SNOMED CT and ICD-10-PCS Surgical Procedures. AMIA Annu Symp Proc. 2018 Apr 16;2017:724-733. eCollection 2017.
    Abstract | PMID:  29854138 | PMCID:  PMC5977651
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  • Kayaalp M. Modes of De-identification. AMIA Annu Symp Proc. 2018 Apr 16;2017:1044-1050. eCollection 2017.
    Abstract | pub9526.pdf | PMID:  29854172 | PMCID:  PMC5977668
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  • Rajaraman S, Antani SK, Poostchi Mohammadabadi M, Silamut K, Hossain MA, Maude RJ, Jaeger S, Thoma GR. Pre-trained convolutional neural networks as feature extractors toward improved malaria parasite detection in thin blood smear images. PeerJ. 2018 Apr 16;6:e4568. doi: 10.7717/peerj.4568. eCollection 2018.
    Abstract | pub9752.pdf | PMID:  29682411 | PMCID:  PMC5907772
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  • 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.
    Abstract | pub9572.pdf | PMID:  29854219 | PMCID:  PMC5977710
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  • Huser V, Shmueli-Blumberg D. Data sharing platforms for de-identified data from human clinical trials. Clin Trials. 2018 Apr 1:1740774518769655. doi: 10.1177/1740774518769655. [Epub ahead of print]
    Abstract | PMID:  29676586
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  • 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
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  • Xue Z, Antani SK, Long LR, Thoma GR. Using deep learning for detecting gender in adult chest radiographs. Proc SPIE 10579, Medical Imaging 2018: Imaging Informatics for Healthcare, Research, and Applications, 105790D (6 March 2018) pp. doi: 10.1117/12.2293027.
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  • 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.
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  • 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).
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  • Tang P, McDonald CJ. Computer-Based Patient-Record Systems - Chapter 9. In Shortliffe E, Perreault L, eds. Medical Informatics. New York: springer. 2001:327-358. DOI: 10.1007/978-0-387-21721-5_9.
    Abstract | pub9718.pdf
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  • 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).
    Abstract | pub9745.pdf
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  • 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
    Abstract | pub9746.pdf
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  • 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
    Abstract | SPIE_2018_tb_fullpaper_final_2.pdf
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  • Xue Z, Antani SK, Long LR, Thoma GR. Using deep learning for detecting gender in adult chest radiographs. SPIE Medical Imaging 2018
    Abstract | SPIE_2018_gender_fullpaper_final.pdf
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  • 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.
    Abstract | PMID:  29274386 | PMCID:  PMC5835197
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  • Lynch P, Wang Y, Kanduru A, Luan X, Mericle L, Lu S, McDonald CJ. On-the-Fly Data Capture Tooling for FHIR/HL7 V2 HL7 January 2018 Working Group Meeting, New Orleans, LA
    Abstract | pub9749.pdf
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  • McDonald CJ. FHIR Overview Presentation by Clement J. McDonald, MD
    Abstract | pub9747.pdf
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  • Zweigenbaum P, Demner-Fushman D. Advanced Literature-Mining Tools. In Edwards D, Stajich J, and Hansen D. (Editors). Bioinformatics: Tools and Applications. Springer 2009.
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  • 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.
    Abstract | PMID:  29381145 | PMCID:  PMC5789866
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  • McDonald CJ. Top LOINC Codes – Orders and Observations
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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.
    Abstract | pub9624.pdf | PMID:  29360430 | PMCID:  PMC5840030
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  • Kayaalp M. Patient Privacy in the Era of Big Data. Balkan Med J. 2018 Jan 20;35(1):8-17. doi: 10.4274/balkanmedj.2017.0966. Epub 2017 Sep 13.
    Abstract | PMID:  28903886 | PMCID:  PMC5820452
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  • 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
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  • 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.
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  • Rajaraman S, Antani SK, Xue Z, Candemir S, Jaeger S, Thoma GR. Visualizing abnormalities in chest radiographs through salient network activations in Deep Learning. Proc. IEEE Life Sciences Conference (LSC), Sydney, Australia, 2017. pp. 71-74, DOI:10.1109/LSC.2017.8268146.
    Abstract | pub9645.pdf
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  • Harpaz R, DuMouchel W, Schuemie M, Bodenreider O, Friedman C, Horvitz E, Ripple A, Sorbello A, White RW, Winnenburg R, Shah NH. Toward multimodal signal detection of adverse drug reactions. J Biomed Inform. 2017 Dec;76:41-49. doi: 10.1016/j.jbi.2017.10.013. Epub 2017 Nov 1.
    Abstract | PMID:  29081385
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  • 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
    Abstract | URL:  https://ieeexplore.ieee.org/document/8218002
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  • 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
    Abstract | pub9621.pdf
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  • Abhyankar S, Schluter P, Bennett K, Vreeman D, McDonald CJ. Enabling Interoperability between Healthcare Devices and EHR Systems. In 2017 AMIA Symposium. Wasington DC: IEEE.
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  • 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
    Abstract | pub9775.pdf
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  • McDonald CJ, Vreeman D, Wang K, Carr C, Colins B, Abhyankar S, Deckard J, Rubin D, Langlotz C. The LOINC/RSNA Radiology Playbook: A unified terminology for radiology procedures. . In 2017 AMIA Symposium. Washington DC.
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  • Raje S, Bhupatiraju R, Abdelrahman H, Busby B. MeSHgram: An Open Source Tool to Visually Browse Co-occurrence of MeSH Terms in PubMed [Poster]. AMIA 2017 Symposium Proceedings.
    Abstract | pub9630.pdf
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  • 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.
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  • Kury F, Baik SH, McDonald CJ. Cardioprotective Drugs and Incident Dementias in Medicare's Big Data. AMIA 2017.
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  • Fallavollita P, Kersten M, Linte CA, Pratt P, Yaniv Z. Guest Editors' Foreword: Special Issue on Augmented Environments for Computer-Assisted Interventions CAI systems enable more precise, safer, and less invasive interventional treatments [Letter]. Healthc Technol Lett. 2017 Oct 27;4(5):149. doi: 10.1049/htl.2017.0078. eCollection 2017 Oct.
    Abstract | PMID:  29184653 | PMCID:  PMC5683192
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  • Chatain GP, Patronas N, Smirniotopoulos J, James G, Piazza M, Benzo S, Ray-Chaudrury A, Sharma S, Lodish M, Nieman L, Stratakis CA, Chittiboina P. Potential utility of FLAIR in MRI-negative Cushing's disease. J Neurosurg. 2017 Oct 13:1-9. doi: 10.3171/2017.4.JNS17234.
    Abstract | PMID:  29027863
    Abstract
  • Fung K, Gutierrez A, Ameye F, D’Have A, Ariel B. Demonstrating the Benefits of Mapping SNOMED CT to ICD-10-PCS through a Prototype Application for End User Implementation. SNOMED Expo Oct 2017, Bratislava, Slovakia pp. 0
    Abstract
    Abstract
  • 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.
    Abstract | pub9623.pdf
    AbstractDownload
  • Moallem G, Jaeger S, Poostchi M, Palaniappan N, Yu H, Silamut K, Maude RJ, Antani SK, Thoma GR. White Blood Cell Detection and Segmentation in Microscopy Images of Thin Blood Smears [Poster]. NIH Research Festival, Poster, 2017
    Abstract | pub9622.pdf
    AbstractDownload
  • Coakley M, Hurt D, Weder N, Mtingwa M, Fincher EC, Alekseyev V, Chen D, Yun A, Gizaw M, Swan J, Yoo TS, Huyen Y. The NIH 3D Print Exchange: A Public Resource for Bioscientific and Biomedical 3D Prints 3D Print Additive Manufacturing, Sep. 1, 2014, 1(3):137-140.
    Abstract
    Abstract
  • Roberts K, Gururaj A, Chen X, Pournejati S, Cohen T, Hersh WR, Demner-Fushman D. Information Retrieval for Biomedical Datasets. 2016 bioCADDIE Challenge. AMIA 2017.
    Abstract
    Abstract
  • Sun H, Li J, Wu Y, Wang L, Fung K. Using an Ontology-Based Approach to Handle Author Affiliations in a Large Biomedical Citation Database. Stud Health Technol Inform. 2017;245:1338.
    Abstract | PMID:  29295419
    Abstract
  • Abhyankar S, Vreeman DJ, Westra BL, Delaney CW. Comments on the Use of LOINC and SNOMED CT for Representing Nursing Data [Letter]. Int J Nurs Knowl. 2017 Aug 30. doi: 10.1111/2047-3095.12183. [Epub ahead of print]
    Abstract | PMID:  28856826
    Abstract
  • Raje S, Bodenreider O. Interoperability of disease concepts in clinical and research ontologies – Contrasting coverage and structure in the Disease Ontology and SNOMED CT. Stud Health Technol Inform. 2017;245:925-929.
    Abstract | PMID:  29295235 | PMCID:  PMC5881393
    Abstract
  • Bhupatiraju R, Fung K, Bodenreider O. MetaMapLite in Excel: Biomedical named-entity recognition for non-technical users. Stud Health Technol Inform (Proc Medinfo): 1252.
    Abstract | PMID:  29295337 | PMCID:  PMC5884681
    Abstract
  • Rajaraman S, Antani SK, Jaeger S. Visualizing Deep Learning Activations for Improved Malaria Cell Classification. Proceedings of The First Workshop in Medical Informatics and Healthcare (MIH 2017), Proceedings of Machine Learning Research (PMLR), v. 69, p. 40-47.
    Abstract | Visualizing_DL_activations_for_improved_malaria_cell_classification.pdf
    AbstractDownload
  • Blake C, Rindflesch TC. Leveraging syntax to better capture the semantics of elliptical coordinated compound noun phrases. J Biomed Inform. 2017 Aug;72:120-131. doi: 10.1016/j.jbi.2017.07.001. Epub 2017 Jul 4.
    Abstract | PMID:  28687199
    Abstract
  • 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.
    Abstract | PMID:  28678823 | PMCID:  PMC5497973
    Abstract
  • Jaeger S. Malaria Datasets
    Abstract
    Abstract
  • 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.
    Abstract | PMID:  28339775 | PMCID:  PMC6080685
    Abstract
  • 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.
    Abstract | PMID:  28339701 | PMCID:  PMC6080681
    Abstract
  • Rindflesch TC, Blake CL, Fiszman M, Kilicoglu H, Rosemblat G, Schneider J, Zeiss CJ. Informatics Support for Basic Research in Biomedicine. ILAR J. 2017 Jul 1;58(1):80-89. doi: 10.1093/ilar/ilx004.
    Abstract | PMID:  28838071 | PMCID:  PMC5886329
    Abstract
  • 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.
    Abstract | PMID:  28339690 | PMCID:  PMC6080677
    Abstract
  • Candemir S, Antani SK, Xue Z, Thoma GR. Novel Method for Storyboarding Biomedical Videos for Medical Informatics. 30th IEEE International Symposium on Computer-Based Medical Systems
    Abstract | pub9571.pdf
    AbstractDownload
  • Vreeman DJ, Abhyankar S, McDonald CJ. Unit conversions between LOINC codes Published June 19, 2017 [Letter]. Journal of the American Medical Informatics Association, 1–3. http://doi.org/10.1093/jamia/ocx087.
    Abstract
    Abstract
  • Kilicoglu H. Biomedical text mining for research rigor and integrity: tasks, challenges, directions. Brief Bioinform. 2017 Jun 13. doi: 10.1093/bib/bbx057.
    Abstract | PMID:  28633401
    Abstract
  • Bush R, Heierman E, Knafel A, Lardin L, McDonald CJ. LIVD – Digital Format for Publication of LOINC to Vendor IVD Test Results. . IVD Industry Connectivity Consortium. http://ivdconnectivity.org/livd/. Published June 1, 2017. Accessed August 9, 2017.
    Abstract
    Abstract
  • Chakrabarti S, Sen A, Huser V, Hruby GW, Rusanova A, Albers DJ, Weng C. An Interoperable Similarity-based Cohort Identification Method Using the OMOP Common Data Model version 5.0. J Healthc Inform Res. 2017 Jun;1(1):1-18. doi: 10.1007/s41666-017-0005-6. Epub 2017 Jun 8.
    Abstract | PMID:  28776047 | PMCID:  PMC5536903
    Abstract
  • McDonald CJ, Maglott D, Abhyankar S, Goodwin R, Kanduru A, Lu S, Lynch P, Vreeman D, Wang Y, Wood G. HL7 Version 2.5.1 Implementation Guide: Lab Results Interface (LRI), Release 1, STU Release 4. US Realm, Chapter 5, Clinical Genomics Results Reporting. Published for May 2017 Ballot.
    Abstract
    Abstract
  • Jaeger S. Chest X-ray Screening System: Segmentation Module – v3
    Abstract
    Abstract
  • Raje S, Bodenreider O. Investigating the coverage of diseases across biomedical research and clinical ontologies. Proceedings of the AMIA Joint Summits on Translational Science CRI: 384-385.
    Abstract
    Abstract
  • 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.
    Abstract | PMID:  28326432 | PMCID:  PMC5373771
    Abstract
  • 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
    Abstract | pub9508.pdf
    AbstractDownload
  • 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.
    Abstract | pub9507.pdf
    AbstractDownload
  • 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.
    Abstract | PMID:  28231809 | PMCID:  PMC5324252
    Abstract
  • 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.
    Abstract | pub9575.pdf
    AbstractDownload
  • 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]
    Abstract | pub9528.pdf
    AbstractDownload
  • Ben Abacha A, Demner-Fushman D. Recognizing Question Entailment for Medical Question Answering. AMIA Annu Symp Proc. 2017 Feb 10;2016:310-318. eCollection 2016.
    Abstract | pub9500.pdf | PMID:  28269825 | PMCID:  PMC5333286
    AbstractDownload
  • Fung K, Xu J, Amey F, Gutierrez AR, D'Have A. Leveraging Lexical Matching and Ontological Alignment to Map SNOMED CT Surgical Procedures to ICD-10-PCS. AMIA Annu Symp Proc. 2017 Feb 10;2016:570-579. eCollection 2016.
    Abstract | PMID:  28269853 | PMCID:  PMC5333287
    Abstract
  • 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.
    Abstract | pub9458.pdf | PMID:  28269888 | PMCID:  PMC5333243
    AbstractDownload
  • Roberts K, Rodriguez L, Shooshan SE, Demner-Fushman D. Resource Classification for Medical Questions. AMIA Annu Symp Proc. 2017 Feb 10;2016:1040-1049. eCollection 2016.
    Abstract | PMID:  28269901 | PMCID:  PMC5333297
    Abstract
  • Workman E, Weir, C, Rindflesch TC. Differentiating Sense through Semantic Interaction Data. AMIA Annu Symp Proc. 2017 Feb 10;2016:1238-1247. eCollection 2016.
    Abstract | PMID:  28269921 | PMCID:  PMC5333208
    Abstract
  • Cahan A, Cimino JJ. Improving precision medicine using individual patient data from trials. CMAJ. 2017 Feb 6;189(5):E204-E207. doi: 10.1503/cmaj.160267. Epub 2016 Aug 29.
    Abstract | PMID:  27573743 | PMCID:  PMC5289871
    Abstract
  • Peters L, Nguyen T, Bodenreider O. Terminology Status APIs - Mapping Obsolete Codes to Current RxNorm, SNOMED CT, and LOINC Concepts. Stud Health Technol Inform. 2017;245:1333.
    Abstract | PMID:  29295414 | PMCID:  PMC5875440
    Abstract
  • 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.
    Abstract | PMID:  28130331
    Abstract
  • 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.
    Abstract
    Abstract
  • 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.
    Abstract
    Abstract
  • 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.
    Abstract | PMID:  29295218 | PMCID:  PMC5881398
    Abstract
  • Dhombres F, Bodenreider O. Trends in Fetal Medicine: A 10-Year Bibliometric Analysis of Prenatal Diagnosis. Stud Health Technol Inform. 2017;245:853-857.
    Abstract | PMID:  29295220 | PMCID:  PMC5884683
    Abstract
  • Lu C, Tormey D, McCreedy L, Browne AC. Enhanced LexSynonym Acquisition for Effective UMLS Concept Mapping. Stud Health Technol Inform. 2017;245:501-505.
    Abstract | pub9776.pdf | PMID:  29295145
    AbstractDownload
  • Nelsonn SD, Parker J, Lario R, Winnenburg R, Erlbaum MS, Lincoln MJ, Bodenreider O. Interoperability of medication classification systems: Lessons learned mapping estab-lished pharmacologic classes (EPCs) to SNOMED CT. Stud Health Technol Inform. 2017;245:920-924.
    Abstract | PMID:  29295234 | PMCID:  PMC5881380
    Abstract
  • Topaz M, Goss F, Blumenthal K, Lai K, Seger DL, Slight SP, Wickner PG, Robinson GA, Fung KW, McClure RC, Spiro S, Acker WW, Bates DW, Zhou L. Towards improved drug allergy alerts: Multidisciplinary expert recommendations. Int J Med Inform. 2017 Jan;97:353-355. doi: 10.1016/j.ijmedinf.2016.10.006. Epub 2016 Oct 6.
    Abstract | PMID:  27729200
    Abstract
  • 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.
    Abstract | PMID:  29295179 | PMCID:  PMC5875427
    Abstract
  • 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.
    Abstract | PMID:  29220453 | PMCID:  PMC5737202
    Abstract
  • 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.
    Abstract | pub9466.pdf | PMID:  28163974 | PMCID:  PMC5248401
    AbstractDownload
  • 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.
    Abstract | pub9450.pdf
    AbstractDownload
  • Kilicoglu H. Inferring Implicit Causal Relationships in Biomedical Literature. Proc 15th Workshop on Biomedical Natural Language Processing. Pages 46-55. 2016.
    Abstract | pub9441.pdf
    AbstractDownload
  • 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.
    Abstract | PMID:  28154833 | PMCID:  PMC5226382
    Abstract
  • 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.
    Abstract | pub9436.pdf
    AbstractDownload
  • Ben Abacha A. NLM_NIH at TREC 2016 Clinical Decision Support Track. Proceedings of TREC 2016, the 25th Text Retrieval Conference, Gaithersburg, MD, USA, November 2016.
    Abstract | pub9489.pdf
    AbstractDownload
  • Wang Y, Lynch P, Kanduru A, Hook J, Mericle L, Ludet C, Vreeman D, McDonald CJ. LHC-Forms and Related Widgets for Capturing and Tuning Health Data [Poster] AMIA Annual Symposium, Chicago IL
    Abstract
    Abstract
  • Ben Abacha A, Demner-Fushman D. NLM_NIH at SemEval-2017 Task 3: from Question Entailment to Question Similarity for Community Question Answering. In Proceedings of the 11th International Workshop on Semantic Evaluation (SemEval@ACL) 2017: 349-352.
    Abstract | pub9538.pdf
    AbstractDownload
  • Ben Abacha A, de Herrera A, Wang Ke, Long LR, Antani SK, Demner-Fushman D. Named entity recognition in functional neuroimaging literature. 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Kansas City, MO, 2017, pp. 2218-2220.
    Abstract
    Abstract
  • Jaeger S, Silamut K, Yu H, Poostchi Mohammadabadi M, Ersoy I, Powell A, Liang Z, Hossain M, Antani SK, Palaniappan K, Maude R, Thoma GR. Reducing the Diagnostic Burden of Malaria Using Microscopy Image Analysis and Machine Learning in the Field [Poster]. Annual Meeting of the American Society of Tropical Medicine & Hygiene (ASTMH), Atlanta, USA, 2016.
    Abstract | pub9432.pdf
    AbstractDownload
  • 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.
    Abstract | pub9433.pdf
    AbstractDownload
  • Madani S, Henderson J, Fung K. Development of an oncology subset of SNOMED CT based on patient notes. AMIA Annu Symp Proc 2016: 91-92.
    Abstract | pub9465.pdf
    AbstractDownload
  • 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
    Abstract | pub9467.pdf
    AbstractDownload
  • Linte CA, Yaniv Z. Image-Guided Interventions: We've come a long way, but are we there? IEEE Pulse. 2016 Nov-Dec;7(6):46-50.
    Abstract | PMID:  27875119
    Abstract
  • McDonald CJ, Wang Y, Lynch P, Kanduru A. Feeding FHIR with LHC-Forms HL7 Partners in Interoperability Mt. Washington Conference Center, Baltimore, MD
    Abstract | pub9748.pdf
    AbstractDownload
  • 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.
    Abstract | pub9421.pdf
    AbstractDownload
  • 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.
    Abstract
    Abstract
  • Borovikov E, Vajda S, Lingappa G, Bonifant MC. Parallel Computing in Face Image Retrieval: Practical Approach to the Real-World Image Search. Multi-Core Computer Vision and Image Processing for Intelligent Applications. IGI Global, 2017. 155-189. Web. 12 Sep. 2016. doi:10.4018/978-1-5225-0889-2.ch006
    Abstract | URL:  http://www.igi-global.com/chapter/parallel-computing-in-face-image-retrieval/163...
    AbstractExternal link
  • Mrabet Y, Vougiouklis P, Kilicoglu H, Gardent C, Demner-Fushman D, Hare J, Simperl E. Aligning Texts and Knowledge Bases with Semantic Sentence Simplification. WebNLG 2016.
    Abstract
    Abstract
  • 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
    Abstract | pub9506.pdf
    AbstractDownload
  • 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.
    Abstract | PMID:  26995600
    Abstract
  • Oellrich A, Collier N, Groza T, Rebholz-Schuhmann D, Shah N, Bodenreider O, Borlan MR, Georgiev I, Liu H, Livingston K, Luna A, Mallon AM, Manda P, Robinson PM, Rustici G, Simonn M, Wang L, Winnenburg R, Dumontier M. The digital revolution in phenotyping. Brief Bioinform. 2016 Sep;17(5):819-30. doi: 10.1093/bib/bbv083. Epub 2015 Sep 29.
    Abstract | PMID:  26420780 | PMCID:  PMC5036847
    Abstract
  • 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.
    Abstract | pub9468.pdf | PMID:  28603299 | PMCID:  PMC5464748
    AbstractDownload
  • 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.
    Abstract
    Abstract
  • Driessen J, Baik SH, Zhang Y. Trends in Off-Label Use of Second-Generation Antipsychotics in the Medicare Population From 2006 to 2012. Psychiatr Serv. 2016 Aug 1;67(8):898-903. doi: 10.1176/appi.ps.201500316. Epub 2016 Apr 15.
    Abstract | PMID:  27079991 | PMCID:  PMC4969167
    Abstract
  • Hristovski D, Kastrin A, Dinevski D, Burgun A, Ziberna L, Rindflesch TC. Using Literature-Based Discovery to Explain Adverse Drug Effects. J Med Syst. 2016 Aug;40(8):185. doi: 10.1007/s10916-016-0544-z. Epub 2016 Jun 18.
    Abstract | PMID:  27318993
    Abstract
  • Homer ML, Palmer NP, Bodenreider O, Cami A, Chadwick L, Mandl KD. The Drug Data to Knowledge Pipeline: Large-Scale Claims Data Classification for Pharmacologic Insight. AMIA Jt Summits Transl Sci Proc. 2016 Jul 20;2016:105-11. eCollection 2016.
    Abstract | pub9334.pdf | PMID:  27570659 | PMCID:  PMC5001754
    AbstractDownload
  • 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.
    Abstract | PMID:  27570676 | PMCID:  PMC5001748
    Abstract
  • 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.
    Abstract | URL:  http://www.lrec-conf.org/proceedings/lrec2016/pdf/152_Paper.pdf
    AbstractExternal link
  • Shin HC, Roberts K, Lu L, Demner-Fushman D. Learning to Read Chest X-Rays: Recurrent Neural Cascade Model for Automated Image Annotation. IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 2016.
    Abstract | URL:  http://arxiv.org/abs/1603.08486
    AbstractExternal link
  • 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)
    Abstract | 1_IJCLA.pdf
    AbstractDownload
  • Hripcsak G, Ryan PB, Duke JD, Shah NH, Park RW, Huser V, Suchard MA, Schuemie MJ, DeFalco FJ, Perotte A, Banda JM, Reich CG, Schilling LM, Matheny ME, Meeker D, Pratt N, Madigan D. Characterizing treatment pathways at scale using the OHDSI network. Proc Natl Acad Sci U S A. 2016 Jul 5;113(27):7329-36. doi: 10.1073/pnas.1510502113. Epub 2016 Jun 6.
    Abstract | PMID:  27274072 | PMCID:  PMC4941483
    Abstract
  • Benedict SH, Hoffman K, Martel MK, Abernethy AP, Asher AL, Capala J, Chen RC, Chera B, Couch J, Deye J, Efstathiou JA, Ford E, Fraass BA, Gabriel PE, Huser V, Kavanagh BD, Khuntia D, Marks LB, Mayo C, McNutt T, Miller RS, Moore KL, Prior F, Roelofs E, Rosenstein BS, Sloan J, Theriault A, Vikram B. Overview of the American Society for Radiation Oncology-National Institutes of Health-American Association of Physicists in Medicine Workshop 2015: Exploring Opportunities for Radiation Oncology in the Era of Big Data. Int J Radiat Oncol Biol Phys. 2016 Jul 1;95(3):873-879. doi: 10.1016/j.ijrobp.2016.03.006.
    Abstract | PMID:  27302503 | PMCID:  PMC4965164
    Abstract
  • 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.
    Abstract | PMID:  27156048 | PMCID:  PMC4923658 | URL:  https://www.sciencedirect.com/science/article/pii/S0895611116300337
    AbstractExternal link
  • Huser V, Cimino JJ. Impending Challenges for the Use of Big Data. Int J Radiat Oncol Biol Phys. 2016 Jul 1;95(3):890-894. doi: 10.1016/j.ijrobp.2015.10.060. Epub 2015 Nov 5.
    Abstract | PMID:  26797535 | PMCID:  PMC4860172
    Abstract
  • 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.
    Abstract | pub9469.pdf
    AbstractDownload
  • Kilicoglu H. Software: Bio-SCoRes
    Abstract
    Abstract
  • Kilicoglu H. Dataset: Sortal Anaphora Dataset
    Abstract
    Abstract
  • 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.
    Abstract | pub9343.pdf
    AbstractDownload
  • KC S, Wendling L, Antani SK, Thoma GR. Overlaid arrow detection for labeling biomedical image regions. IEEE Intelligent Systems, Special Issue on Pattern Recognition, 31(3):66-75, May-June 2016.DOI: 10.1109/MIS.2016.24.
    Abstract | pub9470.pdf
    AbstractDownload
  • Xue Z, Antani SK, Long LR, Demner-Fushman D, Thoma GR. Improving face image extraction by using deep learning technique. Proc. SPIE 9789, Medical Imaging 2016: PACS and Imaging Informatics: Next Generation and Innovations, 97890J (March 25, 2016); doi:10.1117/12.2216278.
    Abstract | pub9332.pdf
    AbstractDownload
  • Kilicoglu H, Rosemblat G, Fiszman M, Rindflesch TC. Sortal anaphora resolution to enhance relation extraction from biomedical literature. BMC Bioinformatics. 2016 Apr 14;17:163. doi: 10.1186/s12859-016-1009-6.
    Abstract | PMID:  27080229 | PMCID:  PMC4832532
    Abstract
  • Fung KW, Richesson R, Smerek M, Pereira KC, Green BB, Patkar A, Clowse M, Bauck A, Bodenreider O. Preparing for the ICD-10-CM Transition: Automated Methods for Translating ICD Codes in Clinical Phenotype Definitions. EGEMS (Wash DC). 2016 Apr 12;4(1):1211. doi: 10.13063/2327-9214.1211. eCollection 2016.
    Abstract | PMID:  27195309 | PMCID:  PMC4862764
    Abstract
  • Hume S, Aerts J, Sarnikar S, Huser V. Current applications and future directions for the CDISC Operational Data Model standard: A methodological review. J Biomed Inform. 2016 Apr;60:352-62. doi: 10.1016/j.jbi.2016.02.016. Epub 2016 Mar 2.
    Abstract | PMID:  26944737 | PMCID:  PMC4837012
    Abstract
  • 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.
    Abstract | PMID:  26774763 | PMCID:  PMC4836984
    Abstract
  • Workman TE, Fiszman M, Cairelli MJ, Nahl D, Rindflesch TC. Spark, an application based on Serendipitous Knowledge Discovery. J Biomed Inform. 2016 Apr;60:23-37. doi: 10.1016/j.jbi.2015.12.014. Epub 2015 Dec 28.
    Abstract | PMID:  26732995
    Abstract
  • 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.
    Abstract | pub9473.pdf
    AbstractDownload
  • 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.
    Abstract | pub9472.pdf
    AbstractDownload
  • 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.
    Abstract | PMID:  26934708 | PMCID:  PMC4774913
    Abstract
  • Baik SH, Hernandez I, Zhang Y. Evaluating the Initiation of Novel Oral Anticoagulants in Medicare Beneficiaries. J Manag Care Spec Pharm. 2016 Mar;22(3):281-92. doi: 10.18553/jmcp.2016.22.3.281.
    Abstract | PMID:  27003558 | PMCID:  PMC5051348
    Abstract
  • Demner-Fushman D, Kohli MD, Rosenman MB, Shooshan SE, Rodriguez L, Antani S, Thoma GR, McDonald CJ. Preparing a collection of radiology examinations for distribution and retrieval. J Am Med Inform Assoc. 2016 Mar;23(2):304-10. doi: 10.1093/jamia/ocv080. Epub 2015 Jul 1.
    Abstract | PMID:  26133894 | PMCID:  PMC5009925
    Abstract
  • 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
    Abstract | pub9344.pdf
    AbstractDownload
  • 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.
    Abstract | pub9474.pdf
    AbstractDownload
  • Dhombres F, Bodenreider O. Interoperability between phenotypes in research and healthcare terminologies--Investigating partial mappings between HPO and SNOMED CT. J Biomed Semantics. 2016 Feb 9;7:3. doi: 10.1186/s13326-016-0047-3. eCollection 2016.
    Abstract | PMID:  26865946 | PMCID:  PMC4748471
    Abstract
  • Yaniv Z. Registration for Orthopaedic Interventions. Chapter 3 in: Zheng G, Li S, editors. Computational Radiology for Orthopaedic Interventions: Lecture Notes in Computational Vision and Biomechanics. Springer International Publishing; c2016. p. 41-70.
    Abstract | URL:  http://www.springer.com/us/book/9783319234816
    AbstractExternal link
  • Guo P, Banerjee K, Stanley RJ, Long LR, Antani SK, Thoma GR, Frazier SR, Moss RH, Stoecker WV. Nuclei-Based Features for Uterine Cervical Cancer Histology Image Analysis with Fusion-based Classification. DOI 10.1109/JBHI.2015.2483318 IEEE Journal of Biomedical and Health Informatics
    Abstract | URL:  http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=7307080
    AbstractExternal link
  • 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.
    Abstract | pub9176.pdf | PMID:  26092662
    AbstractDownload
  • Bodenreider O. Identifying missing hierarchical relations in SNOMED CT from logical definitions based on the lexical features of concept names. Proceedings of the 6th International Conference on Biomedical Ontology (ICBO 2016), 2016: p. (electronic proceedings: http://ceur-ws.org/Vol-1747/IT601_ICBO2016.pdf).
    Abstract
    Abstract
  • 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.
    Abstract
    Abstract
  • Webster RJ, Yaniv Z. Image-Guided Procedures, Robotic Interventions, and Modeling. Proc. SPIE 9786. (ISBN: 9781510600218 ).
    Abstract
    Abstract
  • Roberts K, Shooshan SE, Rodriguez L, Abhyankar S, Kilicoglu H, Demner-Fushman D. The role of fine-grained annotations in supervised recognition of risk factors for heart disease from EHRs. J Biomed Inform. 2015 Dec;58 Suppl:S111-9. doi: 10.1016/j.jbi.2015.06.010. Epub 2015 Jun 26.
    Abstract | pub9188.pdf | PMID:  26122527 | PMCID:  PMC4988795
    AbstractDownload
  • Lu C, Tormey D, MCreedy L, Browne AC. Generating the MEDLINE N-Gram Set [Poster]. AMIA 2015 Annual Symposium, San Francisco, CA, November 14-18, 2015, p. 1569.
    Abstract | pub9345.pdf
    AbstractDownload
  • Cimino JJ, Huser V. Characterization of the Context of Drug Concepts in Research Protocols: An Empiric Study to Guide Ontology Development. AMIA Annu Symp Proc. 2015 Nov 5;2015:441-7. eCollection 2015.
    Abstract | PMID:  26958176 | PMCID:  PMC4765569
    Abstract
  • 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.
    Abstract | pub9258.pdf
    AbstractDownload
  • 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.
    Abstract
    Abstract
  • 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.
    Abstract | pub9333.pdf
    AbstractDownload
  • Antani SK. Automatic x-ray screening for tuberculosis. SPIE Newsroom. October 2015. DOI: 10.1117/2.1201509.006128
    Abstract | pub9265.pdf | URL:  http://spie.org/x115742.xml?highlight=x2416
    AbstractDownloadExternal link
  • Huser V, Sastry C, Breymaier M, Idriss A, Cimino JJ. Standardizing data exchange for clinical research protocols and case report forms: An assessment of the suitability of the Clinical Data Interchange Standards Consortium (CDISC) Operational Data Model (ODM). J Biomed Inform. 2015 Oct;57:88-99. doi: 10.1016/j.jbi.2015.06.023. Epub 2015 Jul 15.
    Abstract | PMID:  26188274 | PMCID:  PMC4714951
    Abstract
  • 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.
    Abstract | PMID:  26730398 | PMCID:  PMC4695659
    Abstract
  • Winnenburg R, Sorbello A, Ripple AM, Harpaz R, Tonning J, Szarfman A, Francis H, Bodenreider O. Leveraging MEDLINE indexing for pharmacovigilance - Inherent limitations and mitigation strategies. J Biomed Inform. 2015 Oct;57:425-35. doi: 10.1016/j.jbi.2015.08.022. Epub 2015 Sep 2.
    Abstract | PMID:  26342964 | PMCID:  PMC4775467
    Abstract
  • 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)
    Abstract | pub9226.pdf
    AbstractDownload
  • Payne TH, Corley S, Cullen TA, Gandhi TK, Harrington L, Kuperman GJ, Makar E, Mattison JE, McCallie DP, McDonald CJ, Tang PC, Tierney WM, Weaver C, Weir CR, Zaroukian MH. Report of the AMIA EHR-2020 Task Force on the status and future direction of EHRs J Am Med Inform Assoc. 2015 Sep;22(5):1102-10. doi: 10.1093/jamia/ocv066. Epub 2015 May 28.
    Abstract | PMID:  26024883 | PMCID:  PMC5009932
    Abstract
  • Dhombres F, Bodenreider O. Investigating the lexico-syntactic properties of phenotype terms – Application to interoperability between HPO and SNOMED CT. Proc Joint Bio-Ontologies and BioLINK ISMB'2015 SIG session "Phenotype Day" 2015:8-11.
    Abstract | pub9335.pdf
    AbstractDownload
  • Ruiz A, Allette K, Francis D, Lamping E, Jaeger S, Folio L, Apolo A. Patterns of soft tissue metastasis in patients with urothelial carcinoma using tumor volume heatmaps [Poster]. NIH Summer Research Program Poster Day, Aug 6, 2015
    Abstract | pub9221.pdf
    AbstractDownload
  • Yaniv Z, Linte CA. Applications of Augmented Reality in the Operating Room. Chapter 19 in Fundamentals of Wearable Computers and Augmented Reality, 2nd ed. CRC Press, 2015.
    Abstract | URL:  https://www.crcpress.com/Fundamentals-of-Wearable-Computers-and-Augmented-Realit...
    AbstractExternal link
  • Candemir S, Borovikov E, KC S, Antani SK, Thoma GR. RSILC: Rotation- and Scale-Invariant, Line-based Color-aware descriptor. Image and Vision Computing, Volume 42, October 2015, Pages 1-12, ISSN 0262-8856. doi:10.1016/j.imavis.2015.06.010.
    Abstract | pub9220.pdf | URL:  http://www.sciencedirect.com/science/article/pii/S0262885615000797#
    AbstractDownloadExternal link
  • Gartrell K, Trinkoff AM, Storr CL, Wilson ML. Electronic Personal Health Record Use Among Nurses in the Nursing Informatics Community. Comput Inform Nurs. 2015 Jul;33(7):306-14. doi: 10.1097/CIN.0000000000000163.
    Abstract | PMID:  26061563
    Abstract
  • 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.
    Abstract | URL:  http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=7167519
    AbstractExternal link
  • KC S, Antani SK, Thoma GR. Stitched Multipanel Biomedical Figure Separation. IEEE, 28th International Symposium on Computer-Based Medical Systems (CBMS), pp. 54-59, 2015.
    Abstract | pub9198.pdf | URL:  http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=7167457
    AbstractDownloadExternal link
  • 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
    Abstract | pub9175.pdf
    AbstractDownload
  • Ayvas S, Horn J, Hassanzadeh O, Zhu Q, Stan J, Tatonetti NP, Vilar S, Brochhausen M8, Samwald M, Rastegar-Mojarad M, Dumontier M, Boyce RD. Toward a complete dataset of drug-drug interaction information from publicly available sources. J Biomed Inform. 2015 Jun;55:206-17. doi: 10.1016/j.jbi.2015.04.006. Epub 2015 Apr 24.
    Abstract | PMID:  25917055 | PMCID:  PMC4464899
    Abstract
  • 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).
    Abstract | pub9223.pdf
    AbstractDownload
  • Vajda S, Rangoni Y, Cecotti H. Semi-automatic ground truth generation using unsupervised clustering and limited manual labeling: Application to handwritten character recognition. Pattern Recognit Lett. 2015 Jun 1;58:23-28.
    Abstract | PMID:  25870463 | PMCID:  PMC4392711
    Abstract
  • 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.
    Abstract | PMID:  25992264 | PMCID:  PMC4436163
    Abstract
  • 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.
    Abstract | PMID:  25964850 | PMCID:  PMC4426554
    Abstract
  • 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".
    Abstract | pub9358.pdf
    AbstractDownload
  • Fung KW, Xu J. An exploration of the properties of the CORE problem list subset and how it facilitates the implementation of SNOMED CT. J Am Med Inform Assoc. 2015 May;22(3):649-58. doi: 10.1093/jamia/ocu022. Epub 2015 Feb 26.
    Abstract | PMID:  25725003 | PMCID:  PMC5566198
    Abstract
  • Gartrell K, Storr CL, Trinkoff AM, Wilson ML, Gurses AP. Electronic personal health record use among registered nurses. Nurs Outlook. 2015 May-Jun;63(3):278-87. doi: 10.1016/j.outlook.2014.11.013. Epub 2014 Nov 28.
    Abstract | PMID:  25982768 | PMCID:  PMC4438260
    Abstract
  • 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.
    Abstract | PMID:  25937884 | PMCID:  PMC4416343
    Abstract
  • Gartrell K, Trinkoff AM, Storr CL, Wilson ML, Gurses AP. Testing the Electronic Personal Health Record Acceptance Model by Nurses for Managing Their Own Health: A Cross-sectional Survey. Appl Clin Inform. 2015 Apr 8;6(2):224-47. doi: 10.4338/ACI-2014-11-RA-0107. eCollection 2015.
    Abstract | PMID:  26171072 | PMCID:  PMC4493327
    Abstract
  • 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.
    Abstract | PMID:  25887792 | PMCID:  PMC4407321
    Abstract
  • Abhyankar S, Goodwin RM, Sontag M, Yusuf C, Ojodu J, McDonald CJ. An update on the use of health information technology in newborn screening. Semin Perinatol. 2015 Apr;39(3):188-93. doi: 10.1053/j.semperi.2015.03.003. Epub 2015 Apr 29.
    Abstract | PMID:  25935354 | PMCID:  PMC4433800
    Abstract
  • 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.
    Abstract | PMID:  25661592 | PMCID:  PMC4888806
    Abstract
  • Zhu X, Cimino JJ. Clinicians' evaluation of computer-assisted medication summarization of electronic medical records. Comput Biol Med. 2015 Apr;59:221-31. doi: 10.1016/j.compbiomed.2013.12.006. Epub 2013 Dec 19.
    Abstract | PMID:  24393492 | PMCID:  PMC4063892
    Abstract
  • Winnenburg R, Mortensen JM, Bodenreider O. Using description logics to evaluate the consistency of drug-class membership relations in NDF-RT. J Biomed Semantics. 2015 Mar 28;6:13. doi: 10.1186/s13326-015-0007-3. eCollection 2015.
    Abstract | PMID:  25866612 | PMCID:  PMC4392727
    Abstract
  • Roberts K, Demner-Fushman D. Toward a Natural Language Interface for EHR Questions. AMIA Jt Summits Transl Sci Proc. 2015 Mar 25;2015:157-61. eCollection 2015.
    Abstract | pub9234.pdf | PMID:  26306260 | PMCID:  PMC4525248
    AbstractDownload
  • Wei W, Demner-Fushman D, Wang S, Jiang X, Ohno-Machado L. Ranking Medical Subject Headings using a factor graph model. AMIA Jt Summits Transl Sci Proc. 2015 Mar 23;2015:56-63. eCollection 2015.
    Abstract | pub9268.pdf | PMID:  26306236 | PMCID:  PMC4525219
    AbstractDownload
  • 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.
    Abstract | PMID:  26306241 | PMCID:  PMC4525230
    Abstract
  • 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.
    Abstract
    Abstract
  • 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.
    Abstract | pub9104.pdf
    AbstractDownload
  • 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.
    Abstract | URL:  http://spie.org/Publications/Proceedings/Paper/10.1117/12.2081456
    AbstractExternal link
  • 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.
    Abstract | pub9103.pdf
    AbstractDownload
  • 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.
    Abstract | PMID:  25592675 | PMCID:  PMC4307891
    Abstract
  • 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).
    Abstract
    Abstract
  • 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).
    Abstract
    Abstract
  • Cohen KB, Demner-Fushman D. Biomedical Natural Language Processing John Benjamins Publishing Company, 2014. DOI: 10.1075/nlp.11
    Abstract
    Abstract
  • 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.
    Abstract | PMID:  25572585
    Abstract
  • 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.
    Abstract | PMID:  26262161
    Abstract
  • Hripcsak G, Duke JD, Shah NH, Reich CG, Huser V, Schuemie MJ, Suchard MA, Park RW, Wong IC, Rijnbeek PR, van der Lei J, Pratt N, Norén GN, Li YC, Stang PE, Madigan D, Ryan PB. Observational Health Data Sciences and Informatics (OHDSI): Opportunities for Observational Researchers. Stud Health Technol Inform. 2015;216:574-8.
    Abstract | PMID:  26262116 | PMCID:  PMC4815923
    Abstract
  • 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
    Abstract | pub8970.pdf
    AbstractDownload
  • 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/.
    Abstract | pub9196.pdf
    AbstractDownload
  • Kilicoglu H, Rogers W. A Hybrid System for Extracting Chemical-Disease Relationships from Scientific Literature. 2015. BioCreative 5 Proceedings.
    Abstract | pub9350.pdf
    AbstractDownload
  • Kury F, Cimino JJ. Identifying Repetitive Institutional Review Board Stipulations by Natural Language Processing and Network Analysis. Stud Health Technol Inform. 2015;216:579-83.
    Abstract | PMID:  26262117
    Abstract
  • 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.
    Abstract | PMID:  26262156
    Abstract
  • Song D, Kim E, Huang X, Patruno J, Munoz-Avila H, Heflin J, Long LR, Antani SK. Multimodal entity coreference for cervical dysplasia diagnosis. IEEE Transactions on Medical Imaging, 34(1), January 2015, 229-245.
    Abstract | URL:  http://dx.doi.org/10.1109/TMI.2014.2352311
    AbstractExternal link
  • Kayaalp M, Dodd Z, Browne AC, Sagan, P, McDonald CJ. Software: NLM-Scrubber
    Abstract | URL:  https://scrubber.nlm.nih.gov/
    AbstractExternal link
  • Cimino JJ, Ayres EJ, Remennik L, Rath S, Freedman R, Beri A, Chen Y, Huser V. The National Institutes of Health's Biomedical Translational Research Information System (BTRIS): design, contents, functionality and experience to date. J Biomed Inform. 2014 Dec;52:11-27. doi: 10.1016/j.jbi.2013.11.004. Epub 2013 Nov 19.
    Abstract | PMID:  24262893 | PMCID:  PMC4026354
    Abstract
  • Jaeger S, Candemir S, Antani SK, Wang Y, Lu P, Thoma GR. Two public chest X-ray datasets for computer-aided screening of pulmonary diseases. Quant Imaging Med Surg. 2014 Dec;4(6):475-7. doi: 10.3978/j.issn.2223-4292.2014.11.20.
    Abstract | pub9356.pdf | PMID:  25525580 | PMCID:  PMC4256233
    AbstractDownload
  • Mishra R, Bian J, Fiszman M, Weir CR, Mostafa J, Fiol GD. Text summarization in the biomedical domain: a systematic review of recent research. J Biomed Inform. 2014 Dec;52:457-67. doi: 10.1016/j.jbi.2014.06.009. Epub 2014 Jul 10.
    Abstract | PMID:  25016293 | PMCID:  PMC4261035
    Abstract
  • Shang N, Xu H, Rindflesch TC, Cohen T. Identifying plausible adverse drug reactions using knowledge extracted from the literature. J Biomed Inform. 2014 Dec;52:293-310. doi: 10.1016/j.jbi.2014.07.011. Epub 2014 Jul 19.
    Abstract | PMID:  25046831 | PMCID:  PMC4261011
    Abstract
  • 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
    Abstract | pub8977.pdf | URL:  http://rsna2014.rsna.org/pdf/Informatics.pdf
    AbstractDownloadExternal link
  • Antani SK. Tuberculosis Chest X-ray Image Data Sets
    Abstract
    Abstract
  • 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.
    Abstract | pub8973.pdf | URL:  http://knowledge.amia.org/56638-amia-1.1540970/t-005-1.1543914/f-005-1.1543915/a...
    AbstractDownloadExternal link
  • Bodenreider O, Rodriguez L. Analyzing U.S. prescription lists with RxNorm and the ATC/DDD Index. AMIA Annu Symp Proc. 2014 Nov 14;2014:297-306. eCollection 2014.
    Abstract | pub9011.pdf | PMID:  25954332 | PMCID:  PMC4419961
    AbstractDownload
  • Browne AC, Kayaalp M, Dodd Z, Sagan, P, McDonald CJ. The Challenges of Creating a Gold Standard for De-identification Research. AMIA Annu Symp Proc. 2014 Nov 14;2014:353-8. eCollection 2014.
    Abstract | pub8927.pdf | PMID:  25954338 | PMCID:  PMC4420002
    AbstractDownload
  • Cimino JJ, Remennick L. Adapting a Clinical Data Repository to ICD-10-CM through the use of a Terminology Repository. AMIA Annu Symp Proc. 2014 Nov 14;2014:405-13. eCollection 2014.
    Abstract | PMID:  25954344 | PMCID:  PMC4419915
    Abstract
  • Culbertson A, Fiszman M, Shin D, Rindflesch TC. Semantic processing to identify adverse drug event information from black box warnings. AMIA Annu Symp Proc. 2014 Nov 14;2014:442-8. eCollection 2014.
    Abstract | PMID:  25954348 | PMCID:  PMC4419903
    Abstract
  • 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.
    Abstract | PMID:  25954361 | PMCID:  PMC4419993
    Abstract
  • Huser, V, Kayaalp M, Dodd Z, Cimino J. Piloting a deceased subject integrated data repository and protecting privacy of relatives. AMIA Annu Symp Proc. 2014 Nov 14;2014:719-28. eCollection 2014.
    Abstract | pub8928.pdf | PMID:  25954378 | PMCID:  PMC4420001
    AbstractDownload
  • 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.
    Abstract | pub8926.pdf | PMID:  25954383 | PMCID:  PMC4419982
    AbstractDownload
  • Lu C, Tormey D, McDreedy L, Browne AC. Using element words to generate (multi)words for the SPECIALIST Lexicon [Poster]. AMIA 2014 Annual Symposium, Washington, DC, November 15-19, 2014, p. 1499. Poster
    Abstract | pub9346.pdf
    AbstractDownload
  • Ozturk S, Kayaalp M, McDonald CJ. Visualization of patient prescription history data in emergency care. AMIA Annu Symp Proc. 2014 Nov 14;2014:963-8. eCollection 2014.
    Abstract | PMID:  25954404 | PMCID:  PMC4419971
    Abstract
  • Pan X, Cimino JJ. Locating relevant patient information in electronic health record data using representations of clinical concepts and database structures. AMIA Annu Symp Proc. 2014 Nov 14;2014:969-75. eCollection 2014.
    Abstract | PMID:  25954405 | PMCID:  PMC4419946
    Abstract
  • 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.
    Abstract | pub8972.pdf | PMID:  25954411 | PMCID:  PMC4420005 | URL:  http://knowledge.amia.org/56638-amia-1.1540970/t-004-1.1544972/f-004-1.1544973/a...
    AbstractDownloadExternal link
  • 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.
    Abstract | PMID:  25954433 | PMCID:  PMC4419968
    Abstract
  • 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.
    Abstract | PMID:  25632348 | PMCID:  PMC4306188
    Abstract
  • Rodriguez L, Huser V, Bodenreider O, Cimino J. Automatic coding of Free-Text Medication Data recorded by Research Coordinators [Poster]. AMIA Annu Symp Proc 2014:1565.
    Abstract | pub9012.pdf
    AbstractDownload
  • Gordon, E, Ersoy, I, Jaeger S, Waisberg, M, Pena, M, Thoma GR, Antani SK, Pierce, S, Palaniappan, K. Retinal Microcirculation Dynamics During an Active Malarial Infection [Poster]. Annual Meeting of the American Society of Tropical Medicine and Hygiene (ASTMH), 2014.
    Abstract
    Abstract
  • 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.
    Abstract
    Abstract
  • McDonald CJ, Callaghan FM, Weissman A, Goodwin RM, Mundkur M, Kuhn T. Use of internist's free time by ambulatory care Electronic Medical Record systems. JAMA Intern Med. 2014 Nov;174(11):1860-3. doi: 10.1001/jamainternmed.2014.4506.
    Abstract | PMID:  25200944
    Abstract
  • Nguyen T, Peters L, Bodenreider O. RxClass - Navigating between drug classes and RxNorm drugs [Poster]. AMIA Annu Symp Proc, 2014: p. 1529.
    Abstract
    Abstract
  • Winnenburg R, Bodenreider O. Desiderata for an authoritative representation of MeSH in RDF. AMIA Annu Symp Proc 2014:1218-1227.
    Abstract
    Abstract
  • 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.
    Abstract | PMID:  25392688 | PMCID:  PMC4216049
    Abstract
  • Bodenreider O, Peters L, Nguyen T. RxClass – Navigating between Drug Classes and RxNorm Drugs (Demo). Prc. ICBO 2014
    Abstract | URL:  http://ceur-ws.org/Vol-1327/icbo2014_paper_49.pdf
    AbstractExternal link
  • Cohen T, Widdows D, Stephan C, Zinner R, Kim J, Rindflesch TC, Davies P. Predicting high-throughput screening results with scalable literature-based discovery methods. CPT Pharmacometrics Syst Pharmacol. 2014 Oct 8;3:e140. doi: 10.1038/psp.2014.37.
    Abstract | PMID:  25295575 | PMCID:  PMC4474167
    Abstract
  • 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.
    Abstract
    Abstract
  • Rondonotti E, Koulaouzidis A, Karargyris A, Giannakou A, Fini L, Soncini M, Pennazio M, Douglas S, Shams A, Lachlan N, Zahid A, Mandelli G, Girelli C. Utility of 3-dimensional image reconstruction in the diagnosis of small-bowel masses in capsule endoscopy (with video). Gastrointest Endosc. 2014 Oct;80(4):642-51. doi: 10.1016/j.gie.2014.04.057. Epub 2014 Jul 3.
    Abstract | PMID:  24998466
    Abstract
  • 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.
    Abstract | PMID:  25705725 | PMCID:  PMC4334137
    Abstract
  • Huser V, Sincan M, Cimino JJ. Developing genomic knowledge bases and databases to support clinical management: current perspectives. Pharmgenomics Pers Med. 2014 Sep 9;7:275-83. doi: 10.2147/PGPM.S49904. eCollection 2014.
    Abstract | PMID:  25276091 | PMCID:  PMC4175027
    Abstract
  • Do T, Murphy G, Earl LA, Del Prete GQ, Grandinetti G, Li GH, Estes JD, Rao P, Trubey CM, Thomas J, Spector J, Bliss D, Nath A, Lifson JD, Subramaniam S. Three-dimensional imaging of HIV-1 virological synapses reveals membrane architectures involved in virus transmission. J Virol. 2014 Sep;88(18):10327-39. doi: 10.1128/JVI.00788-14. Epub 2014 Jun 25.
    Abstract | PMID:  24965444 | PMCID:  PMC4178837
    Abstract
  • 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.
    Abstract | PMID:  24928177 | PMCID:  PMC4147617
    Abstract
  • KC S, Wendling L, Antani SK, Thoma GR. Scalable arrow detection in biomedical images. Pattern Recognition (ICPR), 2014 22nd International Conference; pp 3257-62. DOI: 10.1109/ICPR.2014.561
    Abstract | pub8980.pdf | URL:  http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6977273
    AbstractDownloadExternal link
  • Linte CA, Yaniv Z, Fallavollita P, Abolmaesumi P, Holmes DR III, editors. Augmented Environments for Computer-Assisted Interventions 2014: 9th International AE-CAI Workshop. Held in conjunction with MICCAI 2014. 2014 Sep 14; Boston. Lecture Notes in Computer Science, vol. 8678. Springer; 2014. 149 pages.
    Abstract
    Abstract
  • Nagy DA, Haidegger T, Yaniv Z. A framework for semi-automatic fiducial localization in volumetric images. In: Linte CA, Yaniv Z, Fallavollita P, Abolmaesumi P, Holmes DR III, editors. Augmented Environments for Computer-Assisted Interventions 2014: Proceedings of 9th International AE-CAI Workshop; 2014 Sep 14; Boston. Lecture Notes in Computer Science vol. 8678. Springer; 2014. p. 138-48.
    Abstract | URL:  http://link.springer.com/chapter/10.1007/978-3-319-10437-9_15
    AbstractExternal link
  • Boyce RD, Ryan PB, Noren GN, Schuemie MJ, Reich C, Duke J, Tatonetti NP, Trifiro G, Harpaz R, Overhage JM, Hartzema AG, Kayter M, Voss EA, Lambert CG, Huser V, Dumontier M. Bridging islands of information to establish an integrated knowledge base of drugs and health outcomes of interest. Drug Saf. 2014 Aug;37(8):557-67. doi: 10.1007/s40264-014-0189-0.
    Abstract | PMID:  24985530 | PMCID:  PMC4134480
    Abstract
  • 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.
    Abstract | pub8935.pdf | PMID:  25101165 | PMCID:  PMC4120719
    AbstractDownload
  • Zhang R, Cairelli MJ, Fiszman M, Rosemblat G, Kilicoglu H, Rindflesch TC, Pakhomov SV, Melton GB. Using semantic predications to uncover drug-drug interactions in clinical data. J Biomed Inform. 2014 Jun;49:134-47. doi: 10.1016/j.jbi.2014.01.004. Epub 2014 Jan 19.
    Abstract | PMID:  24448204 | PMCID:  PMC4058371
    Abstract
  • KC S, Candemir S, Jaeger S, Folio L, Karargyris A, Antani SK, Thoma GR. Rotation detection in chest radiographs based on generalized line histogram of rib-orientations. IEEE 27th International Symposium on Computer-Based Medical Systems, New York, NY, USA, May 27-29, 2014: page 138-142.
    Abstract | cameraReady33_cbms0.pdf | URL:  http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6881864
    AbstractDownloadExternal link
  • Kayaalp M, Browne AC, Callaghan FM, Dodd Z, Divita G, Ozturk S, McDonald CJ. The pattern of name tokens in narrative clinical text and a comparison of five systems for redacting them. J Am Med Inform Assoc. 2014 May-Jun;21(3):423-31. doi: 10.1136/amiajnl-2013-001689. Epub 2013 Sep 11.
    Abstract | PMID:  24026308 | PMCID:  PMC3994850 | URL:  http://dx.doi.org/10.1136/amiajnl-2013-001689
    AbstractExternal link
  • Ren H, Campos-Nanez E, Yaniv Z, Banovac F, Abeledo H, Hata N, Cleary K. Treatment planning and image guidance for radiofrequency ablation of large tumors. IEEE J Biomed Health Inform. 2014 May;18(3):920-8. doi: 10.1109/JBHI.2013.2287202. Epub 2013 Oct 24.
    Abstract | PMID:  24235279 | PMCID:  PMC4113118 | URL:  http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=6646232
    AbstractExternal link
  • 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
    Abstract | pub8971.pdf | URL:  http://dx.doi.org/10.1109/CBMS.2014.55
    AbstractDownloadExternal link
  • You D, Antani SK, Demner-Fushman D, Thoma GR. A MRF Model for Biomedical Image Segmentation. CBMS 2014. May 2014.
    Abstract
    Abstract
  • Yaniv Z, Holmes DR III, editors. Medical Imaging 2014: Image-Guided Procedures, Robotic Interventions, and Modeling. Proceedings of conference held 2014 Feb 15-20; San Diego. Proc. SPIE 9036; 2014 Mar 12. 764 pages. ISBN: 9780819498298.
    Abstract
    Abstract
  • 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.
    Abstract | pub8934.pdf | PMID:  25750938 | PMCID:  PMC4350149
    AbstractDownload
  • Linte CA, Yaniv Z. When change happens: computer assistance and image guidance for minimally invasive therapy. Healthcare Technology Letters. 2014 Mar 25;1(1):2-5.
    Abstract | URL:  http://digital-library.theiet.org/content/journals/10.1049/htl.2014.0058
    AbstractExternal link
  • Pedrosa G, Rahman MM, Antani SK, Demner-Fushman D, Long LR, Traina A. Integrating visual words as bunch of n-grams for effective biomedical image classification. Proceedings of IEEE WACV 2014: IEEE Winter Conference on Applications of Computer Vision. Steamboat Springs, CO. March 24-26, 2014.
    Abstract | pub6956.pdf
    AbstractDownload
  • Gong RH, Jenkins B, Sze RW, Yaniv Z. A cost effective and high fidelity fluoroscopy simulator using the image-guided surgery toolkit (IGSTK). In: Yaniv Z, Holmes DR III, editors. Medical Imaging 2014: Image-Guided Procedures, Robotic Interventions, and Modeling; 2014 Feb 15-20; San Diego. Proc. SPIE 9036; 2014 Mar 12:11 pages. DOI: 10.1117/12.2044112.
    Abstract
    Abstract
  • Guler, O, Yaniv Z. A tutorial on image guided therapy. Chapter 11 in: Birkfellner W, editor. Applied Medical Image Processing, Second Edition: A Basic Course. London: CRC Press; 2014. ISBN: 9781466555570.
    Abstract
    Abstract
  • Narayan K, Danielson CM, Lagarec K, Lowekamp BC, Coffman P, Laquerre A, Phaneuf MW, Hope TJ, Subramaniam S. Multi-resolution correlative focused ion beam scanning electron microscopy: applications to cell biology. J Struct Biol. 2014 Mar;185(3):278-84. doi: 10.1016/j.jsb.2013.11.008. Epub 2013 Dec 1.
    Abstract | PMID:  24300554 | PMCID:  PMC3943650
    Abstract
  • 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.
    Abstract | pub6960.pdf | PMID:  24239990
    AbstractDownload
  • Jaeger S, Karargyris A, Candemir S, Folio L, Siegelman J, Callaghan FM, Xue Z, Palaniappan K, Singh RK, Antani SK, Thoma GR, Wang Y, Lu P, McDonald CJ. Automatic tuberculosis screening using chest radiographs. IEEE Trans Med Imaging. 2014 Feb;33(2):233-45. doi: 10.1109/TMI.2013.2284099. Epub 2013 Oct 1.
    Abstract | 2014_TMI_Automatic Tuberculosis.pdf | PMID:  24108713
    AbstractDownload
  • 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.
    Abstract | pub7039.pdf
    AbstractDownload
  • 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.
    Abstract | PMID:  24475099 | PMCID:  PMC3903545
    Abstract
  • Bodenreider O. Multi-lingual features of the Unified Medical Language System. Proc. CLEF-ER 2013 workshop 2013.
    Abstract | 2013-clef_er-ob-abstract.pdf | URL:  http://www.clef2013.org/index.php?page=Pages/proceedings.php
    AbstractDownloadExternal link
  • 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.
    Abstract
    Abstract
  • Huser V, Cimino JJ. Don't take your EHR to heaven, donate it to science: legal and research policies for EHR post mortem. J Am Med Inform Assoc. 2014 Jan-Feb;21(1):8-12. doi: 10.1136/amiajnl-2013-002061. Epub 2013 Aug 21.
    Abstract | PMID:  23966483 | PMCID:  PMC3912713
    Abstract
  • Kastrin A, Rindflesch TC, Hristovski D. Link prediction in a MeSH co-occurrence network: preliminary results. Stud Health Technol Inform. 2014;205:579-83.
    Abstract | PMID:  25160252
    Abstract
  • Kastrin A, Rindflesch TC, Hristovski D. Link prediction on the Semantic MEDLINE Network. Proceedings of the 17th International conference on Discovery Science.
    Abstract
    Abstract
  • McDonald CJ, Tang PC, Hripcsak G. Electronic Health Record Systems. . In: Shortliffe EH, Cimino JJ, editors. Biomedical Informatics: Computer Applications in Healthcare and Biomedicine 4th ED [Internet]. London: Springer London; 2014. p. 391–421. Available from: http://link.springer.com/10.1007/978-1-4471-4474-8.
    Abstract
    Abstract
  • Mork JG, Demner-Fushman D, Schmidt SC, Aronson A. Recent Enhancements to the NLM Medical Text Indexer. BioASQ 2014.
    Abstract
    Abstract
  • Mork JG, Demner-Fushman D, Schmidt SC, Aronson A. Vocabulary Density Method for Personalized Indexing of MEDLINE Journals [Poster]. 2014 AMIA Symposium.
    Abstract
    Abstract
  • Osborne R, Aronson A, Cohen K. A repository of semantic types in the MIMIC II database clinical notes. BioNLP 2014. pp. 93-97.
    Abstract
    Abstract
  • Ripple AM, Mork JG, Schmidt SC, Thomson H, Knecht LS. Performance Comparison of MEDLINE Structured Abstract to Unstructured Abstracts [Poster]. 2014 NIH Research Festival.
    Abstract
    Abstract
  • 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
    Abstract
    Abstract
  • Winnenburg R, Bodenreider O. Coverage of human phenotypes in SNOMED CT [Poster]. SNOMED CT Implementation Showcase, 2014.
    Abstract | URL:  http://ihtsdo.org/fileadmin/user_upload/doc/showcase/show14/SnomedCtShowcase2014...
    AbstractExternal link
  • Winnenburg R, Bodenreider O. Coverage of phenotypes in standard terminologies. Joint Bio-Ontologies and BioLINK ISMB'2014 SIG session "Phenotype Day" 2014:41-44. 
    Abstract | pub8937.pdf
    AbstractDownload
  • 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
    Abstract | pub8936.pdf | URL:  https://drive.google.com/file/d/0B6AZUdKw1IVHeGVtTVZCRXJhbFk/
    AbstractDownloadExternal link
  • Lowekamp BC, Chen DT, Ibáñez L, Blezek D. The Design of SimpleITK. Front Neuroinform. 2013 Dec 30;7:45. doi: 10.3389/fninf.2013.00045. eCollection 2013.
    Abstract | PMID:  24416015 | PMCID:  PMC3874546
    Abstract
  • Bodenreider O. Disease Ontologies In: Dubitzky W, Wolkenhauer O, Cho K-H, Yokota H, editors. Encyclopedia of Systems Biology: Springer; 2013. p. 578-581.
    Abstract | pub2011017.pdf
    AbstractDownload
  • 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.
    Abstract | PMID:  23973273 | PMCID:  PMC3844019
    Abstract
  • 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.
    Abstract | PMID:  24523987 | PMCID:  PMC3920035
    Abstract
  • 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.
    Abstract | PMID:  24307796 | PMCID:  PMC3848150
    Abstract
  • Lowekamp B, Chen D. BinShrink: A multi-resolution filter with cache efficient averaging. Insight Journal. Web. 18 November 2013
    Abstract
    Abstract
  • 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.
    Abstract | PMID:  24551317 | PMCID:  PMC3900117
    Abstract
  • Cairelli MJ, Miller CM, Fiszman M, Workman TE, Rindflesch TC. Semantic MEDLINE for discovery browsing: using semantic predications and the literature-based discovery paradigm to elucidate a mechanism for the obesity paradox. AMIA Annu Symp Proc. 2013 Nov 16;2013:164-73. eCollection 2013.
    Abstract | PMID:  24551329 | PMCID:  PMC3900170
    Abstract
  • Cimino JJ, Overby CL, Devine EB, Hulse NC, Jing X, Maviglia SM, Del Fiol G. Practical choices for infobutton customization: experience from four sites. AMIA Annu Symp Proc. 2013 Nov 16;2013:236-45. eCollection 2013.
    Abstract | PMID:  24551334 | PMCID:  PMC3900175
    Abstract
  • 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.
    Abstract | PMID:  24551339 | PMCID:  PMC3900180
    Abstract
  • Huser V, Cimino JJ. Desiderata for healthcare integrated data repositories based on architectural comparison of three public repositories. AMIA Annu Symp Proc. 2013 Nov 16;2013:648-56. eCollection 2013.
    Abstract | PMID:  24551366 | PMCID:  PMC3900207
    Abstract
  • Lu C, Tormey D, McDreedy L, Browne AC. Implementing comprehensive derivational features in Llexical tools using a systematical approach [Poster]. AMIA 2013 Annual Symposium, Washington, DC, November 16-20, 2013, p. 904
    Abstract | pub9347.pdf
    AbstractDownload
  • 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.
    Abstract | pub8952.pdf | PMID:  24551389 | PMCID:  PMC3900230
    AbstractDownload
  • 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.
    Abstract | PMID:  24551422 | PMCID:  PMC3900160
    Abstract
  • 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.
    Abstract | PMID:  24551423 | PMCID:  PMC3900161
    Abstract
  • 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.
    Abstract | PMID:  24551371 | PMCID:  PMC3900212
    Abstract
  • 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.
    Abstract | Poster5.pdf
    AbstractDownload
  • 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.
    Abstract | poster6.pdf
    AbstractDownload
  • 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.
    Abstract | poster 3.pdf
    AbstractDownload
  • 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.
    Abstract | poster2.pdf
    AbstractDownload
  • 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.
    Abstract | poster4.pdf
    AbstractDownload
  • Le T, Rance B, Bodenreider O. Network visualization of UMLS source vocabularies using semantic groups. AMIA Annu Symp Proc, 2013: p. 90
    Abstract
    Abstract
  • Peters L, Nguyen T, Bodenreider O. Displaying drug classes in RxNav [Poster]. AMIA Annu Symp Proc, 2013: p. 1134.
    Abstract
    Abstract
  • McDonald CJ. Toward electronic medical record alerts that consume less physician time. JAMA Intern Med. 2013 Oct 14;173(18):1755-6. doi: 10.1001/jamainternmed.2013.9332.
    Abstract | PMID:  24126778
    Abstract
  • 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.
    Abstract | PMID:  23810857
    Abstract
  • Gordon E, Waisberg M, Ersoy I, Pena M, Jaeger S, Pierce S. The eye as a window to investigate the CNS microvasculature during a dynamic malaria infection (Abstract). Third Annual Seminar on Molecular Imaging of Infectious Diseases, September 23, 2013.
    Abstract | pub8969.pdf
    AbstractDownload
  • 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.
    Abstract | PMID:  24124345 | PMCID:  PMC3793153
    Abstract
  • Fung K, Kayaalp M, Callaghan FM, McDonald CJ. Comparison of electronic pharmacy prescription records with manually collected medication histories in an emergency department. Ann Emerg Med. 2013 Sep;62(3):205-11. doi: 10.1016/j.annemergmed.2013.04.014. Epub 2013 May 18.
    Abstract | PMID:  23688770 | PMCID:  PMC4697454 | URL:  http://www.sciencedirect.com/science/article/pii/S0196064413003521
    AbstractExternal link
  • 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.
    Abstract | pub7003.pdf | PMID:  23100128 | PMCID:  PMC3756259
    AbstractDownload
  • 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.
    Abstract | PMID:  24083058 | PMCID:  PMC3779392
    Abstract
  • Hersh WR, Weiner MG, Embi PJ, Logan JR, Payne PR, Bernstam EV, Lehmann HP, Hripcsak G, Hartzog TH, Cimino J, Saltz JH. Caveats for the use of operational electronic health record data in comparative effectiveness research. Med Care. 2013 Aug;51(8 Suppl 3):S30-7. doi: 10.1097/MLR.0b013e31829b1dbd.
    Abstract | PMID:  23774517 | PMCID:  PMC3748381
    Abstract
  • Huser V, Cimino JJ. Linking ClinicalTrials.gov and PubMed to track results of interventional human clinical trials. PLoS One. 2013 Jul 9;8(7):e68409. doi: 10.1371/journal.pone.0068409. Print 2013.
    Abstract | PMID:  23874614 | PMCID:  PMC3706420
    Abstract
  • 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.
    Abstract | PMID:  23802936 | PMCID:  PMC3706357
    Abstract
  • Jimeno-Yepes AJ, Sticco JC, Mork JG, Aronson AR. GeneRIF indexing: sentence selection based on machine learning. BMC Bioinformatics. 2013 May 31;14:171. doi: 10.1186/1471-2105-14-171.
    Abstract | PMID:  23725347 | PMCID:  PMC3687823
    Abstract
  • 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.
    Abstract
    Abstract
  • 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.
    Abstract | pub2013-008.pdf | PMID:  23475786 | PMCID:  PMC3628062
    AbstractDownload
  • 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.
    Abstract | PMID:  23631733 | PMCID:  PMC3651320
    Abstract
  • Abhyankar S, McDonald CJ. Overweight, obesity, and all-cause mortality [Letter]. JAMA. 2013 Apr 24;309(16):1680-1. doi: 10.1001/jama.2013.3092.
    Abstract | pub2013-013.pdf | PMID:  23613065 | URL:  http://jama.jamanetwork.com/article.aspx?articleid=1681396
    AbstractDownloadExternal link
  • Schauder DM, Kuybeda O, Zhang J, Klymko K, Bartesaghi A, Borgnia MJ, Mayer ML, Subramaniam S. Glutamate receptor desensitization is mediated by changes in quaternary structure of the ligand binding domain. Proc Natl Acad Sci U S A. 2013 Apr 9;110(15):5921-6. doi: 10.1073/pnas.1217549110. Epub 2013 Mar 25.
    Abstract | PMID:  23530186 | PMCID:  PMC3625259
    Abstract
  • McDonald CJ, Vreeman DJ, Abhyankar S. Comment on "time to integrate clinical and research informatics" [Letter]. Sci Transl Med. 2013 Apr 3;5(179):179le1. doi: 10.1126/scitranslmed.3005700.
    Abstract | PMID:  23552367
    Abstract
  • 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.
    Abstract | PMID:  23026233 | PMCID:  PMC4031661
    Abstract
  • Cimino JJ. Tutorial: meeting data access and reporting requirements with the NIH’s Biomedical Translational Research Information System (BTRIS).
    Abstract
    Abstract
  • 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.
    Abstract | pub6987.pdf | PMID:  23630656 | PMCID:  PMC3636475
    AbstractDownload
  • Liu J, Subramanian KR, Yoo TS. An optical flow approach to tracking colonoscopy video. Comput Med Imaging Graph. 2013 Apr;37(3):207-23. doi: 10.1016/j.compmedimag.2013.01.010. Epub 2013 Mar 13.
    Abstract | PMID:  23490235
    Abstract
  • 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
    Abstract | URL:  http://dx.doi.org/10.1117/12.2007800
    AbstractExternal link
  • Harris AK, Meyerson JR, Matsuoka Y, Kuybeda O, Moran A, Bliss D, Das SR, Yewdell JW, Sapiro G, Subbarao K, Subramaniam S. Structure and accessibility of HA trimers on intact 2009 H1N1 pandemic influenza virus to stem region-specific neutralizing antibodies. Proc Natl Acad Sci U S A. 2013 Mar 19;110(12):4592-7. doi: 10.1073/pnas.1214913110. Epub 2013 Mar 4.
    Abstract | PMID:  23460696 | PMCID:  PMC3607006
    Abstract
  • Hruby GW, Boland MR, Cimino J, Gao J, Wilcox AB, Hirschberg J, Weng C. Characterization of the biomedical query mediation process. AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:89-93. eCollection 2013.
    Abstract | PMID:  24303242 | PMCID:  PMC3845777
    Abstract
  • Huser V, Cimino J. Providing pharmacogenomics clinical decision support using whole genome sequencing data as input. AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:81. eCollection 2013.
    Abstract | PMID:  24303303
    Abstract
  • Manning JD, Marciano BE, Cimino J. Visualizing the data - using lifelines2 to gain insights from data drawn from a clinical data repository. AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:168-72. eCollection 2013.
    Abstract | PMID:  24303258 | PMCID:  PMC3845771
    Abstract
  • Hristovski D, Rindflesch TC, Peterlin B. Using literature-based discovery to identify novel therapeutic approaches. Cardiovasc Hematol Agents Med Chem. 2013 Mar;11(1):14-24.
    Abstract | PMID:  22845900
    Abstract
  • You D, Rahman MM, Antani SK, Demner-Fushman D, Thoma GR. Text- and content-based biomedical image modality classification. Proc. SPIE Medical Imaging. Orlando, FL. February 2013;8674-21.
    Abstract
    Abstract
  • 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.
    Abstract
    Abstract
  • Tran EEH, Kuybeda O, Bartesaghi A, Milne JLS, Subramaniam S. Binding of Neutralizing Antibodies Results in Distinct Quaternary Conformations of Trimeric HIV-1 Envelope Glycoproteins. Biophysical Society 57th Annual Meeting; 2013 Feb 2-6; Philadelphia.
    Abstract
    Abstract
  • 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.
    Abstract | SPIE DRR2013_pointer_segmentation.pdf | URL:  http://proceedings.spiedigitallibrary.org/proceeding.aspx?articleid=1568647
    AbstractDownloadExternal link
  • 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.
    Abstract | URL:  http://proceedings.spiedigitallibrary.org/proceeding.aspx?articleid=1568635
    AbstractExternal link
  • Fung K. Dataset: SNOMED CT to ICD-10 Cross Map
    Abstract
    Abstract
  • Kuybeda O, Frank GA, Bartesaghi A, Borgnia M, Subramaniam S, Sapiro G. A collaborative framework for 3D alignment and classification of heterogeneous subvolumes in cryo-electron tomography. J Struct Biol. 2013 Feb;181(2):116-27. doi: 10.1016/j.jsb.2012.10.010. Epub 2012 Oct 27.
    Abstract | PMID:  23110852 | PMCID:  PMC3565063
    Abstract
  • Harris AK, Meyerson JR, Matsuoka Y, Kuybeda O, Moran A , Bliss D, Das SR, Yewdell J, Sapiro G, Subbarao K, Subramaniam S. Molecular Structures of Native HA Trimers on 2009 H1N1 Pandemic Influenza Virus Complexed with Neutralizing Antibodies. Biophysical Journal. 2013 Jan 29;104(2 Supp 1):414a. 57th Annual Meeting of the Biophysical Society; 2013 Feb 2-6; Philadelphia. DOI: http://dx.doi.org/10.1016/j.bpj.2012.11.2310.
    Abstract
    Abstract
  • Balkanyi L, Schulz S, Cornet R, Bodenreider O. Medical concept representation: the years beyond 2000 [Poster]. Stud Health Technol Inform. 2013;192:1011.
    Abstract | PMID:  23920785 | PMCID:  PMC4300111
    Abstract
  • Bodenreider O, Nguyen D, Chiang P, Chuang P, Madden M, Winnenburg R, McClure R, Emrick S, D'Souza I. The NLM value set authority center (Poster). Stud Health Technol Inform. 2013;192:1224.
    Abstract | PMID:  23920998 | PMCID:  PMC4300102
    Abstract
  • Cimino JJ, Ayres EJ, Beri A, Freedman R, Oberholtzer E, Rath S. Developing a self-service query interface for re-using de-identified electronic health record data. Stud Health Technol Inform. 2013;192:632-6.
    Abstract | PMID:  23920633 | PMCID:  PMC4209406
    Abstract
  • Del Fiol G, Curtis C, Cimino J, Iskander A, Kalluri AS, Jing X, Hulse NC, Long J, Overby CL, Schardt C, Douglas DM. Disseminating context-specific access to online knowledge resources within electronic health record systems. Stud Health Technol Inform. 2013;192:672-6.
    Abstract | PMID:  23920641 | PMCID:  PMC3870015
    Abstract
  • 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.
    Abstract | PMID:  23920539
    Abstract
  • Hunt S, Cimino J, Koziol DE. A comparison of clinicians' access to online knowledge resources using two types of information retrieval applications in an academic hospital setting. J Med Libr Assoc. 2013 Jan;101(1):26-31. doi: 10.3163/1536-5050.101.1.005.
    Abstract | PMID:  23405044 | PMCID:  PMC3543139
    Abstract
  • Jimeno Yepes A, Mork JG, Aronson A. Using the argumentative structure of scientific literature to improve information access [Poster]. BioNLP 2013.
    Abstract
    Abstract
  • Jimeno Yepes AJ, Mork JG, Aronson A. Identifying Publication Types Using Machine Learning. BioASQ Workshop 2013.
    Abstract
    Abstract
  • Maver A, Hristovski D, Rindflesch TC, Peterlin B. Integration of data from omic studies with the literature-based discovery towards identification of novel treatments for neovascularization in diabetic retinopathy. Biomed Res Int. 2013;2013:848952. doi: 10.1155/2013/848952. Epub 2013 Nov 24.
    Abstract | PMID:  24350292 | PMCID:  PMC3857903
    Abstract
  • Montufar-Rueda C, Rodriguez L, Jarquin JD, Barboza A, Bustillo MC, Marin F, Ortiz G, Estrada F. Severe postpartum hemorrhage from uterine atony: a multicentric study. J Pregnancy. 2013;2013:525914. doi: 10.1155/2013/525914. Epub 2013 Dec 2.
    Abstract | PMID:  24363935 | PMCID:  PMC3864080
    Abstract
  • Mork JG, Jimeno Yepes A, Aronson A. The NLM Medical Text Indexer System for Indexing Biomedical Literature. BioASQ 2013.
    Abstract
    Abstract
  • 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.
    Abstract | PMID:  23920645 | PMCID:  PMC4303373
    Abstract
  • 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.
    Abstract | PMID:  23920611 | PMCID:  PMC4296515
    Abstract
  • Winnenburg R, Bodenreider O. Exploring pharmacoepidemiologic groupings of drugs from a clinical perspective. Stud Health Technol Inform. 2013;192:827-31.
    Abstract | PMID:  23920673 | PMCID:  PMC4304656
    Abstract
  • 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.
    Abstract | PMID:  23920677 | PMCID:  PMC3940695
    Abstract
  • 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.
    Abstract
    Abstract
  • Pearson G, Gill MJ. An Evaluation of Motion JPEG 2000 for Video Archiving. Proc. Archiving 2005. Washington, D.C. April 2005:237-43.
    Abstract | pub9302.pdf
    AbstractDownload
  • Kilicoglu H, Shin D, Fiszman M, Rosemblat G, Rindflesch TC. SemMedDB: a PubMed-scale repository of biomedical semantic predications. Bioinformatics. 2012 Dec 1;28(23):3158-60. doi: 10.1093/bioinformatics/bts591. Epub 2012 Oct 8.
    Abstract | PMID:  23044550 | PMCID:  PMC3509487
    Abstract
  • 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.
    Abstract | pub2012-074.pdf
    AbstractDownload
  • Lu C, Browne AC. Development of Sub-Term Mapping Tools (STMT) AMIA 2012 Annual Symposium, Chicago, IL, November 3-7, 2012
    Abstract | pub2012017.pdf
    AbstractDownload
  • Huser V, Cimino JJ. Precision and negative predictive value of links between ClinicalTrials.gov and PubMed. AMIA Annu Symp Proc. 2012;2012:400-8. Epub 2012 Nov 3.
    Abstract | PMID:  23304310 | PMCID:  PMC3540528
    Abstract
  • Kawamoto K, Jacobs J, Welch BM, Huser V, Paterno MD, Del Fiol G, Shields D, Strasberg HR, Huag PJ, Liu Z, Jenders RA, Rowed DW, Chertcoff D, Fehre K, Adlassnig KP, Curtis C. Clinical information system services and capabilities desired for scalable, standards-based, service-oriented decision support: consensus assessment of the Health Level 7 clinical decision support Work Group. AMIA Annu Symp Proc. 2012;2012:446-55. Epub 2012 Nov 3.
    Abstract | PMID:  23304315 | PMCID:  PMC3540445
    Abstract
  • 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.
    Abstract | pub9348.pdf
    AbstractDownload
  • Fung KW, Bodenreider O. Knowledge representation and ontologies. Richesson RL, Andrews JE (Eds.). Clinical Research Informatics, Health Informatics, DOI 10.1007/978-1-84882-448-5_14, Springer-Verlag London Limited Publishing 2012.
    Abstract | pub2012015.pdf
    AbstractDownload
  • Peters L, Nguyen T, Bodenreider O. RxBatch – Batch operations for RxNorm and NDF-RT APIs (Poster). AMIA Annu Symp Proc, 2012: p. 1897.
    Abstract
    Abstract
  • Yoo TS, Bliss D, Lowekamp B, Chen D, Murphy GE, Narayan K, Hartnell LM, Do T, Subramaniam S. Visualizing cells and humans in 3D: Biomedical image analysis at nanometer and meter scales. IEEE Computer Graphics and Applications. 2012 Sep-Oct;32(5):39-49. DOI: 10.1109/MCG.2012.68.
    Abstract | URL:  http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6226336&isnumber=6311364
    AbstractExternal link
  • Bodenreider O. API: Prescribable
    Abstract
    Abstract
  • 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.
    Abstract
    Abstract
  • 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.
    Abstract | pub6687.pdf
    AbstractDownload
  • 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
    Abstract
    Abstract
  • Caban JJ, Rosebrock A, Yoo TS. Automatic identification of prescription drugs using shape distribution models. In: 19th IEEE International Conference on Image Processing (ICIP); 2012 Sep 30-Oct 3; Lake Buena Vista, Florida. p. 1005-8. DOI: 10.1109/ICIP.2012.6467032
    Abstract
    Abstract
  • Jaeger S. An information-theoretic neural model based on concepts in Chinese medicine. 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW).
    Abstract | pub8966.pdf
    AbstractDownload
  • 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.
    Abstract | PMID:  22683993 | PMCID:  PMC3438287
    Abstract
  • Simpson M, You D, Rahman MM, Demner-Fushman D, Antani SK, Thoma GR. ITI's participation in the ImageCLEF 2012 medical retrieval and classification tasks. CLEF 2012 Working Notes. Rome, Italy. September 2012.
    Abstract | pub2012-029.pdf | URL:  http://ims-sites.dei.unipd.it/documents/71612/155385/CLEF2012wn-ImageCLEF-Simpso...
    AbstractDownloadExternal link
  • Callaghan F, Jackson MT, Demner-Fushman D, Abhyankar S, McDonald CJ. NLP-derived information improves the estimates of risk of disease compared to estimates based on manually extracted data alone. 5th International Symposium on Semantic Mining in Biomedicine (SMBM 2012), 2012 Sept 3-4, Zurich, Switzerland.
    Abstract | pub2012-068.pdf | URL:  http://www.zora.uzh.ch/64476/65/smbm12.pdf
    AbstractDownloadExternal link
  • 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.
    Abstract | PMID:  22436890 | PMCID:  PMC3587978
    Abstract
  • 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.
    Abstract | pub6792.pdf | URL:  http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6347110&isnumber=6345844
    AbstractDownloadExternal link
  • Huser V, Taft L, Cimino J. Suitability of LOINC document ontology as a reference terminology for clinical document types: a case report of a research-oriented EHR. NIH Poster Day 2012.
    Abstract | pub2012-072.pdf
    AbstractDownload
  • Abhyankar S, Demner-Fushman D, McDonald CJ. Standardizing clinical laboratory data for secondary use. J Biomed Inform. 2012 Aug;45(4):642-50. doi: 10.1016/j.jbi.2012.04.012. Epub 2012 May 3.
    Abstract | pub2012-070.pdf | PMID:  22561944 | PMCID:  PMC3419308
    AbstractDownload
  • Lin MC, Vreeman DJ, McDonald CJ, Huff SM. Auditing consistency and usefulness of LOINC use among three large institutions - using version spaces for grouping LOINC codes. J Biomed Inform. 2012 Aug;45(4):658-66. doi: 10.1016/j.jbi.2012.01.008. Epub 2012 Jan 28.
    Abstract | PMID:  22306382 | PMCID:  PMC3374914
    Abstract
  • Vreeman D, Chiaravalloti MT, Hook J, McDonald CJ. Enabling international adoption of LOINC through translation. J Biomed Inform. 2012 Aug;45(4):667-73. doi: 10.1016/j.jbi.2012.01.005. Epub 2012 Jan 21.
    Abstract | PMID:  22285984 | PMCID:  PMC3376691
    Abstract
  • Bekhuis T, Demner-Fushman D. Screening nonrandomized studies for medical systematic reviews: a comparative study of classifiers. Artif Intell Med. 2012 Jul;55(3):197-207. doi: 10.1016/j.artmed.2012.05.002. Epub 2012 Jun 5.
    Abstract | PMID:  22677493 | PMCID:  PMC3393813
    Abstract
  • Fung K. Dataset: SNOMED CT to ICD-10-CM Map
    Abstract
    Abstract
  • 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.
    Abstract | pub2012018.pdf
    AbstractDownload
  • McDonald CJ, Vreeman D, Goodwin RM. Dataset: LOINC Top 2000+ Lab Observations and Mapper's Guide
    Abstract
    Abstract
  • Demner-Fushman D, Abhyankar S. Syntactic-semantic frames for clinical cohort identification queries. Data Integration in the Life Sciences (DILS) June 2012, LNBI 7348 proceedings. Lecture Notes in Computer Science. 2012;7348:100-112
    Abstract
    Abstract
  • 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.
    Abstract | pub-2012-048.pdf | URL:  http://jcse.kiise.org/PublishedPaper/topic_abstract.asp?idx=134
    AbstractDownloadExternal link
  • Bodenreider O. Web Interface: RxMix
    Abstract
    Abstract
  • McDonald CJ, Tierney WM. The effect of electronic health records on test ordering [Letter}. Health Aff (Millwood). 2012 Jun;31(6):1365; author reply 1366. doi: 10.1377/hlthaff.2012.0471.
    Abstract | pub2012011.pdf | PMID:  22665848
    AbstractDownload
  • Workman TE, Fiszman M, Hurdle JF. Text summarization as a decision support aid. BMC Med Inform Decis Mak. 2012 May 23;12:41. doi: 10.1186/1472-6947-12-41.
    Abstract | PMID:  22621674 | PMCID:  PMC3461485
    Abstract
  • Fung KW. Dataset: ICD-9-CM to SNOMED CT Map
    Abstract
    Abstract
  • 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.
    Abstract
    Abstract
  • Pan H, Tryka KA, Vreeman DJ, Huggins W, Phillips MJ, Mehta JP, Phillips JH, McDonald C, Junkins HA, Ramos EM, Hamilton CM. Using PhenX measures to identify opportunities for cross-study analysis. Hum Mutat. 2012 May;33(5):849-57. doi: 10.1002/humu.22074. Epub 2012 Apr 3.
    Abstract | PMID:  22415805 | PMCID:  PMC3780790
    Abstract
  • Demner-Fushman D, Abhyankar S. Syntactic-semantic question frames for cohort identification. The 2012 Joint Summits on Translational Science. San Francisco, CA. March 2012.
    Abstract | pub-2012-071.pdf
    AbstractDownload
  • Fung KW. Web Interface: I-Magic SNOMED-CT to ICD-10-CM code mapping tool.
    Abstract
    Abstract
  • Liu J, Subramanian K, Yoo TS. A Phantom Design for Validating Colonoscopy Tracking. Proc. SPIE 8315, Medical Imaging 2012: Computer-Aided Diagnosis, 83151N (23 February 2012); doi: 10.1117/12.912395; http://dx.doi.org/10.1117/12.912395
    Abstract
    Abstract
  • McDonald CJ, McDonald MH. Electronic medical records and preserving primary care physicians' time: comment on "electronic health record-based messages to primary care providers" [Letter]. Arch Intern Med. 2012 Feb 13;172(3):285-7. doi: 10.1001/archinternmed.2011.1678.
    Abstract | PMID:  22332168
    Abstract
  • Jing X, Kay S, Marley T, Hardiker NR, Cimino JJ. Incorporating personalized gene sequence variants, molecular genetics knowledge, and health knowledge into an EHR prototype based on the Continuity of Care Record standard. J Biomed Inform. 2012 Feb;45(1):82-92. doi: 10.1016/j.jbi.2011.09.001. Epub 2011 Sep 17.
    Abstract | pub2012-022.pdf | PMID:  21946299 | PMCID:  PMC3272091
    AbstractDownload
  • 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.
    Abstract | PMID:  22294819 | PMCID:  PMC3250368
    Abstract
  • Wang Y, Halper M, Wei D, Gu H, Perl Y, Xu J, Elhanan G, Chen Y, Spackman KA, Case JT, Hripcsak G. Auditing complex concepts of SNOMED using a refined hierarchical abstraction network. J Biomed Inform. 2012 Feb;45(1):1-14. doi: 10.1016/j.jbi.2011.08.016. Epub 2011 Sep 1.
    Abstract | PMID:  21907827 | PMCID:  PMC3313651
    Abstract
  • Mougin F, Burgun A, Bodenreider O. Comparing Drug-class Membership in ATC and NDF-RT Proc IHI 2012 2012:437-443
    Abstract | pub2012010.pdf
    AbstractDownload
  • Jimeno-Yepes A, Aronson AR. Knowledge-based and knowledge-lean methods combined in unsupervised word sense disambiguation. Proc 2nd ACM SIGHIT International Health Informatics (IHI) Symposium 2012, 733-736.
    Abstract
    Abstract
  • 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.
    Abstract
    Abstract
  • 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.
    Abstract | pub2012-064.pdf
    AbstractDownload
  • Del Fiol G, Huser V, Strasberg HR, Maviglia SM, Curtis C, Cimino JJ. Implementations of the HL7 Context-Aware Knowledge Retrieval ("Infobutton") Standard: challenges, strengths, limitations, and uptake. J Biomed Inform. 2012 Aug;45(4):726-35. doi: 10.1016/j.jbi.2011.12.006.. Epub 2012 Jan 2.
    Abstract | PMID:  22226933 | PMCID:  PMC3334468
    Abstract
  • Adamusiak T, Bodenreider O. Quality assurance in LOINC using Description Logic. AMIA Annu Symp Proc. 2012;2012:1099-108. Epub 2012 Nov 3.
    Abstract | PMID:  23304386 | PMCID:  PMC3540427
    Abstract
  • Cimino J, Jing X, Del Fiol G. Meeting the electronic health record "meaningful use" criterion for the HL7 infobutton standard using OpenInfobutton and the Librarian Infobutton Tailoring Environment (LITE). AMIA Annu Symp Proc. 2012;2012:112-20. Epub 2012 Nov 3.
    Abstract | PMID:  23304279 | PMCID:  PMC3540503
    Abstract
  • Fontelo P, Faustorilla J, Gavino A, Marcelo A. Digital pathology - implementation challenges in low-resource countries. Anal Cell Pathol (Amst). 2012;35(1):31-6. doi: 10.3233/ACP-2011-0024.
    Abstract | PMID:  22233702 | PMCID:  PMC4605723
    Abstract
  • Fung KW, Xu J. Synergism between the mapping projects from SNOMED CT to ICD-10 and ICD-10-CM. AMIA Annu Symp Proc. 2012;2012:218-27. Epub 2012 Nov 3.
    Abstract | amia_2012_symp_0218.pdf | PMID:  23304291 | PMCID:  PMC3540534
    AbstractDownload
  • Kayaalp M. ICU Outcome Predictions using Physiologic Trends in the First Two Days. Computing in Cardiology (39)977–980.
    Abstract | PMCID:  PMC3607431
    Abstract
  • Tran EE, Borgnia MJ, Kuybeda O, Schauder DM, Bartesaghi A, Frank GA, Sapiro G, Milne JL, Subramaniam S. Structural mechanism of trimeric HIV-1 envelope glycoprotein activation. PLoS Pathog. 2012;8(7):e1002797. doi: 10.1371/journal.ppat.1002797. Epub 2012 Jul 12.
    Abstract | PMID:  22807678 | PMCID:  PMC3395603
    Abstract
  • Winnenburg R, Bodenreider O. Issues in creating and maintaining value sets for clinical quality measures. AMIA Annu Symp Proc. 2012;2012:988-96. Epub 2012 Nov 3.
    Abstract | PMID:  23304374 | PMCID:  PMC3540585
    Abstract
  • Xu J, Fung KW. Handling age specification in the SNOMED CT to ICD-10-CM cross-map. AMIA Annu Symp Proc. 2012;2012:1014-22. Epub 2012 Nov 3.
    Abstract | PMID:  23304377 | PMCID:  PMC3540567
    Abstract
  • Xue Z, Antani SK, Long LR, Demner-Fushman D, Thoma GR. Window classification of brain CT images in biomedical articles. AMIA Annu Symp Proc. 2012;2012:1023-9. Epub 2012 Nov 3.
    Abstract | PMID:  23304378 | PMCID:  PMC3540547
    Abstract
  • Cameron D, Kavuluru R, Bodenreider O, Mendes PN, Sheth AP, Thirunarayan K. Semantic predications for complex information needs in biomedical literature BIBM 2011:512-519.
    Abstract | pub2011069.pdf
    AbstractDownload
  • Goodwin RM, Abhyankar S, Zuckerman AE, Copeland SM, Sarkar D, Cuthbert C, Therrell BL, Ojodu J, Lloyd-Puryear MA, Jenders RA, McDonald CJ. Newborn screening health information exchange: updated guidance for coding and HL7 electronic messaging. APHL Newborn Screening and Genetics Testing Symposium. 2011 Nov 7.
    Abstract | pub2011-007.pdf | URL:  http://www.aphl.org/conferences/proceedings/Documents/2011/2011_APHL_NBS_Genetic...
    AbstractDownloadExternal link
  • 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.
    Abstract | pub2011-110.pdf | URL:  http://ii.nlm.nih.gov/MTI_ML/index.shtml
    AbstractDownloadExternal link
  • 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.
    Abstract | PMID:  22185221 | PMCID:  PMC3281188 | URL:  http://www.biomedcentral.com/1471-2105/12/486
    AbstractExternal link
  • 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.
    Abstract
    Abstract
  • Meyerson JR, White TA, Bliss D, Moran A, Bartesaghi A, Borgnia MJ, de la Cruz JV, Schauder D, Hartnell LM, Nandwani R, Dawood M, Kim B, Kim JH, Sununu J, Yang L, Bhatia S, Subramaniam C, Hurt DE, Gaudreault L, Subramaniam S. Determination of molecular structures of HIV envelope glycoproteins using cryo-electron tomography and automated sub-tomogram averaging. J Vis Exp. 2011 Dec 1;(58). pii: 2770. doi: 10.3791/2770.
    Abstract | PMID:  22158337 | PMCID:  PMC3304575
    Abstract
  • Murphy GE, Narayan K, Lowekamp B, Hartnell LM, Heymann JA, Fu J, Subramaniam S. Correlative 3D imaging of whole mammalian cells with light and electron microscopy. J Struct Biol. 2011 Dec;176(3):268-78. doi: 10.1016/j.jsb.2011.08.013. Epub 2011 Sep 1.
    Abstract | PMID:  21907806 | PMCID:  PMC3210386
    Abstract
  • Abhyankar S, Goodwin RM, Zuckerman A, McDonald CJ. Dataset: newborn screening results annotated example HL7 electronic message guidance (v 5.2).
    Abstract
    Abstract
  • Lu C, Browne AC. Converting Unicode Lexicon and Lexical Tools for ASII NLP Applications AMIA Annu Symp Proc 2011:1870.
    Abstract | pub2011070.pdf
    AbstractDownload
  • 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.
    Abstract | pub2011023.pdf | PMID:  22126369 | PMCID:  PMC3298549
    AbstractDownload
  • Abhyankar S, Therrell B, Eaton R, Cuthbert C, Ojodu J, Copeland S, Goodwin RM, McDonald C. Using LOINC and HL7 to standardize hemoglobinopathy screening result reporting. APHL Newborn Screening and Genetics Testing Symposium. 2011 Nov 7.
    Abstract | pub2011-133.pdf | URL:  http://www.aphl.org/conferences/proceedings/Documents/2011/2011_APHL_NBS_Genetic...
    AbstractDownloadExternal link
  • Bodenreider O, Peters L, Nguyen T. Browser and application programming interfaces for drug information sources. AMIA Annu Symp Proc, 2011: p. 2129.
    Abstract
    Abstract
  • Abhyankar S, Goodwin RM, Zuckerman AE, McDonald CJ. Dataset: Newborn screening LOINC panel.
    Abstract
    Abstract
  • Peters L, Nguyen T, Bodenreider O. An application programming interface for NDF-RT AMIA Annu Symp Proc 2011:1922
    Abstract | pub2011021.pdf
    AbstractDownload
  • Demner-Fushman D, Abhyankar S, Callaghan FM, McDonald CJ. Extracting sources of admission and discharge destinations from discharge summaries [Poster]. AMIA 2011 Fall Symposium.
    Abstract | pub2011-117.pdf
    AbstractDownload
  • Sheets L, Gavino A, Fontelo P. Language Fluency and Other Predictors of International Use of PubMed and MedlinePlus. AMIA Annu Symp Proc [Proceedings of the American Medical Informatics Association Annual Symposium]; 2011 Oct 22-26; Washington DC. p. 1779.
    Abstract
    Abstract
  • Cairelli M, Rindflesch TC. Hierarchical Summarization of Concepts for Visual Discovery Browsing - a Pilot Study [abstract and demo]. Procedings of the IEEE VisWeek Workshop on Visual Analytics in Healthcare, October 23, 2011, Providence, RI, 37-40.
    Abstract | URL:  http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CD0QFjAA&url...
    AbstractExternal link
  • Abhyankar S, Goodwin RM, Zuckerman AE, McDonald CJ. Dataset: newborn screening LOINC codes (AHIC panel).
    Abstract
    Abstract
  • Callaghan F, Demner-Fushman D, Abhyankar S, McDonald CJ. Addressing errors in a retrospective observational ICU database [poster]. AMIA 2011 Fall Symposium.
    Abstract | pub2011-086.pdf
    AbstractDownload
  • McDonald CJ, Abhyankar S, Taft L. Dataset: common units of measure - subset of the Unified Code for Units of Measure.
    Abstract
    Abstract
  • 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.
    Abstract | PMID:  21575741 | PMCID:  PMC3170688
    Abstract
  • Rindflesch TC, Kilicoglu H, Fiszman M, Rosemblat G, Shin D. Semantic MEDLINE: An advanced information management application for biomedicine. Information Services and Use, 2011, 31(1): 15-21.
    Abstract | pub-lhncbc-2011-109.pdf | URL:  http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CDUQFjAA&url...
    AbstractDownloadExternal link
  • Bodenreider O, Peters L, Nguyen T. RxNav: Browser and Application Programming Interfaces for Drug Information Sources [Abstract]. AMIA Annu Symp Proc 2011:2129
    Abstract | pub2011018.pdf
    AbstractDownload
  • 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.
    Abstract | PMID:  21822350 | PMCID:  PMC3150552
    Abstract
  • Plaza L, Jimeno-Yepes A, Diaz A, Aronson AR. Studying the correlation between different word sense disambiguation methods and summarization effectiveness in biomedical texts. BMC Bioinformatics. 2011 Aug 26;12:355. doi: 10.1186/1471-2105-12-355.
    Abstract | PMID:  21871110 | PMCID:  PMC3176269
    Abstract
  • 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
    Abstract | pub2011022.pdf
    AbstractDownload
  • Nguyen V, Bodenreider O, Minning T, Sheth AP. The knowledge-driven exploration of integrated biomedical knowledge sources facilitates the generation of new hypotheses Proceedings of the First International Workshop on Linked Science (LISC 2011) 2011:(electronic proceedings: http://ceur-ws.org/Vol-783/)
    Abstract | pub2011019.pdf
    AbstractDownload
  • 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.
    Abstract | pub2011067.pdf | PMID:  21690019
    AbstractDownload
  • Caban JJ, Rheingans P, Yoo TS. An Evaluation of Visualization Techniques to Illustrate Statistical Deformation Models. Computer Graphics Forum. 2011 May-Jun;30(3):821-30. doi:10.1111/j.1467-8659.2011.01931.x.
    Abstract
    Abstract
  • Jimeno-Yepes A, Aronson AR. Self-training and co-training in biomedical word sense disambiguation. BioNLP 2011 Workshop, June 2011, 182-183.
    Abstract | pub-2011-113.pdf | URL:  http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0CDwQFjAB&url...
    AbstractDownloadExternal link
  • Abhyankar S, Callaghan FM, Demner-Fushman D, McDonald CJ. Using informatics tools to study obesity and outcomes after critical illness. NLM Informatics Training Conference 2011, National Institutes of Health (NIH) Campus, Natcher Conference Center, Bethesda, MD, June 28-30, 2011.
    Abstract
    Abstract
  • 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.
    Abstract | pub2010056.pdf | PMID:  21658291 | PMCID:  PMC3111590
    AbstractDownload
  • 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.
    Abstract | PMID:  21658294 | PMCID:  PMC3111593
    Abstract
  • Caban JJ, Yao J, Mollura DJ, Liao D, Yoo TS. Enhancing image analytic tools by fusing quantitative physiological values with image features. In: SIIM [Society for Imaging Informatics in Medicine] 2011 Scientific Abstract Book. SIIM Annual Meeting Learning Track 1 Scientific Sessions: Advanced Visualization: Making Advanced Visualization Tools Work for You; 2011 Jun 2-5; Washington DC/National Harbor, Maryland.
    Abstract
    Abstract
  • McDonald C, Vreeman D, Goodwin RM. Dataset: LOINC Top 300+ Lab Orders
    Abstract
    Abstract
  • Xue Z, Long LR, Antani SK, Thoma GR. Spine x-ray image retrieval using partial vertebral boundaries. 24th International Symposium on Computer-Based Medical Systems. Bristol, UK. June 2011.
    Abstract
    Abstract
  • Jaeger S, Antani S, Thoma GR. Tuberculosis Screening of Chest Radiographs. 2 June 2011, SPIE Newsroom. DOI: 10.1117/2.1201105.003732i.
    Abstract | pub2011-012.pdf
    AbstractDownload
  • 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.
    Abstract | PMID:  21635749 | PMCID:  PMC3123611
    Abstract
  • 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.
    Abstract
    Abstract
  • Gururajan A, Kamalakannan S, Sari-Sharraf H, Shahriar M, Long LR, Antani SK. On the creation of a segmentation library for digitized cervical and lumbar spine radiographs. Comput Med Imaging Graph. 2011 Jun;35(4):251-65. doi: 10.1016/j.compmedimag.2010.11.006. Epub 2011 Mar 5.
    Abstract | PMID:  21377835
    Abstract
  • McDonald CJ, Abhyankar S. Clinical decision support and rich clinical repositories: a symbiotic relationship: comment on "Electronic health records and clinical decision support systems". Arch Intern Med. 2011 May 23;171(10):903-5. doi: 10.1001/archinternmed.2010.518. Epub 2011 Jan 24.
    Abstract | PMID:  21263079 | PMCID:  PMC3101297
    Abstract
  • Luciano JS, Andersson B, Batchelor C, Bodenreider O, Clark T, Denny CK, Domarew C, Gambet T, Harland L, Jentzsch A, Kashyap V, Kos P, Kozlovsky J, Lebo T, Marshall SM, McCusker JP, McGuinness DL, Ogbuji C, Pichler E, Powers RL, Prud'hommeaux E, Samwald M, Schrimi L, Tonellato PJ, Wjetzel JZ, Stephens S, Dumontier M. The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside. J Biomed Semantics. 2011 May 17;2 Suppl 2:S1. doi: 10.1186/2041-1480-2-S2-S1.
    Abstract | pub2011013.pdf | PMID:  21624155 | PMCID:  PMC3102889
    AbstractDownload
  • Fung KW. Dataset: Nursing Problem List Subset of SNOMED CT
    Abstract
    Abstract
  • Yoo TS, Hamilton T, Hurt D, Caban J, Liao D, Chen D. Toward Quantitative X-Ray CT Phantoms of Metastatic Tumors Using Rapid Prototyping Technology. In: Pan X, Liebling M, editors. Proceedings of ISBI 2011: IEEE Computer Society International Symposium on Biomedical Imaging: From Nano to Macro; 2011 Mar 30-Apr 2; Chicago. p. 1770-3. DOI: 10.1109/ISBI.2011.5872749.
    Abstract | URL:  http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5872749&tag=1
    AbstractExternal link
  • Mork J, Peters L, Jimeno-Yepes A, Aronson AR, Bodenreider O. MetaMap in the CALBC Workshop II. CALBC Workshop II, March 2011.
    Abstract | pub-2011-114.pdf | URL:  http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CDUQFjAA&url...
    AbstractDownloadExternal link
  • Butan C, Hartnell LM, Fenton AK, Bliss D, Sockett RE, Subramaniam S, Milne JL. Spiral architecture of the nucleoid in Bdellovibrio bacteriovorus. J Bacteriol. 2011 Mar;193(6):1341-50. doi: 10.1128/JB.01061-10. Epub 2010 Dec 10.
    Abstract | PMID:  21148724 | PMCID:  PMC3067633
    Abstract
  • Antani S, Xue Z, Long LR, Bennett D, Ward S, Thoma GR. Is there a need for biomedical CBIR systems in clinical practice? Outcomes from a usability study. Proceedings of SPIE Medical Imaging 2011: Advanced PACS-based Imaging Informatics and Therapeutic Applications. Orlando, FL. February 2011;7967:796708.
    Abstract | pub2011-078.pdf
    AbstractDownload
  • Caban JJ, Liao D, Yao J, Mollura DJ, Gochuico B, Yoo TS. Enhancing image classification models with multimodal biomarkers. In: Summers RM, van Ginneken B, editors. Proceedings of SPIE Medical Imaging 2011: Computer-Aided Diagnosis; 2011 Feb 12-17; Lake Buena Vista (Orlando area), Florida;7963:9 pages. DOI: 10.1117/12.878084.
    Abstract
    Abstract
  • Liu J, Subramanian KR, Yoo TS. Temporal Volume Flow: An Approach to Tracking Failure Recovery. In: Summers RM, van Ginneken B, editors. Proceedings of SPIE Medical Imaging 2011: Computer-Aided Diagnosis; 2011 Feb 12-17; Lake Buena Vista, Florida;7963. SPIE; 2011 Mar 4. DOI: 10.1117/12.878220.
    Abstract | URL:  http://proceedings.spiedigitallibrary.org/proceeding.aspx?articleid=725186
    AbstractExternal link
  • Mann D, Caban JJ, Stolka PJ, Boctor EM, Yoo TS. Multidimensional transfer functions for effective visualization of streaming ultrasound and elasticity images. In: Wong KH, Holmes DR III, editors. Proceedings of SPIE Medical Imaging 2011: Visualization, Image-Guided Procedures, and Modeling; 2011 Feb 12-17; Lake Buena Vista, Florida;7964:1-8. DOI:10.1117/12.878935.
    Abstract | URL:  http://proceedings.spiedigitallibrary.org/proceeding.aspx?articleid=726207
    AbstractExternal link
  • 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
    Abstract | LHNCBC-2011-002.pdf
    AbstractDownload
  • 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
    Abstract | pub2011009.pdf
    AbstractDownload
  • Doughty E, Kertesz-Farkas A, Bodenreider O, Thompson G, Adadey A, Peterson T, Kann MG. Toward an automatic method for extracting cancer- and other disease-related point mutations from the biomedical literature. Bioinformatics. 2011 Feb 1;27(3):408-15. doi: 10.1093/bioinformatics/btq667. Epub 2010 Dec 7.
    Abstract | pub2011001.pdf | PMID:  21138947 | PMCID:  PMC3031038
    AbstractDownload
  • Campbell JR, Xu J, Fung K. Can SNOMED CT fulfill the vision of a compositional terminology? Analyzing the use case for problem list. AMIA Annu Symp Proc. 2011;2011:181-8. Epub 2011 Oct 22.
    Abstract | PMID:  22195069 | PMCID:  PMC3243203
    Abstract
  • Fung K, Xu J, Rosenbloom ST, Mohr D, Maram N. Testing Three Problem List Terminologies in a simulated data entry environment. AMIA Annu Symp Proc. 2011;2011:445-54. Epub 2011 Oct 22.
    Abstract | PMID:  22195098 | PMCID:  PMC3243193
    Abstract
  • 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.
    Abstract | PMID:  22195224 | PMCID:  PMC3243198
    Abstract
  • Jing X, Cimino JJ. Graphical methods for reducing, visualizing and analyzing large data sets using hierarchical terminologies. AMIA Annu Symp Proc. 2011;2011:635-43. Epub 2011 Oct 22.
    Abstract | PMID:  22195119 | PMCID:  PMC3243153
    Abstract
  • Karargyris A, Antani SK, Thoma GR. Segmenting anatomy in chest x-rays for tuberculosis screening. Conf Proc IEEE Eng Med Biol Soc. 2011;2011:7779-82. doi: 10.1109/IEMBS.2011.6091917.
    Abstract | PMID:  22256142 | URL:  http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6091917&isnumber=6089866
    AbstractExternal link
  • Lin MC, Vreeman DJ, McDonald CJ, Huff SM. A characterization of local LOINC mapping for laboratory tests in three large institutions. Methods Inf Med. 2011;50(2):105-14. doi: 10.3414/ME09-01-0072. Epub 2010 Aug 20.
    Abstract | pub2010039.pdf | PMID:  20725694 | PMCID:  PMC3034110
    AbstractDownload
  • 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.
    Abstract | pub2011020.pdf | PMID:  22195172 | PMCID:  PMC3243188
    AbstractDownload
  • 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.
    Abstract | PMID:  22195216 | PMCID:  PMC3243228
    Abstract
  • Jimeno-Yepes A, Aronson AR. Query expansion for UMLS Metathesaurus disambiguation based on automatic corpus extraction. ICMLA 2010, Dec 2010.
    Abstract | pub2010-089.pdf | URL:  http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=5708977&c...
    AbstractDownloadExternal link
  • 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.
    Abstract | pub2010027.pdf | PMID:  20510585 | PMCID:  PMC2955170
    AbstractDownload
  • Jao CS, Fung KW, Demner-Fushman D. Identifying indications for drugs in drug package inserts. AMIA Annual Symposium Proceedings 2010. November 2010
    Abstract | LHNCBC-2010-059.pdf
    AbstractDownload
  • Lu C, Divita G, Browne AC. Development of Visual Tagging Tool AMIA Annu Symp Proc 2010:1156.
    Abstract | pub2010065.pdf
    AbstractDownload
  • Jimeno-Yepes A, Aronson AR. Knowledge-based biomedical word sense disambiguation: comparison of approaches. BMC Bioinformatics. 2010 Nov 22;11:569. doi: 10.1186/1471-2105-11-569.
    Abstract | pub2010057.pdf | PMID:  21092226 | PMCID:  PMC3001745
    AbstractDownload
  • Cardenas I, Marcelo AB, Fontelo P. Development of a health informatics community-generated, open-source controlled medical vocabulary. AMIA Annu Symp Proc [Proceedings of the American Medical Informatics Association Annual Symposium]; 2010 Nov 13-17; Washington DC. p. 998.
    Abstract
    Abstract
  • Liu F, Fontelo P. Automatic translations of MEDLINE abstracts using Google Translate. AMIA Annu Symp Proc [Proceedings of the American Medical Informatics Association Annual Symposium]; 2010 Nov 13-17; Washington DC. p. 1148.
    Abstract
    Abstract
  • Abhyankar S, Lloyd-Puryear MA, Goodwin R, Copeland S, Eichwald J, Therrell BL, Zuckerman A, Downing G, McDonald CJ. Standardizing newborn screening results for health information exchange. AMIA Annu Symp Proc. 2010 Nov 13;2010:1-5.
    Abstract | pub2010037.pdf | PMID:  21346929 | PMCID:  PMC3041276
    AbstractDownload
  • 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.
    Abstract | pub2010006.pdf | PMID:  21346940 | PMCID:  PMC3041355
    AbstractDownload
  • 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.
    Abstract | pub2010029.pdf | PMID:  21346974 | PMCID:  PMC3041410
    AbstractDownload
  • Lin M-C, Vreeman DJ, McDonald CJ, Huff SM. Correctness of Voluntary LOINC Mapping for Laboratory Tests in Three Large Institutions. AMIA Annu Symp Proc. 2010 Nov 13;2010:447-51.
    Abstract | pub2010042.pdf | PMID:  21347018 | PMCID:  PMC3041457
    AbstractDownload
  • 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.
    Abstract | pub2010010.pdf | PMID:  21347034 | PMCID:  PMC3041405
    AbstractDownload
  • 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.
    Abstract | pub2010011.pdf | PMID:  21347056 | PMCID:  PMC3041346
    AbstractDownload
  • Vreeman DJ, McDonald CJ, Huff SM. Representing Patient Assessments in LOINC®. AMIA Annu Symp Proc. 2010 Nov 13;2010:832-6.
    Abstract | pub2010041.pdf | PMID:  21347095 | PMCID:  PMC3041404
    AbstractDownload
  • Zhang GQ, Bodenreider O. Large-scale, Exhaustive Lattice-based Structural Auditing of SNOMED CT. AMIA Annu Symp Proc. 2010 Nov 13;2010:922-6.
    Abstract | pub2010014.pdf | PMID:  21347113 | PMCID:  PMC3041382
    AbstractDownload
  • 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.
    Abstract | pub2010-066.pdf
    AbstractDownload
  • Zhang G-Q, Bodenreider O. Using SPARQL to Test for Lattices: Application to Quality Assurance in Biomedical Ontologies In: Patel-Schneider PF, Pan Y, Hitzler P, Mika P, Zhang L, Pan JZ, et al., editors. Proceedings of the 9th International Semantic Web Conference (ISWC 2010), Shanghai, China, November 7-11, 2010. Berlin, Heidelberg: Springer; 2010. p. 273-288.
    Abstract
    Abstract
  • Fung K, Scichilone R, Giannangelo K. Benefits and Use Cases of a SNOMED CT to ICD-10 Map. AMIA Annu Symp Proc 2010: 1049.
    Abstract
    Abstract
  • Fung KW, McDonald C, Srinivasan S. The UMLS-CORE project: a study of the problem list terminologies used in large healthcare institutions. J Am Med Inform Assoc. 2010 Nov-Dec;17(6):675-80. doi: 10.1136/jamia.2010.007047.
    Abstract | pub2010043.pdf | PMID:  20962130 | PMCID:  PMC3000762
    AbstractDownload
  • Mork JG, Aronson AR. The Medical Text Indexer (MTI) system for indexing biomedical literature. book chapter submitted to monograph Indexing Specialities: Medicine. Edited by L. Pilar Wyman. Medford, NJ: Information Today, Inc., in association with the American Society of Indexers, Phoenix, AZ. 2010.
    Abstract
    Abstract
  • 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.
    Abstract | PMID:  20962136 | PMCID:  PMC3000749
    Abstract
  • Zhu VJ, Fung K. Extraction and Comparison of Drug Class Information From Standard Terminologies. AMIA Annu Symp Proc. November 2010:1327.
    Abstract
    Abstract
  • 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.
    Abstract | pub2010050.pdf
    AbstractDownload
  • Fung KW. API: RxTerms
    Abstract
    Abstract
  • 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.
    Abstract | PMID:  20936065 | PMCID:  PMC2947139
    Abstract
  • Ducut E, Liu F, Avila JM, Encinas MA, Diwa M, Fontelo P. Virtual Microscopy in a Developing Country: A Collaborative Approach to Building an Image Library. Journal of eHealth Technology and Application. 2010 Sep;8(2):112-5.
    Abstract | URL:  http://web.mit.edu/hst.035/ReadingSupplement/04_26_Yagi/DigitalPathology_eHealth...
    AbstractExternal link
  • Jimeno-Yepes A, Aronson AR. Improving an automatically extracted corpus for UMLS Metathesaurus word sense disambiguation. BioSEPLN 2010, Sept. 2010.
    Abstract | pub2010058.pdf
    AbstractDownload
  • 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.
    Abstract | pub2010047.pdf | PMID:  20819859 | PMCID:  PMC2995679
    AbstractDownload
  • 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
    Abstract | pub2010051.pdf
    AbstractDownload
  • 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
    Abstract | pub2010030k.pdf
    AbstractDownload
  • Resnick MP, Ripple AM, Auston I, Rindflesch TC. An Ontology for Public Health to Support Enhanced Information Retrieval AMIA Annu Symp Proc. 2010
    Abstract | pub2010031.pdf
    AbstractDownload
  • Demner-Fushman D, Mork JG, Shooshan SE, Aronson AR. UMLS content views appropriate for NLP processing of the biomedical literature vs. clinical text. J Biomed Inform. 2010 Aug;43(4):587-94. doi: 10.1016/j.jbi.2010.02.005. Epub 2010 Feb 10.
    Abstract | pub2009040.pdf | PMID:  20152935 | PMCID:  PMC2890296
    AbstractDownload
  • Murphy GE, Lowekamp B, Zerfas PM, Chandler RJ, Narasimha R, Venditti CP, Subramaniam S. Ion-abrasion scanning electron microscopy reveals distorted liver mitochondrial morphology in murine methylmalonic acidemia. J Struct Biol. 2010 Aug;171(2):125-32. doi: 10.1016/j.jsb.2010.04.005. Epub 2010 Apr 23.
    Abstract | PMID:  20399866 | PMCID:  PMC2885563
    Abstract
  • 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
    Abstract | pub2010052.pdf
    AbstractDownload
  • Fung KW. Dataset: SNOMED CT route of administration subset.
    Abstract
    Abstract
  • Felts RL, Narayan K, Estes JD, Shi D, Trubey CM, Fu J, Hartnell LM, Ruthel GT, Schneider DK, Nagashima K, Bess JW Jr, Bavari S, Lowekamp B, Bliss D, Lifson JD, Subramaniam S. 3D visualization of HIV transfer at the virological synapse between dendritic cells and T cells. Proc Natl Acad Sci U S A. 2010 Jul 27;107(30):13336-41. doi: 10.1073/pnas.1003040107. Epub 2010 Jul 12.
    Abstract | PMID:  20624966 | PMCID:  PMC2922156
    Abstract
  • 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
    Abstract
    Abstract
  • Caban JJ, Rheingans P, Yoo TS. An MRF-based Statistical Deformation Model for Morphological Image Analysis. IEEE Computer Society Workshop on Mathematical Models in Biomedical Image Analysis (MMBIA); 2010 Jun 14; San Francisco:31-8.
    Abstract | URL:  http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5543441&tag=1
    AbstractExternal link
  • 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.
    Abstract | PMID:  20172792
    Abstract
  • Qian X, Tagare HD, Fulbright RK, Long LR, Antani SK. Optimal embedding for shape indexing in medical image databases. Med Image Anal. 2010 Jun;14(3):243-54. doi: 10.1016/j.media.2010.01.001. Epub 2010 Jan 20.
    Abstract | PMID:  20163981 | PMCID:  PMC2854880
    Abstract
  • 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.
    Abstract | pub2010-095.pdf
    AbstractDownload
  • 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.
    Abstract | pub2010033.pdf | PMID:  20442139 | PMCID:  PMC2995713
    AbstractDownload
  • Chen D, Chittajallu DR, Passalis G, Kakadiaris IA. Computational tools for quantitative breast morphometry based on 3D scans. Ann Biomed Eng. 2010 May;38(5):1703-18. doi: 10.1007/s10439-010-9971-z. Epub 2010 Mar 19.
    Abstract | PMID:  20300850
    Abstract
  • Friedlin J, McDonald CJ. An evaluation of medical knowledge contained in Wikipedia and its use in the LOINC database. J Am Med Inform Assoc. 2010 May-Jun;17(3):283-7. doi: 10.1136/jamia.2009.001180.
    Abstract | pub2010040.pdf | PMID:  20442145 | PMCID:  PMC2974620
    AbstractDownload
  • 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
    Abstract | pub2010016.pdf
    AbstractDownload
  • 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
    Abstract | pub2010017.pdf
    AbstractDownload
  • Xue Z, Antani S, Long LR, Thoma GR. Web-accessible Cervigram Automatic Segmentation Tool SPIE Medical Imaging Conference. March 2010;7628
    Abstract | pub2010018.pdf
    AbstractDownload
  • Liu J, Subramanian K, Yoo TS. Accurate motion parameter estimation for colonoscopy tracking using a regression method. In: Karssemeijer N, Summer RM, editors. Proceedings of SPIE Medical Imaging 2010: Computer-Aided Diagnosis; 2010 Feb 13-18; San Diego;7624:11 pages. DOI: 10.1117/12.844433.
    Abstract | URL:  http://spie.org/x648.html?product_id=844433
    AbstractExternal link
  • 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
    Abstract | pub2010003.pdf
    AbstractDownload
  • 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
    Abstract | pub2010028.pdf
    AbstractDownload
  • Dumontier M, Andersson B, Batchelor C, Domarew C, Jentzsch A, Luciano J, Pichler E, Prud'hommeaux E, Whetzel PL, Bodenreider O, Clark T, Harland L, Kashyap V, Kos P, Kozlovsky J, McGurk J, Ogbuji C, Samwald M, Schriml L, Tonellato PJ, Zhao J, Stephens S. The Translational Medicine Ontology: Driving Personalized Medicine by Bridging the Gap from Bedside to Bench Proceedings of the 13th ISMB'2010 SIG meeting Bio-ontologies 2010:120-123
    Abstract | pub2010004.pdf
    AbstractDownload
  • 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
    Abstract | pub2011005.pdf
    AbstractDownload
  • Sahoo SS, Bodenreider O, Hitzler P, Sheth A, Thirunarayan K. Provenance Context Entity (PaCE): Scalable Provenance Tracking for Scientific RDF Data SSDBM: Springer, 2010. p. 461-470
    Abstract | pub2010012.pdf
    AbstractDownload
  • Zuckerman AE, Downs SM, McDonald CJ, Weisman JL, Ross DA. Newborn Screening as the Model for Interoperable Genetic Data AMIA Annu Symp Proc. 2010
    Abstract | pub2010035.pdf
    AbstractDownload
  • Cardillo E, Hernandez, Jr G, Bodenreider O. Integrating consumer-oriented vocabularies with selected professional ones from the UMLS using Semantic Web Technologies. Proceedings of the eHealth 2010 conference, 2010: p. (paper 10579 - electronic proceedings).
    Abstract
    Abstract
  • Bodenreider O, Burgun A. A framework for comparing phenotype annotations of orthologous genes. Stud Health Technol Inform. 2010;160(Pt 2):1309-13.
    Abstract | pub2010005.pdf | PMID:  20841896
    AbstractDownload
  • Downs SM, van Dyck PC, Rinaldo P, McDonald CJ, Howell RR, Zuckerman A, Downing G. Improving newborn screening laboratory test ordering and result reporting using health information exchange. J Am Med Inform Assoc. 2010 Jan-Feb;17(1):13-8. doi: 10.1197/jamia.M3295.
    Abstract | pub2010038.pdf | PMID:  20064796 | PMCID:  PMC2995628
    AbstractDownload
  • 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.
    Abstract | pub2010007.pdf | PMID:  20841786
    AbstractDownload
  • 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.
    Abstract | pub2010008.pdf | PMID:  20841778
    AbstractDownload
  • Liu J, Subramanian K, Yoo TS. Region flow: a multi-stage method for colonoscopy tracking. Med Image Comput Comput Assist Interv. 2010;13(Pt 2):505-13.
    Abstract | PMID:  20879353
    Abstract
  • Mortensen J, Bodenreider O. Comparing Pharmacologic Classes in NDF-RT and SNOMED CT. Proc SMBM 2010:119-124.
    Abstract
    Abstract
  • Neve L, Long LR, Antani SK. Software: Boundary Marking Tool 2 (BMT2)
    Abstract
    Abstract
  • Vreeman DJ, McDonald C, Huff SM. LOINC® - A Universal Catalog of Individual Clinical Observations and Uniform Representation of Enumerated Collections. Int J Funct Inform Personal Med. 2010;3(4):273-291. Epub 2011 May 23.
    Abstract | pub2010061.pdf | PMID:  22899966 | PMCID:  PMC3418707
    AbstractDownload
  • Wei D, Bodenreider O. Using the abstraction network in complement to description logics for quality assurance in biomedical terminologies - a case study in SNOMED CT. Stud Health Technol Inform. 2010;160(Pt 2):1070-4.
    Abstract | pub2010013.pdf | PMID:  20841848
    AbstractDownload
  • 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.
    Abstract | PMID:  20841653
    Abstract
  • Baorto D, Li L, Cimino JJ. Practical Experience with the Maintenance of a Large Ontology for an Academic Medical Center Journal of Biomedical Informatics; 2009 Jun;42(3):494-503)
    Abstract
    Abstract
  • Lowekamp B, Chen D. A Framework for Improved Regression Testing Based Upon CTest and CDash. The Insight Journal. Web. 2009 Jul-Dec.
    Abstract | URL:  http://hdl.handle.net/10380/3116
    AbstractExternal link
  • Humphrey SM, Névéol A, Gobeil J, Ruch P, Darmoni SJ, Browne AC. Comparing a Rule Based vs. Statistical System for Automatic Categorization of MEDLINE Documents According to Biomedical Specialty. J Am Soc Inf Sci Technol. 2009 Dec 1;60(12):2530-2539.
    Abstract | PMID:  19956557 | PMCID:  PMC2782854
    Abstract
  • Mork JG, Bodenreider O, Demner-Fushman D, Doagan RI, Lang F-M, Lu Z, Névéol A, Peters L, Shooshan SE, Aronson AR. NLM's I2B2 tool system description. Third i2b2 Workshop on Natural Language Processing Challenges for Clinical Records, November, San Francisco, 2009
    Abstract | pub2010032.pdf
    AbstractDownload
  • Encinas MA, Ducut E, Liu F, Avila JM, Diwa M, Fontelo P. Development of a Virtual Slide Library in a Developing Country. AMIA Annu Symp Proc; 2009 Nov 14-18; San Francisco. p. 836.
    Abstract | pub2009052.pdf
    AbstractDownload
  • Liu F, Fontelo P. Infobuttons Linked to Indivo, a Patient Controlled Health Record. AMIA Annu Symp Proc; 2009 Nov 14-18; San Francisco. p. 940.
    Abstract | pub2009050.pdf
    AbstractDownload
  • Lu C, Humphrey SM, Rogers W, Browne AC. Development of a semantic type based WSD tool [Abstract]. AMIA Annu Symp Proc 2009:943.
    Abstract | pub2009067.pdf
    AbstractDownload
  • 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).
    Abstract
    Abstract
  • 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.
    Abstract | pub2009056.pdf
    AbstractDownload
  • Aronson AR, Lang FM. The Evolution of MetaMap, a Concept Search Program for Biomedical Text AMIA Annu Symp Proc. 2009 Nov:22
    Abstract | pub2009041.pdf
    AbstractDownload
  • Bodenreider O. Using SNOMED CT in combination with MedDRA for reporting signal detection and adverse drug reactions reporting. AMIA Annu Symp Proc. 2009 Nov 14;2009:45-9.
    Abstract | pub2009026.pdf | PMID:  20351820 | PMCID:  PMC2815504
    AbstractDownload
  • Burgun A, Mougin F, Bodenreider O. Two approaches to integrating phenotype and clinical information. AMIA Annu Symp Proc. 2009 Nov 14;2009:75-9.
    Abstract | pub2009027.pdf | PMID:  20351826 | PMCID:  PMC2815427
    AbstractDownload
  • Cimino JJ. The contribution of observational studies and clinical context information for guiding the integration of infobuttons into clinical information systems. AMIA Annu Symp Proc. 2009 Nov 14;2009:109-13.
    Abstract | PMID:  20351832 | PMCID:  PMC2815416
    Abstract
  • Cohen T, Schvaneveldt R, Rindflesch TC. Predication-based semantic indexing: permutations as a means to encode predications in semantic space. AMIA Annu Symp Proc. 2009 Nov 14;2009:114-8.
    Abstract | pub2009044.pdf | PMID:  20351833 | PMCID:  PMC2815384
    AbstractDownload
  • Geller J, Morrey CP, Xu J, Halper M, Elhanan G, Perl Y, Hripcsak G. Comparing inconsistent relationship configurations indicating UMLS errors. AMIA Annu Symp Proc. 2009 Nov 14;2009:193-7.
    Abstract | PMID:  20351848 | PMCID:  PMC2815406
    Abstract
  • Haerian K, McKeeby J, DiPatrizio G, Cimino JJ. Use of clinical alerting to improve the collection of clinical research data. AMIA Annu Symp Proc. 2009 Nov 14;2009:218-22.
    Abstract | PMID:  20351853 | PMCID:  PMC2815392
    Abstract
  • Hristovski D, Kastrin A, Peterlin P, Rindflesch TC. Semantic relations for interpreting DNA microarray data. AMIA Annu Symp Proc. 2009 Nov 14;2009:255-9.
    Abstract | pub2009045.pdf | PMID:  20351860 | PMCID:  PMC2815475
    AbstractDownload
  • 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
    Abstract | PMID:  25635265 | PMCID:  PMC4307020
    Abstract
  • Bodenreider O. Provenance information in biomedical knowledge repositories – A use case. Proceedings of the First International Workshop on the role of Semantic Web in Provenance Management (SWPM 2009), 2009: p. (electronic proceedings: http://ceur-ws.org/Vol-526/).
    Abstract
    Abstract
  • Fung K, Berglund D, Scichilone R, Brear H, Giannangelo K. SNOMED CT to ICD-10 map development process diagram. Meeting of the WHO Collaborating Centers for the Family of International Classifications. October 2009.
    Abstract | URL:  http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CDUQFjAA&url...
    AbstractExternal link
  • Fung K, Berglund D, Scichilone R, Brear H, Giannangelo K. SNOMED CT to ICD-10 mapping project update - a joint task for IHTSDO and WHO-FIC. Meeting of the WHO Collaborating Centers for the Family of International Classifications. October 2009.
    Abstract | URL:  http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&sqi=2&ved=0CDIQFj...
    AbstractExternal link
  • Yoo TS, Silver D, Correa C, Chen D, Moran A. Volumetric Bodies - the Exhibition. IEEE VisWeek 2009 Interactive Demo & Art Exhibit; 2009 Oct 12-16; Atlantic City, New Jersey.
    Abstract
    Abstract
  • 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.
    Abstract | pub2009039.pdf | PMID:  19671694 | PMCID:  PMC2765257
    AbstractDownload
  • Demner-Fushman D, Chapman WW, McDonald CJ. What can natural language processing do for clinical decision support? J Biomed Inform. 2009 Oct;42(5):760-72. doi: 10.1016/j.jbi.2009.08.007. Epub 2009 Aug 13.
    Abstract | PMID:  19683066 | PMCID:  PMC2757540
    Abstract
  • 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.
    Abstract | PMID:  19022398 | PMCID:  PMC2776079
    Abstract
  • Lowekamp B, Chen D, Santoroski J, Yaniv Z, Yoo TS. Software: SimpleITK.
    Abstract
    Abstract
  • 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.
    Abstract | pub2009038.pdf | PMID:  19166973 | PMCID:  PMC2818245
    AbstractDownload
  • Simonaitis L, McDonald CJ. Using National Drug Codes and drug knowledge bases to organize prescription records from multiple sources. Am J Health Syst Pharm. 2009 Oct 1;66(19):1743-53. doi: 10.2146/ajhp080221.
    Abstract | pub2010034.pdf | PMID:  19767382 | PMCID:  PMC2965522
    AbstractDownload
  • Bennett AE, Narayan K, Shi D, Hartnell LM, Gousset K, He H, Lowekamp BC, Yoo TS, Bliss D, Freed EO, Subramaniam S. Ion-abrasion scanning electron microscopy reveals surface-connected tubular conduits in HIV-infected macrophages. PLoS Pathog. 2009 Sep;5(9):e1000591. doi: 10.1371/journal.ppat.1000591. Epub 2009 Sep 25.
    Abstract | PMID:  19779568 | PMCID:  PMC2743285
    Abstract
  • Chen Y, Gu H, Perl Y, Halper M, Xu J. Expanding the extent of a UMLS semantic type via group neighborhood auditing. J Am Med Inform Assoc. 2009 Sep-Oct;16(5):746-57. doi: 10.1197/jamia.M2951. Epub 2009 Jun 30.
    Abstract | PMID:  19567802 | PMCID:  PMC2744725
    Abstract
  • Fung KW. Dataset: CORE problem list of SNOMED CT.
    Abstract
    Abstract
  • Xu X, Lee DJ, Antani SK, Long LR, Archiband JK. Using Relevance Feedback with Short-term Memory for Content-based Spine X-ray Image Retrieval. J Neurocomputing. June 2009;72(10-12):2259-69.
    Abstract
    Abstract
  • 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.
    Abstract | PMID:  19394440 | PMCID:  PMC2722378
    Abstract
  • Cimino JJ, Hayamizu TF, Bodenreider O, Davis B, Stafford GA, Ringwald M. The caBIG terminology review process. J Biomed Inform. 2009 Jun;42(3):571-80. doi: 10.1016/j.jbi.2008.12.003. Epub 2008 Dec 25.
    Abstract | PMID:  19154797 | PMCID:  PMC2729758
    Abstract
  • 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.
    Abstract | PMID:  19303057
    Abstract
  • 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.
    Abstract | PMID:  19475724 | PMCID:  PMC2891883
    Abstract
  • Zhu X, Fan JW, Baort D, Weng C, Cimino JJ. A review of auditing methods applied to the content of controlled biomedical terminologies. J Biomed Inform. 2009 Jun;42(3):413-25. doi: 10.1016/j.jbi.2009.03.003. Epub 2009 Mar 12.
    Abstract | PMID:  19285571 | PMCID:  PMC3505841
    Abstract
  • McDonald CJ, Fung K, Wang Y, Lynch P, Hook J, Vreeman D. Towards a standardized HL7 clinical data capture tool – with a trial implementation in NLM’s personal health record. 10th International HL7 Interoperability Conference. May 2009.
    Abstract
    Abstract
  • Lowekamp B. IO Streaming in ITK. Kitware Source. 2009 Apr;9:5-7.
    Abstract | URL:  http://www.kitware.com/media/html/IOStreamingInITK.html
    AbstractExternal link
  • Xue Z, Long LR, Antani SK, Jeronimo J, Thoma GR. Image-retrieval System Aids Cervical Cancer Studies SPIE Newsroom. April 2009
    Abstract
    Abstract
  • 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.
    Abstract | PMID:  19217754
    Abstract
  • Heymann JAW, Shi D, Kim S, Bliss D, Milne JLS, Subramaniam S. 3D imaging of mammalian cells with ion-abrasion scanning electron microscopy. J Struct Biol. 2009 Apr;166(1):1-7. doi: 10.1016/j.jsb.2008.11.005. Epub 2008 Dec 10.
    Abstract | PMID:  19116171
    Abstract
  • 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
    Abstract | PMID:  19244017
    Abstract
  • McDonald CJ. Protecting Patients In Health Information Exchange: A Defense Of The HIPAA Privacy Rule. Health Aff (Millwood). 2009 Mar-Apr;28(2):447-9. doi: 10.1377/hlthaff.28.2.447.
    Abstract | PMID:  19276002 | PMCID:  PMC2953709
    Abstract
  • Overby CL, Tarczy-Hornoch P, Demner-Fushman D. The potential for automated question answering in the context of genomic medicine: An assessment of existing resources and properties of answers Summit on Translat Bioinforma. 2009 Mar 1;2009:1-25.
    Abstract | PMID:  21347155 | PMCID:  PMC3041571
    Abstract
  • Xue Z, Long LR, Antani SK, Jeronimo J, Thoma GR. Segmentation of Mosaicism in Cervicographic Images Using Support Vector Machines Proc. SPIE 7259, Medical Imaging 2009, Lake Buena Vista, Florida, United States: Image Processing, 72594X (27 March 2009); doi: 10.1117/12.812318; http://dx.doi.org/10.1117/12.812318.
    Abstract
    Abstract
  • McDonald CJ, Hill G. IUPAC Silver Book- Compendium of Terminology and Nomenclature of Properties in Clinical Laboratory Sciences - Chapter 8 - Kinds-of-Quantity of Dimension One. SI Unit 1. Royal Society of Chemistry; 2009. doi:10.1039/978178262245.1-00075.
    Abstract
    Abstract
  • Anne A, Bagayoko C, Fontelo P. Evaluation de BabelMeSH en Francais. IRBM 2009. DOI: 10.1016/j.irbm.2009.06.006.
    Abstract | pub2009048.pdf
    AbstractDownload
  • Bodenreider O, Burgun A. Desiderata for an Ontology of Diseases for the Annotation of Biological Datasets Proc ICBO 2009:39-42
    Abstract | pub2009023.pdf
    AbstractDownload
  • Collins SA, Currie LM, Bakken S, Cimino JJ. Information needs, infobutton manager use, and satisfaction by clinician type: a case study. J Am Med Inform Assoc. 2009 Jan-Feb;16(1):140-2. Epub 2008 Oct 24.
    Abstract | PMID:  18952943 | PMCID:  PMC2605588
    Abstract
  • 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
    Abstract | pub2009005.pdf
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  • Hristovski D, Kastrin A, Peterlin B, Rindflesch TC. Combining Semantic Relations and DNA Microarray Data for Novel Hypotheses Generation Lecture Notes in Bioinformatics. Springer
    Abstract | pub2009060.pdf
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  • Kilicoglu H, Demner-Fushman D, Rindflesch TC, Wilczynski NL, Haynes RB. Towards Automatic Recognition of Scientifically Rigorous Clinical Research Evidence J Am Med Inform Assoc. 2009 Jan-Feb;16(1):25-31. Epub 2008 Oct 24.
    Abstract | PMID:  18952929 | PMCID:  PMC2605595
    Abstract
  • 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.
    Abstract | PMID:  19381547 | PMCID:  PMC2719765
    Abstract
  • 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
    Abstract | PMID:  19478019 | PMCID:  PMC2687948
    Abstract
  • 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
    Abstract
    Abstract
  • Zweigenbaum P, Demner-Fushman D. Bioinformatics: Tools and Applications. Springer 2009.
    Abstract
    Abstract
  • 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
    Abstract | PMID:  19965054
    Abstract
  • 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
    Abstract | PMID:  20523757 | PMCID:  PMC2879660
    Abstract
  • Pontet F, Magdal Petersen U, Fuentes-Arderiu X, Nordin G, Bruunshuus I, Ihalainen J, Karlsson D, Forsum U, Dybkaer R, Schadow G, Kuelpmann W, Ferard G, Kang D, McDonald C, Hill G. Clinical laboratory sciences data transmission: the NPU coding system. Stud Health Technol Inform. 2009;150:265-9.
    Abstract | pub2009062.pdf | PMID:  19745311 | PMCID:  PMC3082954
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  • Du H, Yoo TS, Qin H. PDE-based medial axis extraction and shape manipulation of arbitrary meshes. Journal of Systems Science and Complexity. 2008 Dec;21(4):601-17.
    Abstract
    Abstract
  • 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.
    Abstract | PMID:  18660879 | PMCID:  PMC2592252
    Abstract
  • Bodenreider O. Comparing SNOMED CT and the NCI Thesaurus through Semantic Web Technologies Proc. KR-MED 2008
    Abstract
    Abstract
  • Bodenreider O. Ontologies and Data Integration in Biomedicine: Success Stories and Challenging Issues In: Bairoch A, Cohen-Boulakia S, Froidevaux C, editors. Proceedings of the Fifth International Workshop on Data Integration in the Life Sciences (DILS 2008); Berlin Heidelberg New York: Springer; 2008. p. 1-4
    Abstract | pub2008024.pdf
    AbstractDownload
  • Bodenreider O. Semantic Web for Translational Biomedicine: Two Pilot Experiments [Abstract]. Proc. MIA Summit on Translational Bioinformatics 2008:141
    Abstract | pub2008025.pdf
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  • Burgun A, Bodenreider O. Accessing and Integrating Data and Knowledge for Biomedical Research Yearb Med Inform. 2008:91-101
    Abstract | pub2008027.pdf | PMID:  18660883 | PMCID:  PMC2553094
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  • Huang KC, Geller J, Halper M, Perl Y, Xu J. Using WordNet synonym substitution to enhance UMLS source integration. Artif Intell Med. June 2009;46(2):97-109. doi: 10.1016/j.artmed.2008.11.008. Epub 2008 Dec 30.
    Abstract | PMID:  19117739 | PMCID:  PMC2755556
    Abstract
  • Kilicoglu H, Fiszman M, Rodriguez A, Shin D, Ripple AM, Rindflesch TC. Semantic MEDLINE: A Web Application for Managing the Results of PubMed Searches Proc. Third Int'l Symposium for Semantic Mining in Biomedicine, 69-76
    Abstract
    Abstract
  • 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
    Abstract | pub2008009.pdf
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  • 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
    Abstract | pub2008028.pdf
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  • Peters L, Bodenreider O. Using the RxNorm Web Services API for Quality Assurance Purposes AMIA Annu Symp Proc. 2008 Nov 6:591-5.
    Abstract | PMID:  18999038 | PMCID:  PMC2656097
    Abstract
  • Rogers J, Bodenreider O. SNOMED CT: Browsing the Browsers Proc of the Third International Conference on Knowledge Representation in Medicine (KR-MED 2008) 2008:30-36
    Abstract
    Abstract
  • Zeng K, Bodenreider O, Kilbourne J, Nelson SJ. Standards, Security and Usability: Experience with MyMedicationList [Abstract]. Proc. AMIA Spring Congress 2008
    Abstract | pub2008035.pdf
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  • 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/).
    Abstract
    Abstract
  • Hansen RA, Wanzhu T, Wang J, Ambuehl R, McDonald CJ, Murray MD. Risk of adverse gastrointestinal events from inhaled corticosteroids. 2008 Nov;28(11):1325-34.
    Abstract | pub2008073.pdf |