Refereed Publications

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    Refereed Journal Articles and Book Chapters

  1. Jean J, Goldberg S, Khare R., Bailey, LC, et al. Retrospective analysis of Candida-related conditions in infancy and early childhood caries, 2017
  2. Callahan T, Bauck AE, Bertoch D, Brown J, Khare R., et al. A Comparison Of Data Quality Assessment Checks In Six Data Sharing Networks, eGEMS, 2017
  3. Khare R., Utidjian L, Ruth B, et al. A longitudinal study of data quality in a large pediatric data research network, Journal of American Medical Informatics Association, 2017(link)
  4. Huser V, DeFalco F, Schuemie M, Ryan P, Shang N, Velez M, Park RW, Boyce RD, Duke J, Khare R., Utidjian L, Bailey C. Multi-site Evaluation of a Data Quality Tool for Patient-Level Clinical Datasets, eGEMS, 2016
  5. Leaman, R., Khare, R., Lu, Z., Challenges in Clinical Natural Language Processing for Automated Disorder Normalization, Journal of Biomedical Informatics, 2015
  6. Khare, R., Good, B., Leaman, R., Su, A., Lu, Z., Crowdsourcing in Biomedicine: Challenges and Opportunities, (link)
  7. Khare, R., Burger, J. D., Aberdeen, J. S., Tresner-Kirsch, D. W., Corrales, T., Hirschman, L., Lu, Z., Scaling Drug Indication Curation through Crowdsourcing, Database Oxford Journal, 2015 (link)
  8. Khare, R., Li, J., Lu, Z., LabeledIn: Cataloging Labeled Indications for Human Drugs, Journal of Biomedical Informatics, 2014 (link)
  9. Comeau, D.C., Batista-Navarro, R. T., Dai, H-J., Doğan, R. I., Jimeno, A., Khare, R., Lu, Z., Marques, H., Mattingly C.J., Neves, M., Peng, Y., Rak, R., Rinaldi, F., Tsai, R. T-H., Verspoor, K., Wiegers, T.C., Wu, C.H., Wilbur, W.J. BioC Interoperability Track Overview, Database Oxford Journal, 2014 (link)
  10. Khare, R., Wei, C-H., Mao, Y., Leaman, R., Lu, Z., tmBioC: Improving Interoperability of Text Mining Tools with BioC, Database Oxford Journal, 2014 (link)
  11. Burger, J., Doughty, E.K., Khare, R., Wei, C-H., Mishra, R., Aberdeen, J.,Tresner-Kirsch, D.,Wellner, B., Kann, M.G., Lu, Z., Hirschman, L., Hybrid curation of gene-mutation relations combining automated extraction and crowdsourcing, Database Oxford Journal, 2014. (pdf)
  12. Khare, R., Leaman, R., Lu, Z., Accessing Biomedical Literature in the Current Information Landscape, Biomedical Literature Mining - Methods in Molecular Biology, Volume - 1159, Edition 2014. (link)
  13. Khare, R., An, Y., Song, I-Y., Understanding Deep Web Search Interfaces: A Survey, SIGMOD Record, 39(1):33-40, 2010.(pdf). (Supplementary Page)

    Peer-Reviewed Full Conference Papers

  14. Khare, R , Ruth, BJ, Miller, M., Tucker, J., Utidjian, LH, Razzaghi, H., Patibandla, N., Burrows, EK, Bailey, LC., Predicting Causes of Data Quality Issues in a Clinical Data Research Network, AMIA Joint Summits 2018, March 15-20, 2018, San Francisco CA, USA
  15. Khare, R., Burger, J. D., Aberdeen, J. S. et al, Biocuration meets text mining and crowdsourcing, BC2 Basel Computational Biology Conference, June 7-10, 2015, Congress Center Basel, Switzerland
  16. Khare, R., Wei, C-H, Lu, Z., Automatic Extraction of Drug Indications from FDA Drug Labels, AMIA Annual Symposium 2014, November 15-20, 2014, Washington DC, USA (Acc. Rate 47%)
  17. Khare, R., Sahai, E., Pramanick, I., Remote Mentoring Young Females in STEM through MAGIC, The Sixth Conference of MIT's Learning International Networks Consortium (LINC 2013), June 16-19, 2013, Cambridge, MA, USA. (pdf)
  18. Khare, R., An, Y., Wolf, S., Nyirjesy, P., Liu, L., Chou, E., Understanding the EMR Error Control Practices among Gynecologic Physicians, iConference 2013, February 12-15, 2013, Fort Worth, TX, USA. (pdf)
  19. Khare, R., An, Y., Li, J., Song, I-Y., Hu, X.,Exploiting Semantic Structure for Mapping User-specified Form Terms to SNOMED CT Concepts, 2nd ACM International Health Informatics Conference (IHI 2012), January 28-30, 2012, Miami, FL, USA. **Acc. Rate 18%** (pdf)
  20. An, Y., Khare, R., Song, I-Y., Hu, X. Automatically Mapping and Integrating Multiple Data Entry Forms into a Database, 30th International Conference on Conceptual Modeling (ER 2011), October 31-November 3, 2011, Brussels, Belgium. **Acc. Rate 16%** (pdf)
  21. Khare, R., An, Y., Song, I-Y., Hu, X.,Can Clinicians Create High-Quality Databases? A Study on A Flexible Electronic Health Record (fEHR) System, 1st ACM International Health Informatics Conference (IHI 2010),November 11-12, 2010, Arlington, VA, USA. **Acc. Rate 17%** (pdf)
  22. Khare, R., An, Y., An Empirical Study on Using Hidden Markov Model for Search Interface Segmentation, 18th ACM International Conference on Information and Knowledge Management (CIKM2009), November 3-5, 2009, Hong Kong. **Acc. Rate 14.5%** (pdf).
  23. Song, I-Y., Khare, R., An, Y., Hilsbos, M., A Multi-level Method for Developing UML Sequence Diagrams, 27th International Conference on Conceptual Modeling (ER2008), October 20-23, 2008, Barcelona, Spain. **Acc. Rate 25%** (pdf).
  24. Song, I-Y., Khare, R., An, Y., Lee, S., Kim, S-P., Kim, J., Moon, Y-S., SAMSTAR: An Automatic Tool for Generating Star Schemas from an Entity-Relationship Diagram. 27th International Conference on Conceptual Modeling(ER 2008), October 20-23, 2008, Barcelona, Spain.(pdf).

    Peer-Reviewed Short Conference Papers, Panels, and Abstracts

  25. Khare, R., Razzaghi, L., Utidjian L, Miller M, Bailey, Understanding the gaps between data quality checks and research capabilities of a pediatric data research network, AMIA Joint Summits on Translational Informatics 2017, San Francisco, CA, USA. (Acc. Rate 41%)
  26. Bailey, L.C. Kahn, M., Deaknye, S., Khare, R., Deans, K., PEDSnet: from building a high-quality CDRN to conducting science, AMIA Annual Symposium 2016, Chicago, IL, USA
  27. Khare, R., Utidjian, L., Schulte, G., Marsolo, K., Bailey, C., Identifying and Understanding Data Quality Issues in a Pediatric Distributed Research Network, AMIA Annual Symposium 2015, November 14-18, 2015, San Francisco, CA, USA. (Acc. Rate 35%)
  28. Khare, R., Li, J., Lu, Z., Annotating FDA Drug Labels for Drug Indications, AMIA Joint Summits on Translational Science, April 07-09, 2014, San Francisco, CA, USA. **Translational Bioinformatics Late-Breaking Abstract (Acc. Rate 20%)
  29. Khare, R., Li, J., Lu, Z., Toward Creating a Gold Standard of Drug Indications from FDA Drug Labels, IEEE International Conference on Health Informatics (ICHI), September 09-11, 2013, Philadelphia, PA, USA. (pdf)
  30. Gong, X., Ke, W., Khare, R., Studying Scatter/Gather Browsing for Web Search, The American Society for Information Science and Technology (ASIST 2012 Annual Meeting), October 26-30, 2012, Baltimore, MD.(pdf)
  31. An, Y., Khare, R., Song, I-Y., Hu, X., Bridging Encounter Forms and Electronic Medical Record Databases: Annotation, Mapping, and Integration, IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2012), October 4-7, 2012, Philadelphia, USA. (Acc. Rate 21) (pdf)
  32. Li, J., Khare, R., Lu, Zhiyong, Improving Online Access to Drug-related Information, IEEE Healthcare Informatics, Imaging, and Systems Biology Conference (HISB 2012), September 27-28, 2012, La Jolla, CA. (pdf)
  33. An, Y., Khare, R., Song, I-Y., Hu, X.. Data Exploration and Knowledge Discovery in a Patient Wellness Tracking (PWT) System at a Nurse-Managed Health Services Center, 2nd ACM International Health Informatics Conference (IHI 2012), January 28-30, 2012, Miami, FL, USA. (Acc. Rate 18%) (pdf)

    Peer-Reviewed Workshop and Demo Papers

  34. Utidjian, L., Khare, R., et al., Identifying and Understanding Data Quality Issues in a Pediatric Distributed Research Network, American Academy of Pediatrics (AAP) National Conference & Exhibition, Council on Clinical Information Technology, October 23-27, 2015, Washington, DC, USA
  35. Kim, J., Kim, D., Lee, S., Moon, Y-S., Song, I-Y.,Khare, R., An, Y. ,SAMSTARplus: An Automatic Tool for Generating Multi-Dimensional Schemas from an Entity Relationship Diagram, 28th International Conference on Conceptual Modeling (ER2009) November 9-12, 2009, Gramado, Brazil. (pdf).
  36. Song, I-Y., Khare, R., Dai, B., SAMSTAR: A Semi-Automated Lexical Method for Generating STAR Schemas from an ER diagram, Data warehousing and Online Analytical Processing (DOLAP) workshop held in conjunction with CIKM 2007, November 9, 2007, Lisbon, Portugal. (pdf).

    Technical Reports and Articles

  37. Khare, R., Wei, C-H, Mao, Y., Leaman, R., Lu, Z., Improving Interoperability of Text Mining Tools with BioC, BioCreative IV Workshop, October 07-09, 2013, Bethesda, MD. (pdf)
  38. Leaman, R., Khare, R., Lu, Z., NCBI at ShARe/CLEF eHealth Shared Task: Disorder Normalization in Clinical Notes with DNorm, CLEFeHealth 2013 - Task 1: Identification and Normalization of Disorders in Clinical Reports, September 23-26, 2013, Valencia, Spain. (pdf) (Highest Performance in Disease Normalization Task)
  39. Desikan, P., Khare, R., Srivastava, J., Kaplan, R., Ghosh, J., Liu, L., Gopal, V., Predictive Modeling in Healthcare: Challenges and Opportunities, IEEE Life Sciences Newsletter November 2013. (link)
  40. Desikan, P. and Khare, R., Data Mining for Healthcare: DMH 2013 Workshop Summary, IEEE International Conference on Health Informatics (ICHI), September 9-11 2013.
  41. Khare, R., Careers in Bioinformatics, 2013 NIH Career Symposium. (pdf)
  42. Khare, R., A Framework for Mapping User Designed Forms to Relational Databases, Doctoral Dissertation Report, Drexel University, December 2011 (pdf) (Drexel Most Outstanding Promise Dissertation Award)