2013

• M. Yetisgen-Yildiz, C.A. Bejan, L. Vanderwende, F. Xia, H.L. Evans, M.M. Wurfel. Automated Tools for Phenotype Extraction from Medical Records. To appear in Proceedings of the American Medical Informatics Association Clinical Research Informatics Summit (AMIA CRI'13). San Francisco, CA, March, 2013.
• M. Yetisgen-Yildiz, M.L. Gunn, F. Xia, T.H. Payne. A Text Processing Pipeline to Extract Recommendations from Radiology Reports. To appear in Journal of Biomedical Informatics, 2013.
• C.A. Bejan, L. Vanderwende, F. Xia, M. Yetisgen-Yildiz. Assertion modeling and its role in clinical phenotype identification. To appear in Journal of Biomedical Informatics, 2013.

2012

• C.A. Bejan, L. Vanderwende, M.M. Wurfel, and M. Yetisgen-Yildiz. Assessing Pneumonia Identification from Time-Ordered Narrative Reports. To appear in Proceedings of the American Medical Informatics Association Fall Symposium (AMIA'12). Chicago, IL, November, 2012.
• M. Tepper, F. Xia, and M. Yetisgen-Yildiz. Smoking Status Detection Across Domains. To appear in Proceedings of the American Medical Informatics Association Fall Symposium (AMIA'12). Chicago, IL, November, 2012.
• J. Huh, M. Yetisgen-Yildiz, A. Hartzler, D. McDonald, A. Park and W. Pratt. Toward Automatic Weaving of Medical Advice with Patient Experiences Using Text Classification. To appear in Proceedings of the American Medical Informatics Association Fall Symposium (AMIA'12). Chicago, IL, November, 2012.
• C.A. Bejan, L. Vanderwende, F. Xia, M. Wurfel, M. Yetisgen-Yildiz. Pneumonia identification using statistical feature selection. To appear in J Am Med Inform Assoc., 2012.
• F. Xia, M. Yetisgen-Yildiz. Clinical corpus annotation: challenges and strategies. Proceedings of Third Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM'2012) of the International Conference on Language Resources and Evaluation (LREC), Istanbul, May, 2012.
• M. Tepper, D. Capurro, F. Xia, L. Vanderwende, M. Yetisgen-Yildiz. Statistical Section Segmentation in Free-Text Clinical Records. Proceedings of the International Conference on Language Resources and Evaluation (LREC), Istanbul, May, 2012.

2011

• M. Yetisgen-Yildiz, B.J. Glavan, F. Xia, L. Vanderwende, M.M. Wurfel. Identifying Patients with Pneumonia from Free-Text Intensive Care Unit Reports. Proceedings of Learning from Unstructured Clinical Text Workshop of ICML'2011. Bellevue, WA, July, 2011.
• M. Yetisgen-Yildiz, B.J. Glavan, F. Xia, L. Vanderwende, M.M. Wurfel. Extraction of Pneumonia Cases from Free-Text Intensive Care Unit Reports. Proceedings of American Medical Informatics Association Fall Symposium (AMIA'2011). Washington, D.C., November, 2011.
• M. Yetisgen-Yildiz, M.L. Gunn, F. Xia, T.H. Payne. Automatic Identification of Critical Follow-Up Recommendation Sentences in Radiology Reports. Proceedings of the American Medical Informatics Association Fall Symposium (AMIA'11). Washington D.C. November, 2011.
• Z. Luo, M. Yetisgen-Yildiz, C. Weng. Dynamic Categorization of Clinical Research Eligibility Criteria by Hierarchical Clustering, Journal of Biomedical Informatics, 2011, 44(6):927-35.

2010

• M. Yetisgen-Yildiz, I. Solti, F. Xia. Using Amazon's Mechanical Turk for Annotating Medical Named Entities. Proceedings of American Medical Informatics Association Fall Symposium (AMIA'2010). Washington, D.C., November, 2010.
• M. Yetisgen-Yildiz, I. Solti, F. Xia, S.R. Halgrim. Preliminary Experiments with Amazon's Mechanical Turk for Annotating Medical Named Entities. Proceedings of Creating Speech and Language Data with Amazon's Mechanical Turk Workshop of NAACL'2010, 2010.
• N. Lawson, K. Eustice, M. Perkowitz, M. Yetisgen-Yildiz. Annotating Large Email Datasets for Named Entity Recognition with Mechanical Turk. Proceedings of Creating Speech and Language Data with Amazon's Mechanical Turk Workshop of NAACL'2010, 2010.

2009

• M. Yetisgen-Yildiz and W. Pratt. A New Evaluation Methodology for Literature-Based Discovery. Journal of Biomedical Informatics. Journal of Biomedical Informatics, 2009, Vol. 42, No. 4, pp. 633-643.
• M. Yetisgen-Yildiz and W. Pratt. Evaluation of Literature-Based Discovery Systems. P. Bruza and M. Weeber (eds) Literature-Based Discovery. Springer's series on Information Science and Knowledge Management, 2009.

2008

• M. Yetisgen-Yildiz and W. Pratt. Finding the meaning of medical concept correlations. Proceedings of the American Medical Informatics Association Fall Symposium (AMIA'08). Washington D.C., November, 2008.

2007

• M. Yetisgen-Yildiz and W. Pratt. Extracting the meaning of medical concept correlations. Proceedings of the International Conference on Knowledge Capture (K-Cap'07). Whistler, BC, October, 2007.

2006

• M. Yetisgen-Yildiz and W. Pratt. Using Statistical and Knowledge Based Approaches for Literature-Based Discovery. Journal of Biomedical Informatics, 2006, Vol. 39, No. 6, pp. 600-611.
• M. Yetisgen-Yildiz. LitLinker: A System for Searching Potential Discoveries in Biomedical Literature. Proceedings of 29th Annual International ACM SIGIR Conference on Research & Development on Information Retrieval (SIGIR'06) Doctoral Consortium. Seattle, WA, August, 2006.

2005

• M. Yetisgen-Yildiz and W. Pratt. Feature Representation and Category Relationship Issues in Medline Document Classification. Proceedings of the American Medical Informatics Association Fall Symposium (AMIA'05). Washington D.C., October, 2005.
• M. Skeels, K. Henning, M. Yetisgen-Yildiz, and W. Pratt. Interaction Design for Literature-Based Discovery. Proceedings of the International Conference for Human-Computer Interaction (CHI'05). Portland, April, 2005.

2003

• W. Pratt and M. Yetisgen-Yildiz. LitLinker: Capturing Connections across the Biomedical Literature. Proceedings of the International Conference on Knowledge Capture (K-Cap'03). Florida, October 2003.
• W. Pratt and M. Yetisgen-Yildiz. A Study of Biomedical Concept Identification: MetaMap vs. People. Proceedings of the American Medical Informatics Association Fall Symposium (AMIA'03). Washington D.C. November, 2003.