1. Lee HT, Xu H, Ota-Setlik A, Emala CW. Oxidant preconditioning protects human proximal tubular cells against lethal oxidant injury via p38 MAPK and heme oxygenase-1. Am J Nephrol. 2003 Sep-Oct; 23(5):324-33.
2. Lee HT, Xu H, Siegel CD, Krichevsky IE. Local Anesthetics Induce Human Renal Cell Apoptosis. Am J Nephrol. 2003 May-Jun; 23(3):129-39.
3. Xu, H, Anderson, K, Grann, V, Friedman, C. Facilitating Cancer Research using Natural Language Processing of Pathology Reports. In Proceedings of Medinfo. 2004; 565-72.
4. Xu H, Markatou M, Dimova R, Liu H, Friedman C. Machine learning and word sense disambiguation in the biomedical domain: design and evaluation issues. BMC Bioinformatics. 2006; 7:334.
5. Karina Tulipano P, Tao Y, Millar WS, Zanzonico P, Kolbert K, Xu H, Yu H, Chen L, Lussier YA, Friedman C. Natural language processing and visualization in the molecular imaging domain. J Biomed Inform. 2007; 40:3, 270-281.
6. Fan JW, Xu H, Friedman C. Classifying biomedical concepts using contextual and lexical features. BMC Bioinformatics. 2007; 8: 264.
7. Fan JW, Xu H, Friedman C. Using Distributional Analysis to Semantically Classify UMLS Concepts. In Proceedings of Medinfo. 2007; 519-23.
8. Xu H, Jung-Wei Fan, Friedman C. Combine multiple evidence for gene symbol disambiguation. ACL 2007, BioNLP Workshop, p41-48.
9. Xu H, Fan JW, Hripcsak G, Mendonca EA, Markatou M, Friedman C. Gene symbol disambiguation using knowledge-based profiles. Bioinformatics, 2007 23(8):1015-1022.
10. Xu H, Stetson P, Friedman C. A Study of Abbreviations in Clinical Notes. AMIA Annu Symp Proc. 2007; 821-5.
11. Chen ES, Hripcsak G, Xu H, Markatou M, Friedman C. Automated Acquisition of Disease-Drug Knowledge from Biomedical and Clinical Documents. JAMIA 2008; 15(1):87-98.
12. Xu H, Stetson P, Friedman C. Methods for Building Sense Inventories of Abbreviations in Clinical Notes. JAMIA, 2009 16(1):103-108.
13. Denny JC, Peterson JF, Choma NN, Xu H, Miller RA, Bastarache L, Peterson NB. Development of a Natural Language Processing System to Identify Timing and Status of Colonoscopy Testing in Electronic Medical Records. AMIA 2009 accepted, pending JAMIA review.
14. Xu H, Stenner SP, Doan S, Johnson KB, Waitman LR, Denny JC. MedEx - A Medication Information Extraction System for Clinical Narratives. AMIA 2009 accepted, pending JAMIA review.
15. Xu H, Doan S, Birdwell KA, Cowan JD, Vincz AJ, Haas DW, Basford MA, Denny JC. An automated approach to calculating the daily dose of tacrolimus in electronic health records. 2010 AMIA Summit on Clinical Research Informatics.
16. Denny JC, Peterson JF, Choma NN, Xu H, Miller RA, Bastarache L, Peterson NB. Development of a Natural Language Processing System to Identify Timing and Status of Colonoscopy Testing in Electronic Medical Records. JAMIA 2010; 17(4): 393-8
17. Doan S, Bastarache L, Klimkowski S, Denny JC, Xu H. Integrating Existing NLP Tools for Medication Extraction from Discharge Summaries. JAMIA 2010; 17:528-31.
18. Doan S and Xu H. Recognizing Medication related Entities in Hospital Discharge Summaries using Support Vector Machine. COLING 2010, the 23rd International Conference on Computational Linguistics, 259-266.
19. Xu H, Lu Y, Jiang M, Liu M, Denny JC, Dai Q, Peterson NB. Mining Biomedical Literature for Terms related to Epidemiologic Exposures. AMIA Annu Symp Proc. 2010 (in press).
20. Denny JC, Speltz P, Maddox R, Stein G, Xu H, Spickard A. Comparing Content Coverage in Medical Curriculum to Trainee-Authored Clinical Notes. AMIA Annu Symp Proc. 2010 (in press)
21. Wilke RA, Xu H, Denny JC, Roden DM, Krauss RM, McCarty CA, Davis RL, Skaar T, Lamba J, and Savova G. The emerging role of electronic medical records in pharmacogenomics. Clin Pharmacol Ther. 2011, 89(3): 379-86.
22. Rosenbloom ST, Denny JC, Xu H, Lorenzi N, Stead WW, Johnson KB. Data from clinical notes: a perspective on the tension between structure and flexible documentation. J Am Med Inform Assoc. 2011, 18(2):181-6.
23. Jiang M, Chen Y, Liu M, Rosenbloom ST, Mani S, Denny JC, Xu H. A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries. J Am Med Inform Assoc. 2011 Apr 20.
24. Xu H, Jiang M, Oetjens M, Bowton EA, Ramirez AH, Jeff JM, Basford MA, Pulley JM, Cowan JD, Wang X, Ritchie MD, Masys DR, Roden DM, Crawford DC, Denny JC. Facilitating pharmacogenetic studies using electronic health records and natural language processing: a case study of warfarin. J Am Med Inform Assoc. 2011; 18(4): 387-91
25. Xu H, Fu Z, Shah A, Chen Y, Peterson NB, Chen Q, Mani S, Levy MA, Dai Qi, Denny JC. Extracting and integrating data from entire electronic health records for detecting colorectal cancer cases. AMIA Annu Symp Proc 2011.
26. Liu M, Kawai VK, Stein CM, Roden DM, Xu H. A framework to determine patient drug exposure from EMR: an application to warfarin. AMIA Annu Symp Proc 2011.
27. Chen Y, Mani S, Xu H. Applying active learning to assertion classification of concepts in clinical text. AMIA Annu Symp Proc 2011.
28. Wu Y, Rosenbloom ST, Denny JC, Miller RA, Mani S, Giuse DA, Xu H. Detecting abbreviations in discharge summaries using machine learning methods. AMIA Annu Symp Proc 2011.
29. Xu H, AbdelRahman S, Lu Y, Denny JC, Doan S. Applying semantic-based probabilistic context free grammar to medical language processing-a preliminary study on parsing medication sentences. Journal of Biomedical Informatics 2011 Aug 12.
30. Delaney JT, Ramirez AH, Bowton EA, Pulley JM, Basford MA, Schildcrout JS, Shi Y, Zink R, Oetjens M, Xu H, Cleator JH, Jahangir E, Ritchie MD, Masys DR, Roden DM, Crawford DC, Denny JC. Predicting clopidogrel response using DNA samples linked to an electronic health record. Accepted to Clinical Pharmacology & Therapeutics, 2011.
31. Use of a DNA Biobank Linked to Electronic Medical Records to Characterize Pharmacogenomic Predictors of Tacrolimus Dose Requirement in Kidney Transplant Recipients. Birdwell KA, Grady B, Choi L, Xu H, Denny JC, Jiang M, Vranic G, Vranic G, Basford BA, Cowan JD, Richardson DM, Robinson MP, Ikizler TA, Ritchie MD, Stein CM, Haas DW. Accepted to Pharmacogenetics and Genomics, 2011.
32. An Initial Study of Full Parsing of Clinical Text using the Stanford Parser. Xu H, AbdelRahman S, Jiang M, Fan JW, Huang Y. Accepted to International Workshop on Biomedical and Health Informatics, IEEE Conference of Bioinformatics and Biomedicine (BIBM), 2011.
33. Wu Y, Liu M, Zheng W, Zhao Z, Xu H. Ranking gene-drug relationships in biomedical literature using latent dirichlet allocation. Accepted to Pacific Symposium on Biocomputing, 2012.
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