John Wilbur, MD, PhD Contact Information
Building 38A, Room 6S606
8600 Rockville Pike
MSC 6075
Bethesda, MD 20894-6075
Tel: 301-435-5926
Fax: 301-480-2288
wilbur@ncbi.nlm.nih.gov

Ph.D. University of California, Davis,California, 1967 M.D. Loma Linda University, California, 1977 ABIM Diplomate, American Board of Internal Medicine, 1980

W. John Wilbur, MD, PhD

Computational Biology Branch
NCBI, NLM, NIH

Research Interests

  • Statistical natural language processing;
  • Machine learning; and
  • Information retrieval.

Select Recent Publications

  • Sunghwan Sohn, Donald Comeau, Won Kim and W J Wilbur, Abbreviation Definition Identification Based On Automatic Precision Estimates, BMC Bioinformatics, 2008, 9:402.
  • W. John Wilbur and Won Kim, The Ineffectiveness of Within-Document Term Frequency in Text Classification, Information Retrieval, 2009, 12:5, 509.
  • Lana Yeganova, Don Comeau, Won Kim, W. John Wilbur, How To Interpret PubMed Queries And Why It Matters, Journal of the American Society for Information Science and Technology, 2009, 60(2):264-274.
  • Smith LH, Tanabe L, Johnson nee Ando R, Kuo C, Chung I, Hsu C, Lin Y, Klinger R, Friedrich CM, Ganchev K, Torii M, Liu H, Haddow B, Struble CA, Povinelli RJ, Vlachos A, Baumgartner Jr WA, Hunter L, Carpenter R, Tsai RT, Dai H, Liu F, Chen Y, Sun C, . . ., Wilbur WJ (2008) Overview of BioCreative II gene mention recognition. Genome Biology 9(Suppl 2):S2.1-19.
  • Krallinger M, Morgan A, Smith LH, Leitner F, Tanabe L, Wilbur WJ, Hirschman L, Valencia A (2008) Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge. Genome Biology 9(Suppl 2):S1.1-9.
  • Zhiyong Lu, Won Kim, and W. John Wilbur, Evaluating Relevance Ranking Strategies for MEDLINE Retrieval, Journal of the American Medical Informatics Association, 2009 16(1):32-6.
  • Zhiyong Lu and W. John Wilbur, Improving accuracy for identifying related PubMed queries by an integrated approach, Journal of Biomedical Informatics,2008, doi:10.1016/j.jbi.2008.12.006.
  • Larry Smith and W. John Wilbur, The value of parsing as feature generation for gene mention recognition, Journal of Biomedical Informatics,2009, doi:10.1016/j.jbi.2009.03.011.
  • Andrey Rzhetsky, Hagit Shatkay, and W. John Wilbur, How to Get the Most out of Your Curation Effort, PLoS Computational Biology, (2009), 5(5): e1000391. doi:10.1371/journal.pcbi.1000391.
  • Zhiyong Lu, W. John Wilbur, Johanna R McEntyre, Alexey Iskhakov, Lee Szilagyi, Finding Query Suggestions for PubMed, AMIA Annual Symposium, (2009), 396-400.
  • Zhiyong Lu, Natalie Xie, and W. John Wilbur, Identifying related journals through log analysis, Bioinformatics, (2009), 3038-9.
  • Neveol, A, Kim W, Wilbur, WJ, Lu Z, Exploring two biomedical text genres for disease recognition, in Proceedings of the BioNLP 2009 Workshop, Boulder, CO, 2009.
  • Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Mizrachi I, Ostell J, Panchenko A, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Slotta D, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Wang Y, John Wilbur W, Yaschenko E, Ye J. Nucleic Acids Res. 2010 Jan;38(Database issue):D5-16.
  • Larry Smith and W. John Wilbur, Finding related sentence pairs in MEDLINE, Information Retrieval, (2010), in press, DOI: 10.1007/s10791-010-9126-8.
  • Zhiyong Lu and W. John Wilbur, Overview of BioCreative III Gene Normalization, in Proceedings of BioCreative III Workshop, Bethesda, MD, 2010, pp. 24-44.
  • Sun Kim and W. John Wilbur, Improving Protein-Protein Interaction Article Classification Performance by Utilizing Grammatical Relations, in Proceedings of BioCreative III Workshop, Bethesda, MD, 2010, pp. 83-88.
  • Won Kim and W. John Wilbur, Improving a gold standard: treating human relevance judgments of MEDLINE document pairs, Proceedings of the Ninth International Conference on Machine Learning and Applications, 2010, pp. 491-498.
  • Lana Yeganova, Don C. Comeau, and W. John Wilbur, Identifying abbreviation definitions - machine learning with naturally labeled data, Proceedings of the Ninth International Conference on Machine Learning and Applications, 2010, pp. 499-505.
  • W. John Wilbur and Won Kim, Improving a gold standard: treating human relevance judgments of MEDLINE document pairs, BMC Bioinformatics. 2011 Jun 9;12 (Suppl 3):S5.
  • Yeganova L, Comeau DC, Wilbur WJ, Machine learning with naturally labeled data for identifying abbreviation definitions, BMC Bioinformatics 2011 Jun 9; 12(Suppl 3):S6.
  • Yeganova, Lana, Comeau, Donald C., Kim, Won and Wilbur, W. John, Text Mining Techniques for Leveraging Positively Labeled Data, Proceedings of BioNLP 2011 Workshop, Portland, Oregon, June 2011: 155—163.

Publications in PubMed

Group Members

Group Alumni

  • Myung Chung
  • Hagit Shatkay
Support Center

Last updated: 2017-12-20T18:57:39Z