Lorraine Tanabe
Computational Biology Branch
National Center for Biotechnology Information
National Institutes of Health
Building 38A
8600 Rockville Pike
Bethesda, MD 20894
Phone +1-301-594-3218
Fax +1-301-480-2290
tanabe@ncbi.nlm.nih.gov

Ph.D. Computational Sciences and Informatics, George Mason University, 2003

Research:

  • Natural language processing for molecular biology
  • Text mining the biomedical literature
  • Semantic tagging
Publications:
  • Tanabe, L., Thom, L.H., Matten, W., Comeau, D.C. and Wilbur, W.J. SemCat: Semantically Categorized Entities for Genomics. AMIA Annual Symposium, 2006.
  • Tanabe, L. and Wilbur, W.J. A Priority Model for Named Entities. To appear in HLT-NAACL 2006 Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis (BioNLP'06).
  • Tanabe, L. 2005. The Genomic Data Mine. In: Chen H, Fuller SS, Friedman C, Hersh W, editors. Medical Informatics: Knowledge Management and Data Mining in Biomedicine. New York. Springer. p 547-571.
  • Smith, L.H., Tanabe, L., Rindflesch, T. and Wilbur, W.J. MedTag: a Collection of Biomedical Annotations. ISMB BioLink Workshop, 2005.
  • Tanabe, L., Xie, N., Thom, L.H., Matten, W. and Wilbur, W.J. GENETAG: a Tagged Corpus for Gene/Protein Named Entity Recognition. BMC Bioinformatics 6:Supp. 1, 2005. [pdf]
  • Aronson, A.R., Demner, D., Humphrey, S.H., Ide, N.C., Kim, W., Loane, R.R., Mork, J.G., Smith, L.H., Tanabe, L., Wilbur, W.J., Xie, N. Knowledge-Intensive and Statistical Approaches to the Retrieval and Annotation of Genomics MEDLINE Citations. Proceedings of the 13th Text Retrieval Conference (TREC-2004), 2004. [pdf]
  • Cohen, K.B., Tanabe, L., Kinoshita, S. and Hunter, L. A Resource for Constructing Customized Test Suites for Molecular Biology Entity Identification Systems. HLT/NAACL BioLink Workshop, 2004. [pdf]
  • Tanabe, L., and Wilbur, W.J. Generation of a Large Gene/Protein Lexicon by Morphological Pattern Analysis. Journal of Bioinformatics and Computational Biology, 2:1-16, 2004.[pubmed] [download]
  • Kayaalp, M., Aronson, A.R., Humphrey, S.M., Ide, N.C., Tanabe, L., Smith, L.H., Demner, D., Loane, R.R., Mork, J.G., and Bodenreider, O. Methods for Accurate Retrieval of MEDLINE citations in Functional Genomics, Proceedings of the 12th Text Retrieval Conference (TREC-2003), 2003. [pdf]
  • Tanabe, L. Text Mining the Biomedical Literature for Genetic Knowledge, Ph.D. diss., George Mason University, 2003.
  • Tanabe, L., and Wilbur, W.J. Tagging Gene and Protein names in Full Text Biomedical Articles. Proceedings of the Workshop on Natural Language Processing in the Biomedical Domain (ACL-2002), 9-13, 2002.[pdf]
  • Tanabe, L., and Wilbur, W.J. Tagging Gene and Protein Names in Biomedical Text. Bioinformatics, 18:1124-1132, 2002.[pdf] [download] [training data]
  • Weinstein J.N., Scherf U., Lee J.K., Nishizuka S., Gwadry F., Bussey A.K., Kim S., Smith L.H., Tanabe L., Richman S., Alexander J., Kouros-Mehr H., Maunakea A., Reinhold W.C. The Bioinformatics of Microarray Gene Expression Profiling. Cytometry. 2002 Jan 1;47(1):46-9.
  • Tanabe, L. What's Behind Bioinformatics. Trends in Biotechnology, 19:2:81, 2001.
  • Scherf, U., Ross, D.T., Waltham, M., Smith, L.H., Lee, J.K., Tanabe, L., Kohn, K.W., Reinhold, W.C., Myers, T.G., Andrews, D.T., Scudiero, D.A., Eisen M.B., Sausville, E.A., Pommier, Y., Botstein, D., Brown, P.O. and Weinstein, J.N. A Gene Expression Database for the Molecular Pharmacology of Cancer. Nature Genetics 24:236-244, 2000.[pdf]
  • Rindflesch, T.C., Tanabe, L., Weinstein, J.N. and Hunter, L. EDGAR: Extraction of Drugs, Genes and Relations from Biomedical Literature. Proceedings of the Pacific Symposium on Biocomputing 5:514-525, 2000.[pdf]
  • Tanabe, L., Scherf, U., Smith, L.H., Lee, J.K., Hunter, L., Weinstein, J.N. MedMiner: An Internet Text-Mining Tool for Biomedical Information, with Application to Gene Expression Profiling. Biotechniques 27:1210-1217, 1999.[pdf] [tool]