Larry Smith
Staff Scientist
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
lsmith@ncbi.nlm.nih.gov

Ph.D. Mathematics, Indiana University, 1998.

Research Interests:

  • Language modeling.
  • Information retrieval and extraction.

    • Related Sites:

  • Dr. John Wilbur
  • Dr. Lorrie Tanabe
  • Ftp site with research data and the latest versions of MedPost and MedTag.
  • Personal web page

    • Current Publications:

  • Smith LH, Wilbur WJ. (2008) The value of parsing as feature generation for gene mention recognition. Biomedical Informatics, to appear.
  • Smith LH, et al. (2008) Overview of BioCreative II Gene Mention Recognition. Genome Biology, 2008, 9(Suppl 2):S2. [pdf]
  • Wilbur JW, Smith LH and Tanabe LK. (2007) BioCreative 2. Gene Mention Task. In Proceedings of the Second BioCreative Challenge Evaluation Workshop, pp. 7-16. Madrid, April, 2007. [pdf]
  • Demner-Fushman D, et al. (2007) Combining Resources to Find Answers to Biomedical Questions. In Proceedings of the Text Retrieval Conference (TREC-2007), [pdf]
  • Demner-Fushman D, et al. (2006) Finding Relevant Passages in Scientific Articles: Fusion of Automatic Approaches vs. an Interactive Team Effort. In Proceedings of the Text Retrieval Conference (TREC-2006), [pdf]
  • Aronson AR, et al. (2006) Fusion of knowledge-intensive and statistical approaches for retrieving and annotating textual genomics documents. In Proceedings of the Text Retrieval Conference (TREC-2005), [pdf]
  • Smith LH, Tanabe L, Rindflesch T and Wilbur WJ. (2005) MedTag: A Collection of Biomedical Annotations. In Proceedings of the ACL-ISMB Workshop on Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics, pp. 32-37. Detroit, June 2005. [pdf]
  • Smith L, Rindflesch T and Wilbur WJ. (2005) The Importance of the Lexicon in Tagging Biological Text. Natural Language Engineering, 12(2), 1-17. [pdf]
  • Smith LH. (2005) "Exploratory Genomic Data Analysis", in Medical Informatics, Knowledge Management and Data Mining in Biomedicine, Chen, H. et al., Eds., Springer, 2005. [book]
  • Aronson AR, et al. (2005) Knowledge-intensive and statistical approaches to the retrieval and annotation of genomics MEDLINE citations. In Proceedings of the Text Retrieval Conference (TREC-2004), NIST Special Publication 500-261. [pdf]
  • Smith L and Wilbur WJ. (2004) Retrieving definitional content for ontology development. Computational Biology and Chemistry, 28(2004), 387-391. [pdf]
  • Smith L, Rindflesch T and Wilbur WJ. (2004) MedPost: a Part of Speech Tagger for Biomedical Text. Bioinformatics, 20(14), 2320-2321. [pdf]
  • Yeganova L, Smith L and Wilbur WJ. (2004) Identification of related gene/protein names based on an HMM of name variations. Computational Biology and Chemistry, 28(2), 97-107. [pdf]
  • Kayaalp M, Aronson AR, Humphrey SM, Ide NC, Tanabe LK, Smith LH, Demner D, Loane RR, Mork JG, Bodenreider O. (2003) Methods for accurate retrieval of MEDLINE citations in functional genomics. In Proceedings of the Text Retrieval Conference (TREC-2003), NIST Special Publication 500-255, pp. 441-450. [pdf]
  • Smith L, Yeganova L and Wilbur WJ. (2003) Hidden Markov models and optimized sequence alignment. Computational Biology and Chemistry, 27(1), 77-84. [pdf]

    • Other Publications:

  • Smith LH. (2005) On ordering free groups. Journal of Symbolic Computation, 40(6), 1285-1290. [pdf]
  • Smith LH. (2005) Review of The Turing Test, Verbal Behavior as the Hallmark of Intelligence, by Stuart Shieber. Linguist List 16.1815. [web]
  • Lee JK, Bussey KJ, Gwadry FG, Reinhold W, Riddick G, Pelletier SL, Nishizuka S, Szakacs G, Annereau J-P, Shankavaram U, Lababidi S, Smith LH, Gottesman MN, Weinstein JN. (2003) Comparing cDNA and Oligonucleotide Array Data: Concordance of Gene Expression Across Platforms for the NCI-60 Cancer Cells. Genome Biol, 4(12), R82. [pdf]
  • Smith LH and Nelson DJ. (2002) Multiple-tube resonance model. In Proceedings of SPIE, 4791, pp. 33-42. [pdf]
  • Nelson DJ and Smith LH. (2002) Tuning Time-Frequency methods for the detection of metered HF speech. In Proceedings of SPIE, 4791, pp. 71-79. [pdf]
  • Zhou Y, Gwadry FG, Reinhold WC, Miller LD, Smith LH, Scherf U, Liu ET, Kohn KW, Pommier Y, Weinstein JN. (2002) Transcriptional Regulation of Mitotic Genes by Camptothecin-Induced DNA Damage: Microarray Analysis of Dose- and Time-Dependent Effects. Cancer Res, 62(6), 1688-1695. [pdf]
  • Weinstein JN, Scherf U, Lee JK, Nishizuka S, Gwadry F, Bussey AK, Kim S, Smith LH, Tanabe L, Richman S, Alexander J, Kouros-Mehr H, Maunakea A, Reinhold WC. (2002) The Bioinformatics of Microarray Gene Expression Profiling. Cytometry. 47(1), 46-49. [pdf]
  • Lee JK, Scherf U, Smith LH, Tanabe L, Weinstein JN. (2001) Analysis of gene expression data of the NCl 60 cancer cell lines using Bayesian hierarchical effects model. In Proceedings of SPIE, 4266, pp. 228-235. [pdf]
  • Scherf U, Ross DT, Waltham M, Smith LH, Lee JK, Tanabe L, Kohn KW, Reinhold WC, Myers TG, Andrews DT, Scudiero DA, Eisen MB, Sausville EA, Pommier Y, Botstein D, Brown PO and Weinstein JN. (2000) A Gene Expression Database for the Molecular Pharmacology of Cancer. Nature Genetics, 24(3), 236-244. [pdf]
  • Tanabe L, Smith LH, Lee JK, Scherf U, Hunter L and Weinstein JN. (1999) MedMiner: An internet tool for filtering and organizing biomedical information, with application to gene expression profiling. Biotechniques, 27, 1210-1217. [pdf]