Table of Contents

1. Lawrence Hunter

   Artificial Intelligence & Molecular Biology

- pp.1-46

2. Genomics and Its Impact on Medicine and Society a 2001 Primer

3. Mark D. Yandell & William H. Majoros

   Genomics and Natural Language Processing

- Nature Reviews Genetics, 2002

4. Lynette Hirschman, Jong C. Park, Junichi Tsujii, Limsoon Wong

  Accomplishments and Challenges in Literature Data Mining for Biology

- Bioinformatics, vol.18(12), pp1-12, 2002

5. Berry de Bruijn & Joel Martin

  Getting to the (C)ore of knowledge: mining biomedical literature

- International Journal of Medical Informatics, vol.67, pp.7-18, 2002

6. K. Fukuda, T. Tsunoda, A. Tamura, T. Takagi

  Toward Information Extraction: Identifying protein names from biological papers

- Pac Symp Biocomput, 1998

7. Lorraine Tanabe & W. John Wilbur

  Tagging gene and protein names in biomedical text

- Proceedings of the Workshop on Natural Language Processing in the Biomedical

  Domain, vol.18(8), pp. 1124-1132, 2002

8. Daniel Hanisch, Juliane Fluck, Heinz-theodor Mevissen

   Playing Biology's Name Game: Identifying Protein Names In Scientific Text

- Pacific Symposium on Biocomputing, January, 2003

9. K.Bretonnel Cohen, Andrew E. Dolbey, George K. Acpuaah-Mensah, Lawrence   

   Hunter

   Contrast And Variability In Gene Names

- Proceedings of the Workshop on Natural Language Processing in the Biomedical 

   Domain, pp.14-20, July 2003 

10. Jun'ichi Kazama, Takaki Makino, Yoshihiro Ohta, Jun'ichi Tsujii

   Tuning Support Vector Machines for Biomedical Named Enitiy Recognition

- Proceedings of the Workshop on Natural Language Processing in the Biomedical 

   Domain, pp.1-8, July 2002

11. James Thomas, David Milward, Christos Ouzounis, Stephen, Mark Carroll

    Automatic Extraction of Protein Interactions form Scientific Abstracts

  - Pac Symp Biocomput , 2002

12. B.J STAPLEY & G. BENOIT

    Biobibliometrics: Information Retrieval and Visualization From Co-occurrences of

    Gene Names in Medline Abstracts

  - Pac Symp Biocomput, pp.529-540, 2000

13. Akane Yakushiji, Yuka Tateisi, Yusuke Miyao

    Event Extraction from Biomedical Papers Using a Full Parser

  - Pac Symp Biocomput, 2001

14. J. Pustejovsky, J. Castano, J. Zhang     

   Robust Relational parsing over Biomedical Literature: Extracting Inhibit Relations

  - Pac Symp Biocomput, pp.505-516, 2002

15. Jong C. Park, Hyun Sook Kim, Jung Jae Kim

    Bidirectional Incremental Parsing for Automatic Pathway Identification with 

    Combinatory Categorial Grammar

  - Pac Symp Biocomput, 2001

16. Kevin Humphreys, George Demetriou, Robert Gaizauskas

    Two Applications of Information Extraction to Biological Science Journal

    Articles: Enzyme Interactions and Protein Structures

  - Pac Symp Biocomput, 2002

17. Vasileios Hatzivassiloglou, Pablo A. Duboue and Andrey Rzhetsky

    Disambiguating Proteins, Genes, and RNA in text: A Machine Learning Approach

  - Bioinformatics, vol.17 Suppl 1: S97-S106, 2001

18. L. Tanabe, U. Scherf, L.H. Smith, J.K. Lee, L. Hunter, J.N. Weinstein

   MedMiner: An Internet Text-Mining Tool for Biomedical Information, with

    Application to Gene Expression profiling

  - Biotechnipues, vol.27(6): 1210-4, 1216-7, December 1999

19. Limsoon Wong

    PIES, a Protein Interaction Extraction System

  - Pac Symp Biocomput, pp.520-531, 2001

20. Thomas C. Rindflesch, Lorraine Tanabe, John N. Weinstein

    Edgar: Extraction of Drugs, Genes and Relations form the Biomedical Literature

  - Pac Symp Biocomput, pp.517-528, 2000

21. G. Leroy, H. Chen

    Filling Preposition-Based Templates to Capture Information from Medical

    Abstracts

  - Pac Symposium on Biocomputing, 2002

22. See-Kiong Ng, Marie Wong

    Toward Routine Automatic Pathway Discovery from On-line Scientific Text     

    Abstracts

- Genome Informatics, vol.10: 104-112, 1999

23. Carol Friedman, Pauline Kra, Hong Yu, Michael Krauthammer, Andrey Rzhetsky

    Genies: a Natural-language Processing system for the Extraction of Molecular

    pathways from journal articles

  - Bioinformatics, vol.17 Suppl. 1,  pp.S74-S82, 2001

24. Betsy L. Humphreys, MLS, Donald A. B. Lindberg, MD Harold M. Schoolm

    and G. Octo Barnett, MD

    The Unified Medical Language System: an Informatics Research Collaboration

  - J Am Med Inform Assoc, vol.5(1): 1-11, January 1998

25. M. Ashburner, Catherine A. Ball, Judith A. Blake, David Botstein, Heather       

    Butler, J. Michael Cherry, Allan P. Davis, Kara Dolinski, Selina S. Dwight, Janan 

    T. Eppig, Midori A. Harris, David P. Hill, Laurie Lssel-Tarver, Andrew         

    Kasarskis, Suzanna Lewis, John C. Matese, Joel E. Richardson, Martin Ringwald, 

    Gerald M. Rubin, Gavin Sherlock

    Gene ontology: Tool for the unification of biology

  - Nat Genet, vol.25(1), pp.25-29, 2000

26. Wolfgang Fleischmann, Steffen Moller, Alain Gateau, Rolf Apweiler

    A Novel Method for Automatic Functional Annotation of Proteins

  - Bioinformatics, vol.15(3), pp.228-233, 1999

27.  I. N. Sarkar, M.N. C무색, R. Gelman, F. Hartel, Y.A. Lussier

     Linking Biomedical Language Information and Knowledge Resources: Go and   

     Umls

  - Pacific Symposium on Biocomputing, January 2003

28. Frank Eisenhaber & Peer Bork

    Evaluation of Human-readable Annotation in Biomolecular Sequence Databases  

    with Biological Rule Libraries

  - Bioinformatics, vol.15, pp.528-535, 1999

29. Soumya Raychaudhuri, Jeffey T. Chang, Patrick D. Sutphin, Russ B. Altman

    Associating Genes with Gene Ontology Codes Using a Maximum Entropy        

    Analysis of Biomedical Literature

- Genome Res, vol.12(1), pp.203-214, 2002

30. Jeffey T. Chang, Soumya Raychaudhuri, Russ B.

    Including Biological Literature Improves Homology Search

  - Pac Symp Biocompt, pp.374-383, 2001

31. George Hripcsak, MD, Gilad J. Kuperman, Md, PhD, carol Friedman, PhD, Daniel 

    F. Heitjan, PhD

    A Reliability Study for Evaluating Information Extraction from Radiology Reports

  - J Am Med Inform Assoc. vol.6(2), pp,143-150, 1999

32. Udohahn Martin Romacker & Stefan Schulz

    Creating Knowledge Repositories from Biomedical Reports: the Medsyndikate   

    Text Mining System

-  Pacific Symposium on Biocomputing, 2002

33.  B.J. Stapley, L.A. Kelley, M.J.E. Sternberg

     Predicting The Sub-Cellular Location of Proteins from Text Using Support     

     Vector Machines

  - Pac Symp Biocomput, 2002

34. Olivier Bodenrdider, Thomas C. Rindflesch, Anita Burgun

    Unsupervised, Corpus-based Method for Extending a Biomedical Terminology   

  - Proceedings of the Workshop on Natural Language Processing in the Biomedical 

    Domain, pp53-56, July 2002

35. Olivier Bodenreider, Anita Burgun, Thomas C. Rindflesch

   Assessing the Consistency of a biomedical Terminology Through Lexical        

    Knowledge

- International Journal of Medical Informatics, vol.67, pp.85-95, 2002

36. Ariel S. Schwartz, Marti A. Hearst

    A Simple Algorithm for Identifying Abbreviation Definitions Biomedical Text

- Pac Symp Biocomput, pp.451-462, 2003

37. Shin-ichi Usuzaka, Kim Lan Sim, Miyako Tanaka, Hiroshi Matsuno, Satoru      

    Miyano

    A Machine Learning Approach to Reducing the Work of Experts in Article      

    Selection form Database: A Case Study for Regulatory Relations of S. cerevisiae 

    Genes in MEDLINE

-  Genome Inform Ser Workshop Genome Inform, vol.9, pp.91-101, 1998

38. Javier Tamames, Dominic Clark, Javier Herrero, Joaquin Dopazo, Christian      

    Blaschke, Jose M. Fernandez, Juan C. Oliveros, Alfonso Valencia

    Bioinformatics Methods for the Analysis of Expression Arrays: Data Clustering  

    and Information Extraction

-  Journal of Biotechnology, vol.98, pp.269-283, 2002

39. Hagit Shatkay, Stephen Edwards, W. John Wilbur, Mark Boguski

    Genes, Themes and Microarrays Using Information Retrieval for Large-scale    

    Gene Analysis

  - ISMB 2000