IBM Skip to main content
  Home     Products & services     Support & downloads     My account  
  Select a country  
Journals Home  
  Systems Journal  
  ·  Current Issue  
  ·  Recent Issues  
  ·  Papers in Progress  
  ·  Search/Index  
  ·  Orders  
  ·  Description  
  ·  Author's Guide  
Journal of Research
and Development
  Staff  
  Contact Us  
  Related links:  
     IBM Life Sciences  
     GeneMine  
IBM Systems Journal  
Volume 40, Number 2, 2001
Deep computing for the life sciences
 Table of contents: arrowHTML arrowPDF arrowASCII   This article: arrowHTML arrowPDF arrowASCII arrowCopyright info
   

The GeneMine system for genome/proteome annotation and collaborative data mining - References
by C. Lee and K. Irizarry

Cited references

  1. C. Lee, LOOK: A Software System for Integrated Macromolecular Sequence—Structure Analysis and Modeling, Molecular Applications Group, Palo Alto, CA (1993).
  2. M. Mueller and C. Lee, The GeneMine System for Automated Gene Function Analysis and Rich Structure-Function Annotation, Molecular Applications Group, Palo Alto, CA (1995).
  3. C. Marcazzo et al., “Identifying Gene Function and Features Through Comprehensive Automated Analysis,” Hilton Head Conference (1997).
  4. S. F. Altschul et al., “Basic Local Alignment Search Tool,” Journal of Molecular Biology 215, 403–410 (1990).
  5. K. H. Buetow, M. N. Edmonson, and A. B. Cassidy, “Reliable Identification of Large Numbers of Candidate SNPs from Public EST Data,” Nature Genetics 21, 323–325 (1999).
  6. K. Irizarry et al., “Genome-Wide Analysis of Single-Nucleotide Polymorphisms in Human Expressed Sequences,” Nature Genetics 26, 233–236 (2000).
  7. R. Durbin and J. Thierry Mieg, A C. elegans Database, Medical Research Council, Cambridge, UK (1991).
  8. V. M. Markowitz and O. Ritter, “Characterizing Heterogeneous Molecular Biology Database Systems,” Journal of Computational Biology 2, 547–556 (1995).
  9. S. B. Davidson et al., “BioKleisli: A Digital Library for Biomedical Researchers,” Journal of Digital Libraries 1, 36–53 (1997).
  10. L. C. J. Bailey et al., “GAIA: Framework Annotation of Genomic Sequence,” Genome Research 8, 234–250 (1998).
  11. A. Kosky, E. Szeto, and V. M. Markowitz, OPM Data Management Tools for CORBA Compliant Environments, Lawrence Berkeley National Laboratories, Berkeley, CA (1996).
  12. T. Gaasterland and C. W. Sensen, “MAGPIE: Automated Genome Interpretation,” Trends in Genetics 12, 76–78 (1996).
  13. D. Frishman and H.-W. Mewes, “PEDANTic Genome Analysis,” Trends in Genetics 13, 415–416 (1997).
  14. M. A. Andrade et al., “Automated Genome Sequence Analysis and Annotation,” Bioinformatics 15, 391–412 (1999).
  15. V. Brusic and J. Zeleznikow, “Knowledge Discovery and Data Mining in Biological Databases,” Knowledge Engineering Review 14, 257–277 (1999).
  16. M. S. Chen, J. Han, and P. S. Yu, Data Mining: An Overview from Database Perspective, IBM T. J. Watson Research Center, Yorktown Heights, NY (1996).
  17. M. Hansen, D. Meads, and A. Pang, “Comparative Visualization of Structure-Sequence Alignments,” IEEE Conference on Information Visualization, Research Triangle Park, NC (1998).
  18. D. A. Payne et al., “OmniViz Pro: Applying Multiple Interactive Visualizations for the Life and Chemical Sciences,” IEEE Conference on Information Visualization, Salt Lake City, UT (2000).
  19. C. Lee and S. Subbiah, “Prediction of Protein Side-Chain Conformation by Packing Optimization,” Journal of Molecular Biology 217, 373–388 (1991).
  20. M. Levitt, “Accurate Modeling of Protein Conformation by Automatic Segment Matching,” Journal of Molecular Biology 226, 507–533 (1992).
  21. C. Lee, “Predicting Protein Mutant Energetics by Self-Consistent Ensemble Optimization,” Journal of Molecular Biology 236, 918–939 (1994).
  22. Y. Wang et al., “Cn3D: Sequence and Structure Views for Entrez,” Trends in Biochemical Sciences 25, 300–302 (2000).
  23. S. B. Needleman and C. D. Wunsch, “A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins,” Journal of Molecular Biology 48, 443–453 (1970).
  24. T. F. Smith and M. S. Waterman, “Identification of Common Molecular Subsequences,” Journal of Molecular Biology 147, 195–197 (1981).
  25. M. S. Boguski, T. M. Lowe, and C. M. Tolstoshev, “dbEST—Database for 'Expressed Sequence Tags',” Nature Genetics 4, 332–333 (1993).
  26. A. Bairoch, P. Bucher, and K. Hofmann, “The PROSITE Database, Its Status in 1995,” Nucleic Acids Research 24, 189–196 (1995).
  27. A. G. Murzin et al., “SCOP: A Structural Classification of Proteins Database for the Investigation of Sequences and Structures,” Journal of Molecular Biology 247, 536–540 (1995).
  28. J. I. Garrels, “YPD—A Database for the Proteins of Saccharomyces Cerevisiae,” Nucleic Acids Research 24, 46–49 (1996).
  29. C. A. Orengo et al., “CATH—A Hierarchic Classification of Protein Domain Structures,” Structure 5, 1093–1108 (1997).
  30. A. Bairoch and R. Apweiler, “The SWISS-PROT Protein Sequence Data Bank and Its Supplement TrEMBL in 1998,” Nucleic Acids Research 26, 38–42 (1998).
  31. K. Nakai and P. Horton, “PSORT: A Program for Detecting Sorting Signals in Proteins and Predicting Their Subcellular Localization,” Trends in Biochemical Sciences 24, 34–36 (1999).
  32. E. L. Sonnhammer, G. von Heijne, and A. Krogh, “A Hidden Markov Model for Predicting Transmembrane Helices in Protein Sequences,” Proceedings of the 6th International Conference on Intelligent Systems for Molecular Biology (ISMB) 6, 175–182 (1998).
  33. S. Henikoff and J. G. Henikoff, “Protein Family Classification Based on Searching a Database of Blocks,” Genomics 19, 97–107 (1994).
  34. F. Corpet et al., “ProDom and ProDom-CG: Tools for Protein Domain Analysis and Whole Genome Comparisons,” Nucleic Acids Research 28, 267–269 (2000).
  35. W. M. Gelbart et al., “FlyBase: A Drosophila Database. The FlyBase Consortium,” Nucleic Acids Research 25, 63–66 (1997).
  36. W. R. Pearson and D. J. Lipman, “Improved Tools for Biological Sequence Comparison,” Proceedings of the National Academy of Sciences (USA) 85, 2444–2448 (1988).
  37. K. Hofmann et al., “The PROSITE Database, Its Status in 1999,” Nucleic Acids Research 27, 215–219 (1999).
  38. K. L. B. Borden and P. S. Freemont, “The RING Finger Domain: A Recent Example of a Sequence-Structure Family,” Current Opinion in Structural Biology 6, 395–401 (1996).
  39. L. H. Castilla et al., “Mutations in the BRCA1 Gene in Families with Early-Onset Breast and Ovarian Cancer,” Nature Genetics 8, 387–391 (1994).
  40. L. S. Friedman et al., “Confirmation of BRCA1 by Analysis of Germline Mutations Linked to Breast and Ovarian Cancer in Ten Families,” Nature Genetics 8, 399–404 (1994).
  41. M. Pantoliano et al., “Multivalent Ligand-Receptor Binding Interactions in the Fibroblast Growth Factor System Produce a Cooperative Growth Factor and Heparin Mechanism for Receptor Dimerization,” Biochemistry 10229–10248 (1994).
  42. P. Sengupta, H. A. Colbert, and C. L. Bargmann, “The C. elegans Gene odr-7 Encodes an Olifactory-Specific Member of the Nuclear Receptor Superfamily,” Cell 79, 971–980 (1994).
  43. J. J. Chou et al., “Solution Structure of the RAIDD CARD and Model for CARD/CARD Interaction in Caspase-2 and Caspase-9 Recruitment,” Cell 94, 171–180 (1998).
  44. C. Oxvig and T. A. Springer, “Experimental Support for a Beta-Propeller Domain in Integrin Alpha-Subunits and a Calcium Binding Site on Its Lower Surface,” Proceedings of the National Academy of Sciences (USA) 95, 4870–4875 (1998).
  45. M. J. Shields et al., “The Effect of Human 2-Microglobulin on Major Histocompatibility Complex I Peptide Loading and the Engineering of a High Affinity Variant: Implications for Peptide-Based Vaccines,” Journal of Biological Chemistry 273, 28010–28018 (1998).
  46. J. M. Goldberg and R. L. Baldwin, “A Specific Transition State for S-peptide Combining with Folded S-protein and Then Refolding,” Proceedings of the National Academy of Sciences (USA) 96, 2019–2024 (1999).
About IBM | Privacy | Legal | Contact