Publications

Bada, M. and Hunter, L. (2006) Enrichment of OBO Ontologies. Accepted into Journal of Biomedical Informatics. [doc]

Lu, Z., Bada, M., Ogren, P., Cohen, K., and Hunter, L. (2006) Improving biomedical corpus annotation guidelines. Proceedings of the Joint BioLINK and 9th Bio-Ontologies Meeting. [pdf]

Johnson, H. L., Cohen, K. B., Baumgartner, Jr., W. A., Lu Z., Bada, M., Kester, T., Kim, H., and Hunter, L. (2006) Evaluation of Lexical Methods for Detecting Relationships Between Concepts from Multiple Ontologies. Proceedings of the Pacific Symposium on Biocomputing 11, 28-39. [PubMed]

Bada, M., Turi, D., McEntire, R., and Stevens, R. (2004) Using Reasoning to Guide Annotation with Gene Ontology Terms in GOAT. ACM SIGMOD Record 33(2), 27-32. [pdf]

Bada, M., Stevens, R., Goble, C., Gil., Y., Ashburner, M., Blake, J. A., Cherry, J. M., Harris, M., and Lewis, S. (2004) A short study on the success of the Gene Ontology. Journal of Web Semantics 1(2), 235-240. [pdf]

Bada, M., McEntire, R., Wroe, C., and Stevens, R. (2003) GOAT: The Gene Ontology Annotation Tool. Proceedings of the 2003 UK e-Science All Hands Meeting, 514-519. [pdf]

Gabashvili, I. S., Whirl-Carrillo, M., Bada, M., Banatao, D. R., and Altman, R. B. (2003) Ribosomal dynamics inferred from variations in experimental measurements. RNA 9, 1301-1307. [PubMed]

Whirl-Carrillo, M., Gabashvili, I. S., Bada, M., Banatao, D. R., and Altman, R. B. (2002) Mining biochemical information: Lessons taught by the ribosome. RNA 8, 279-289. [PubMed]

Bada, M. A. and Altman, R. B. (2000) Computational Modeling of Structural Experimental Data. Methods of Enzymology 317, 470-491. [pdf]

Bada, M., Walther, D., Arcangioli, B., Doniach, S., and Delarue, M. (2000) Solution structural studies and low-resolution model of the Schizosaccharomyces pombe sap1 protein. Journal of Molecular Biology 300, 563-574. [PubMed]

Altman, R. B., Bada, M., Chai, X. J., Carillo, M. W., Chen, R. O., and Abernethy, N. F. (1999) RiboWeb: An Ontology-Based System for Collaborative Molecular Biology. IEEE Intelligent Systems, September/October 1999, 68-76. [pdf]

Sayre, L. M., Naismith, R. T., 2nd, Bada, M. A., Li, W. S., Klein, M. E., and Tennant, M. D. (1996) trans-2-phenylcyclopropylamine is a substrate for and inactivator of horseradish peroxidase. Biochimica et Biophysica Acta 1296, 250-256. [PubMed]