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Drena L. Dobbs
Professor

Drena Dobbs

Professor Dobbs received her B.S. in Biology from the University of Georgia in 1977 and her Ph.D. in Molecular Biology from the University of Oregon in 1983. She received an NIH Postdoctoral Fellowship in 1984, and worked with Elizabeth Blackburn at the University of California, Berkeley. Dr. Dobbs joined Iowa State University in 1987. From 1999 through 2001, she served as the first Chair of the Bioinformatics and Computational Biology (BCB) Graduate Program at ISU. Currently, she serves as Director of ISU's NSF IGERT Training Program in Computational Molecular Biology

Research Description

Long-term research goals of the Dobbs group are to understand how proteins and nucleic acids achieve their functional three-dimensional structures and to elucidate mechanisms that determine recognition and regulate interactions among proteins, nucleic acids and other molecules in cells. We use both computational and wet-lab experimental approaches to explore the structure and function of important macromolecular complexes, in close collaboration with several groups at Iowa State, University of Minnesota, and Harvard University.

Current areas of focus include: development of novel antiviral therapies against HIV-1 and other lentiviruses; rational design of zinc finger proteins (ZFPs) as tools for genomic modification and gene therapy; prediction of epitopes and nucleic acid binding residues in proteins; and prediction and experimental validation of structural and functional effects of mutations and SNPs in proteins. For details, please visit the Dobbs Lab website: http://ddobbs.public.iastate.edu/

Contact Information

3112 Molecular Biology
Ames, IA 50011-3260
515-294-1112 voice
515-294-6755 fax

Web Site

http://ddobbs.public.iastate.edu/

Education

B.S., University of Georgia, 1977
Ph.D., University of Oregon, 1983

Publications

  • Towfic, F., Caragea, C., Dobbs, D., Honavar, V. In press. Struct-NB: Predicting protein-RNA binding sites using structural features. Int. J. Data Min Bioinform .
  • Fu, F., Sander, J.D., Maeder, M., Thibodeau-Beganny, S., Joung, J.K., Dobbs, D., Miller, L., Voytas, D.F. 2009. Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays. Nucleic Acids Res 37(D):279-283.
  • Sander, J.D., Zaback, P., Joung, J.K., Voytas, D.F., Dobbs, D. 2009. An affinity-based scoring scheme for predicting DNA-binding activities of modularly assembled zinc-finger proteins. Nucleic Acids Res 37:506-515.
  • Ihm, Y., Sparks, W.O., Lee, J.H., Cao, H., Culver, G., Carpenter, S., Wang, C.Z., Ho, K.M., Dobbs, D. 2009. Structural model of the Rev regulatory protein from equine infectious anemia virus . PLoS ONE 3:e4178.
  • Caragea, C., Sinapov, J., Dobbs, D., Honavar, V. 2008. Using global sequence similarity to enhance biological sequence labeling. IEEE Int. Conf. Bioinf. Biomed. (BIBM 2008) :104-111.
  • Lee, J.-H., Hamilton, M., Gleeson, C., Caragea, C., Zaback, P., Sander, J.D., Li, X., Wu, F., Terribilini, M., Honavar, V., Dobbs, D. 2008. Striking similarities in structure and nucleic acid binding sites of diverse telomerase proteins revealed by combining structure prediction and machine learning approaches. Pac. Symp. Biocomput. (PSB 2008) 13:501-512.
  • EL-Manzalawy, Y., Dobbs, D., Honavar, V. 2008. Predicting protective linear B-cell epitopes using evolutionary information. IEEE Int. Conf. Bioinf. Biomed. (BIBM 2008) :289-292.
  • EL-Manzalawy, Y., Dobbs, D., Honavar, V. . 2008. Predicting linear B-cell epitopes using string kernels. J. Mol. Recognit 21:243-255.
  • Maeder, ML., Thibodea-Beganny, S., Osiak, A., Wright, DA., Anthony, RM., Eichtinger, M., Jiang, T., Foley, JE., Winfrey, RJ., Townsend, JA., Unger-Wallace, E., Sander, JD., Dobbs, D., Cathomen, T., Voytas, DF., Joung, JK. 2008. Efficient gene modification modification enabled by an OPEN (Oligomerized Pool ENgineering) platform for constructing zinc finger nucleases. Mol. Cell 31:294-301.
  • Dunn-Thomas, T., Dobbs, D.L., Sakaguchi, D., Young, M.J., Honavar, V., Greenlee, H.M.W. 2008. Proteomic differentiation between murine retinal and brain derived progenitor cells. Stem Cells Dev 17:119-132.
  • Yan, C., Wu, F., Jernigan, R., Dobbs, D., Honavar, V. 2008. Characterization of protein-protein interfaces. Protein J 27:59-70.
  • El-Manzalawy, Y., Dobbs., Honavar, V. 2008. On evaluating MHC-II binding peptide prediction methods. PLoS ONE 3:e3268.
  • Lee, J.-H., Culver, G., Carpenter, S., Dobbs, D. 2008. Analysis of the EIAV Rev-responsive element (RRE) reveals a conserved RNA motif required for high affinity Rev binding in both HIV-1 and EIAV. PLoS ONE 3:e2272.
  • Wu, F., Towfic, F., Dobbs, D., Honavar, V . 2007. Analysis of protein-protein dimeric interfaces. In: Computational Structural Bioinformatics Workshop (CSBW), IEEE Int. Conf. Bioinf. Biomed. (BIBM 2007) :35-47.
  • Towfic, F., Gemperline, D.C., Caragea, C., Wu, F., Dobbs, D., Honavar, V. 2007. Structural characterization of RNA-binding sites of proteins: preliminary results. In: Computational Structural Bioinformatics Workshop (CSBW), IEEE Int. Conf. Bioinf. Biomed. (BIBM 2007) .
  • EL-Manzalawy, Y., Dobbs, D., Honavar, V. 2007. AUC-optimized protein sequence motifs. Comput. Syst. Bioinformatics Conf. (CSB 2007) .
  • Caragea, C., Sinapov, J., Honavar, V., Dobbs, D. 2007. Assessing the performance of macromolecular sequence classifiers. Proc. 7th IEEE Int. Conf. Bioinf. Bioeng. (BIBE 2007) :320-326.
  • Caragea, C., Sinapov, J., Silvescu, A., Dobbs, D., Honavar, V. 2007. Glycosylation site prediction using ensembles of support vector machine classifiers. BMC Bioinformatics 8:438.
  • Andorf, C., Dobbs, D., Honavar, V. 2007. Exploring inconsistencies in genome-wide protein function annotations. BMC Bioinformatics 8:284.
  • Terribilini, M., Sander, J., Lee, J.-H., Zaback, P., Jernigan, R., Honavar, V., Dobbs, D. 2007. RNABindR: A server for analyzing and predicting RNA binding sites in proteins. Nucleic Acids Res. (Web Server issue) 35:W578-584.
  • Sander, JD. Zaback, P., Joung, JK., Voytas, DF., Dobbs, D. 2007. Zinc Finger Targeter (ZiFiT): An engineered zinc finger/target site design tool . Nucleic Acids Res. (Web Server issue) 35:W599-605.
  • Wu, F., Olson, B., Dobbs, D., Honavar, V. 2006. Comparing kernels for predicting protein binding sites from amino acid sequence. IEEE Joint Conf. on Neural Networks, Vancouver (IJCNN 2006) :2921-2925.
  • Terribilini, M., Lee, J.H., Yan, C., Jernigan, R., Carpenter, S., Honavar, V., and Dobbs, D. 2006. Identifying interaction sites in "recalcitrant" proteins: Predicted protein and RNA binding sites in Rev proteins of HIV and EIAV agree with experimental data. Pac. Symp. Biocomput. (PSB06) 11:415-426.
  • Wright, D.A., Thibodeau-Beganny, S., Sander, J.D., Ronnie J. Winfrey, R.J., Hirsh, A.S., Eichtinger, M., Fu, F., Porteus, M.H, Dobbs, D., Voytas, D.F., Joung, J.K. 2006. Standardized reagents and protocols for engineering zinc finger nucleases by modular design assembly. Nature Protoc 1:1637-1652.
  • Cao H.B., Wang C.Z., Dobbs D, Ihm Y., Ho K.M. 2006. Codability criterion for picking protein-like structures from random three-dimensional configurations. Phys Rev E 74:031921.
  • Yan, C., Terribilini, M., Wu, F., Jernigan, R.L., Dobbs, D., Honavar, V. 2006. Predicting DNA-binding sites of proteins from amino acid sequence. BMC Bioinformatics 7:262.
  • Lee, J.H., Murphy, S.C., Belshan, M., Sparks, W.O., Wannemuehler, Y., Liu, S., Hope, T.J., Dobbs, D., Carpenter, S. 2006. Characterization of functional domains of equine infectious anemia virus Rev suggests a bipartite RNA-binding domain. J Virol 80:3844-3852.
  • Terribilini, M., Lee, J.H., Yan, C., Jernigan, R.L., Honavar, V., Dobbs, D. 2006. Prediction of RNA binding sites in proteins from amino acid sequence. RNA 12:1450-1462.
  • Lonosky, P.M., Zhang, X.,.Honavar, V.G., Dobbs, D.L., Fu A., and Rodermel, S.R. 2004. A proteomic analysis of chloroplast biogenesis in maize. Plant Physiol 134:560-574.
  • Cao H., Ihm Y., Wang, C.Z., Morris, J.R., Su, M., Dobbs, D. and Ho, K.M. 2004. Three-dimensional threading approach to protein structure recognition. Polymer 45:687-697.
  • Wang, X., Schroeder, D., Dobbs, D., and Honavar, V. 2003. Data-driven discovery of motif-based protein function classifiers. Information Sciences 155:1-18.