Dobbs Lab Publications (Recent)

2007

Sander, J. Zaback, P., Joung, J., Voytas, D., Dobbs, D. (2007)   Zinc Finger Targeter (ZiFiT):
An engineered zinc finger/target site design tool. Nucleic Acids Res., [Epub ahead of print]. In press.

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., [Epub ahead of print]. In press.

Andorf, C., Dobbs, D. and Honavar, V. (2007) Exploring inconsistencies in genome-wide protein function annotations. BMC Bioinformatics. In press.

EL-Manzalawy, Y., Dobbs, D., Honavar, V. (2007) PepMIL: A novel method for predicting flexible length MHC-II binding peptides. BMC Bioinformatics. In press

Yan, C., Wu, F., Jernigan, R., Dobbs, D. and Honavar, V. (2007) Characterization of protein-protein interfaces. Protein J. In press.

2006

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.

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. (free at PubMed Central)

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.

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.  

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.

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. 10th Pacific Symposium on Biocomputing. Hawaii (PSB 2006), v.11, pp. 415-426.

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), pp. 2921-2925.