Iowa State University

Department of Genetics, Development and Cell Biology

Dobbs Lab Publications (Recent)

2014

Walia, R.R., Xue, L.C., Wilkins, K., El-Manzalawy, Y., Dobbs, D., Honavar, V. (2014). RNABindRPlus: A Predictor that Combines Machine Learning and Sequence Homology-Based Methods to Improve the Reliability of Predicted RNA-Binding Residues in Proteins. PLoS ONE 9(5): e97725. doi:10.1371/journal.pone.0097725

 

2013

Muppirala, U.K., Lewis, B.A., Dobbs, D. (2013). Computational Tools for Investigating RNA-Protein Interaction Partners. Journal of Computer Science and Systems Biology 6, 182-187.

 

Xue, L.C., Jordan, R.A., El-Manzalawy, Y., Dobbs, D., Honavar, V. (2013). DockRank: Ranking docked conformations using partner-specific sequence homology-based protein interface prediction. Proteins: Structure, Function, and Bioinformatics

 

2012

Walia, R.R., Caragea, C., Lewis, B.A., Towfic, F.G., Terribilini, M., El-Manzalawy, Y., Dobbs, D., Honavar, V. (2012). Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art. BMC Bioinformatics 13, 89. (Highly accessed)

 

Jordan, R.A., El-Manzalawy, Y., Dobbs, D., Honavar, V. (2012). Predicting protein-protein interface residues using local surface structural similarity. BMC Bioinformatics 13, 41. (Highly accessed)

 

2011

Muppirala, U.K., Honavar, V., Dobbs, D. (2011). Predicting RNA-Protein Interactions Using Only Sequence Information. BMC Bioinformatics 12, 489. (Highly accessed)

 

Xue, L.C., Dobbs, D., Honavar, V. (2011). HomPPI: a class of sequence homology based protein-protein interface prediction methods. BMC Bioinformatics 12, 244.

 

Steczkiewicz, K., Zimmermann, M.T., Kurcinski, M., Lewis, B.A., Dobbs, D., Kloczkowski, A., Jernigan, R.L., Kolinski, A., Ginalski, K. (2011). Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization step. Proc Natl Acad Sci U S A 108, 9443-9448.

 

Sander JD, Dahlborg EJ, Goodwin MJ, Cade L, Zhang F, Cifuentes D, Curtin SJ, Blackburn JS, Thibodeau-Beganny S, Qi Y, Pierick CJ, Hoffman E, Maeder ML, Khayter C, Reyon D, Dobbs D, Langenau DM, Stupar RM, Giraldez AJ, Voytas DF, Peterson RT, Yeh JR, Joung JK (2011). Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nat Methods 8, 67-69.

 

Reyon, D., Kirkpatrick, J.R., Sander, J.D., Zhang, F., Voytas, D.F., Joung, J.K., Dobbs, D., Coffman, C.R. (2011). ZFNGenome: a comprehensive resource for locating zinc finger nuclease target sites in model organisms. BMC Genomics 12, 83. (Highly accessed)

 

Lewis, B.A., Walia, R.R., Terribilini, M., Ferguson, J., Zheng, C., Honavar, V., Dobbs, D. (2011). PRIDB: a Protein-RNA Interface Database. Nucleic Acids Res 39, D277-282.

 

EL-Manzalawy, Y., Dobbs, D., Honavar, V. (2011). Predicting MHC-II binding affinity using multiple instance regression. IEEE/ACM Trans Comput Biol Bioinform 8, 1067-1079.

 

Curtin SJ, Zhang F, Sander JD, Haun WJ, Starker C, Baltes NJ, Reyon D, Dahlborg EJ, Goodwin MJ, Coffman AP, Dobbs D, Joung JK, Voytas DF, Stupar RM. (2011). Targeted mutagenesis of duplicated genes in soybean with zinc-finger nucleases. Plant Physiol 156, 466-473.

 

 

2010

Zhang F, Maeder ML, Unger-Wallace E, Hoshaw JP, Reyon D, Christian M, Li X, Pierick CJ, Dobbs D, Peterson T, Joung JK, Voytas DF. (2010). High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases. Proc Natl Acad Sci U S A 107, 12028-12033.

 

Towfic, F., Caragea, C., Gemperline, D.C., Dobbs, D., Honavar, V. (2010). Struct-NB: predicting protein-RNA binding sites using structural features. Int J Data Min Bioinform 4, 21-43.

 

Sander JD, Reyon D, Maeder ML, Foley JE, Thibodeau-Beganny S, Li X, Regan MR, Dahlborg EJ, Goodwin MJ, Fu F, Voytas DF, Joung JK, Dobbs D (2010). Predicting success of oligomerized pool engineering (OPEN) for zinc finger target site sequences. BMC Bioinformatics 11, 543.

 

Sander, J.D., Maeder, M.L., Reyon, D., Voytas, D.F., Joung, J.K., Dobbs, D. (2010). ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool. Nucleic Acids Res 38, W462-468.

 

Carpenter, S., Dobbs, D. (2010). Molecular and biological characterization of equine infectious anemia virus Rev. Curr HIV Res 8, 87-93.

 

2009

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., 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 4, e4178.

 

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, D279-283.

 

Caragea, C., Sinapov, J., Dobbs, D., Honavar, V. (2009). Mixture of experts models to exploit global sequence similarity on biomolecular sequence labeling. BMC Bioinformatics 10 Suppl 4, S4.

 

2008

Yan, C., Wu, F., Jernigan, R.L., Dobbs, D., Honavar, V. (2008). Characterization of protein-protein interfaces. Protein J 27, 59-70.

 

Maeder ML, Thibodeau-Beganny S, Osiak A, Wright DA, Anthony RM, Eichtinger M, Jiang T, Foley JE, Winfrey RJ, Townsend JA, Unger-Wallace E, Sander JD,Müller-Lerch F, Fu F, Pearlberg J, Göbel C, Dassie JP, Pruett-Miller SM, Porteus MH, Sgroi DC, Iafrate AJ, Dobbs D, McCray PB Jr, Cathomen T, Voytas DF, Joung JK. (2008). Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification. Mol Cell 31, 294-301.

 

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 diverse telomerase proteins revealed by combining structure prediction and machine learning approaches. Pac Symp Biocomput, 13:501-512.

 

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.

 

El-Manzalawy, Y., Dobbs, D., Honavar, V. (2008). Predicting flexible length linear B-cell epitopes. Comput Syst Bioinformatics Conf 7, 121-132.

 

El-Manzalawy, Y., Dobbs, D., Honavar, V. (2008). Predicting linear B-cell epitopes using string kernels. J Mol Recognit 21, 243-255.

 

El-Manzalawy, Y., Dobbs, D., Honavar, V. (2008). On evaluating MHC-II binding peptide prediction methods. PLoS One 3, e3268.

 

Dunn-Thomas, T.E., Dobbs, D.L., Sakaguchi, D.S., Young, M.J., Honavar, V.G., Greenlee, M.H. (2008). Proteomic differentiation between murine retinal and brain-derived progenitor cells. Stem Cells Dev 17, 119-131.