faculty & research

Home Page >Faculty & Research  

Taner Z. Sen
Assistant Professor (Collaborator)

Taner Sen

Research Description

Analysis, interpretation, and representation of maize genetic and genomic data; protein sequence and structure-based methods to understand function as part of the elaborate networks of cellular interactions; protein modeling and dynamics to elucidate structure-function relationships; development and improvement of secondary and tertiary structure prediction methods; protein-protein binding site predictions; structural and functional interpretations of protein-protein interaction networks.

Contact Information

1025 Crop Genome Informatics Lab
Ames, IA 50011
515-294-5326 voice

Web Site

http://www.public.iastate.edu/~taner/

Education

B.S., Bogazici University, 1996
M.S., Bogazici University, 1998
Ph.D., University of Akron, 2003

Publications

  • Cheng, H., Sen, T.Z., Jernigan, R.L., Kloczkowski, A. 2007. Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: Combining GOR V and Fragment Database Mining (FDM). Bioinformatics, in press .
  • Myron, P., Sen, T.Z., Jernigan, R.L., Kloczkowski, A. 2007. Generation and enumeration of compact conformations on the 2D triangular and 3D fcc lattices. Journal of Chemical Physics, in press .
  • Sulkowska, J.I., Kloczkowski, A., Sen, T.Z., Cieplak, M., Jernigan, R.L.. 2007. Predicting the order in which contacts are broken during single molecule protein stretching experiments. Proteins, in press .
  • Mark, J.E, Abou-Hussein, R., Sen, T.Z., Kloczkowski, A. 2007. Monte Carlo Simulations on Nanoparticles in Elastomers. Effects of the Particles on the Dimensions of the Polymer Chains and the Mechanical Properties of the Networks. Macromolecular Symposia, in press .
  • Sen, T.Z., Kloczkowski, A., Jernigan, R.L. 2006. A DNA-centric look at protein-DNA complexes. Structure 14(9):1341-1342.
  • Sen, T.Z., Cheng, H., Kloczkowski, A., Jernigan, R.L.. 2006. The Consensus Data Mining (CMD) secondary structure prediction method by combining GOR V and Fragments Database Mining. Protein Science 15:2499-2506.
  • Sen, T.Z., Kloczkowski, A., Jernigan, R.L. 2006. Functional clustering of yeast proteins from the protein-protein interaction network. BMC Bioinformatics 7(355).
  • Sen, T.Z., Feng, Y., Garcia, J.V., Kloczkowski, A., Jernigan, R.L.. 2006. The extent of cooperativity of protein motions observed with elastic network models is similar for atomic and coarser-grained models. Journal of Chemical Theory and Computation 2:696-704.
  • Sharaf, M.A., Kloczkowski, A., Sen, T.Z., Jacob, K.I., Mark, J.E.. 2006. Molecular Modeling of Matrix Chain Deformation in Nanofiber Filled Composites. Colloid and Polymer Science 284(7):700-709.
  • Sharaf, M.A., Kloczkowski, A., Sen, T.Z., Jacob, K.I., Mark, J.E.. 2006. Filler-induced deformations of amorphous polyethylene chains. The effects of the deformations on elastomeric properties, and some comparisons with experiments. European Polymer Journal 42:796-806.
  • Fernandez, A., Tawfik, D.S., Berkhout, B., Sanders, R., Kloczkowski, A., Sen, T.Z., Jernigan, R..L.. 2005. Protein Promiscuity: Drug Resistance and Native Functions -- HIV-1 Case. J. Biomol. Struct. Dyn. 22(6):615-624.
  • Sen, T.Z., Jernigan, R.L., Garnier, J., Kloczkowski, A.. 2005. The GOR V server for protein secondary structure assignment. Bioinformatics 21(11):2787-2788.
  • Cheng, H., Sen, T.Z., Kloczkowski, A., Margaritis, D., Jernigan, R.L.. 2005. Prediction of protein secondary structure by mining fragments database. Polymer 46:4314-4321.
  • Mark, J.E, Abou-Hussein, R., Sen, T.Z., Kloczkowski, A.. 2005. Some simulations on filler reinforcement in elastomers. Polymer 46(21):8894-8904.
  • Sen, T.Z., Sharaf, M.A., Mark, J.E., Kloczkowski, A.. 2005. Modeling the elastomeric properties of stereoregular polypropylenes in nanocomposites with spherical fillers. Polymer 46(18):Polymer.
  • Kloczkowski, A., Sen, T.Z., Sharaf, M.A.. 2005. The largest eigenvalue method for stereo-regular vinyl chains. Polymer 46:4373-4383.
  • Sen, T.Z., Kloczkowski, A., Jernigan, R.L., Yan, C., Honavar, V., Ho, K.-M., Wang, C.-Z., Ihm, Y., Cao, H., Gu, X, Dobbs, D.. 2004. Predicting binding sites of hydrolase-inhibitor complexes by combining several methods. BMC Bioinformatics 5(205).
  • Varshney, V., Dirama, T.E., Sen, T.Z., Carri, G.A.. 2004. A Minimal Model for the Helix-Coil Transition of Worm-like Polymers. Insights from Monte Carlo Simulations and Theoretical Implications. Macromolecules 37:8794-8804.
  • Kloczkowski, A., Sen,T.Z., Jernigan, R.L.. 2004. The transfer matrix method for lattice proteins-an application with cooperative interactions. Polymer 45:707-716.
  • Valladares, D., Toki, S., Sen, T.Z., Yalcin, B., Cakmak, M.. 2002. Real time birefringence, true stress and true strain behavior of natural rubber: Effect of crosslink density. Macromolecular Symposia 185:149-166.
  • Konuklar, F. A. S., Aviyente, V., Sen, T.Z., Bahar, I.. 2001. Modeling the deamidation of asparagine residues via succinimide intermediates. Journal of Molecular Modeling 7(5):147-160.
  • Sen, T. Z., Bahar, I., Erman, B., Lauprêtre, F., Monnerie, L.. 1999. Local chain dynamics of cis-1,4-polybutadiene and cis-1,4-polyisoprene. A comparative study based on Cooperative Kinematics theory and NMR experiments. Macromolecules 32:3017-3024.