Taner Z Sen

People
Assistant Professor (Collaborator/Affiliate Faculty)

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
taner@iastate.edu

Publications

  • Sen, T.Z., “Sampling errors: Aristotle’s suspect statistical skills”, Nature, 513(7518), 315, 2014. (comment)
  • Walsh, J.R., Sen, T.Z., Dickerson, J.A., “A computational platform to maintain and migrate manual functional annotations for BioCyc databases”, BMC Systems Biology, 8(1):115, 2014.
  • Ilgu, M., Fulton, B.D., Yennamalli, R.M., Lamm, M.H., Sen, T.Z., Nilsen-Hamilton, M., “An adaptable pentaloop defines a robust neomycin-B RNA aptamer with conditional Ligand-bound structures”, RNA, 20, 815-824, 2014.
  • Yennamalli, R.M., Rader, A.J., Kenny, A.J., Wolt, J.D., Sen, T.Z., “Endoglucanases: Insights into Thermostability and Biofuel Applications”, Biotechnology for Fuels, 6:136, 2013. (review)
  • Andorf, C.M., Honavar, V., Sen, T.Z., “”Predicting the binding patterns of hub proteins:  A case study using yeast protein interaction networks”, PLoS ONE, 8(2):e56833, 2013.
  • Monaco, M.K., Sen, T.Z., Dharmawardhana, P.D., Ren, L., Schaeffer, M., Naithani, S., Amarasinghe, V., Thomason, J., Harper, L., Gardiner, J., Cannon, E.K.S., Lawrence, C.J., Ware, D., Jaiswal, P., “Maize Metabolic Network Construction and Transcriptome Analysis”, The Plant Genome, 6(1), 2013.
  • Panos, M., Sen, T.Z., Ahunbay, M.G., “Molecular Simulation of Fibronectin Adsorption onto Polyurethane Surfaces”, Langmuir, 34, 12619-28, 2012.
  • Rader, A.J., Yennamalli, R.M., Harter, A.K., Sen, T.Z., “A rigid network of long-range contacts increases thermostability in a mutant endoglucanase”, Journal of Biomolecular Structure and Dynamics, 30(6), 628-637,2012.
  • Cannon, E.K., Birkett, S.M., Braun, B.L., Kodavali, S., Jennewein, D.M., Yilmaz, A., Antonescu, V., Antonescu, C., Harper, L.C., Gardiner, J.M., Schaeffer, M.L., Campbell, D.A., Andorf, C.M., Andorf, D., Lisch, D., Koch, K.E., McCarty, D.R., Quackenbush, J., Grotewold, E., Lushbough, C.M., Sen, T.Z., Lawrence, C.J., “POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data”, International Journal of Plant Genomics, 2011:923035, 2011.
  • Yennamalli, R.M., Wolt, J.D., Sen, T.Z., “Dynamics of endoglucanase catalytic domains: implications towards thermostability”, Journal of Biomolecular Structure and Dynamics, 29(3), 509-526, 2011.
  • Schaeffer, M.L., Harper, L.C., Gardiner, J., Andorf, C.M., Campbell, D.A., Cannon, E.K.S., Sen, T.Z., Lawrence, C.J., “MaizeGDB: curation and outreach go hand-in-hand”, Database: The Journal of Biological Databases and Curation, doi: 10.1093/database/bar022, 2011.
  • Harper, L.C., Schaeffer, M.L., Thistle, J.,Gardiner, J., Andorf, C.M., Campbell, D.A., Cannon, E.K.S., Braun, B.L., Birkett, S., Lawrence, C.J., Sen, T.Z., “The MaizeGDB Genome Browser Tutorial: One Example of Database Outreach to Biologists via Video”, Database: The Journal of Biological Databases and Curation, doi: 10.1093/database/bar016, 2011.
  • Yennamalli R.M., Rader A.J., Wolt J.D., Sen T.Z., “Thermostability in Endoglucanases is Fold-Specific”, BMC Structural Biology, 11(1):10, 2011.
  • International Arabidopsis Informatics Consortium (Sen T.Z. and 50 other authors), “An International Bioinformatics Infrastructure to Underpin the Arabidopsis Community”, Plant Cell, 22(8), 2530-2536. 2010.
  • Sen T.Z., Harper L.C., Schaeffer M.L., Seigfried, T.E., Andorf, C.M., Lawrence C.J, “Choosing a Genome Browser for a Model Organism Database (MOD): Surveying the Maize Community”, Database: The Journal of Biological Databases and Curation, doi: 10.1093/database/baq007, 2010.
  • Andorf, C.M., Harper L.C., Schaeffer M.L., Seigfried, T.E., Andorf, C.M., Lawrence C.J, Sen, T.Z. “The Locus Lookup Tool at MaizeGDB: Identification of Genomic Regions in Maize by Integrating Sequence Information with Physical and Genetic Maps”, Bioinformatics, 26, 434-436, 2010.
  • Sen T.Z., Andorf C.M., Schaeffer M.L., Harper L.C., Sparks M.E., Duvick J., Brendel V.P., Cannon, E., Campbell D.A., Lawrence C.J., “MaizeGDB becomes ‘sequence-centric’”, Database, 2009; doi: 10.1093/database/bap020.
  • Kurkcuoglu O, Doruker P., Sen T.Z., Kloczkowski, A., Jernigan R.L., “The ribosome shape directs mRNA translocation through entrance and exit dynamics”, Physical Biology, 5(4), 40005, 2008.
  • Lawrence, C. J., Harper, L.C., Schaeffer, M.L., Sen, T.Z., Seigfried, T.E., Campell, D.A., “MaizeGDB: the Maize Model Organism Database for Basic, Translational, and Applied Research”, International Journal of Plant Genomics, 2008.
  • Sen, T.Z., Kloster, M., Kloczkowski, A., Kolinski, A., Bujnicki, J.M., Jernigan, R.L., “Structure prediction and normal mode analysis of the outer membrane transporter FecA”, Biophysical Journal, 94(7), 2482–2491, 2008.
  • Sulkowska, J.I., Kloczkowski, A., Sen, T.Z., Cieplak, M., Jernigan, R.L. “Predicting the order in which contacts are broken during single molecule protein stretching experiments”, Proteins, 71, 45-60, 2008.
  • Cheng, H., Sen, T.Z., Jernigan, R.L., Kloczkowski, A., “Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: Combining GOR V and Fragment Database Mining (FDM)”, Bioinformatics, 23(19), 2628-2630, 2007.
  • Peto, M., Sen, T.Z., Jernigan, R.L., Kloczkowski, A., “Generation and enumeration of compact conformations on the 2D triangular and 3D fcc lattices”, Journal of Chemical Physics, 127(4):044101, 2007.
  • Mark, J.E, Abou-Hussein, R., Sen, T.Z., Kloczkowski, A., “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, 256, 40-47, 2007.
  • 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.
Education: 
B.S., Bogazici University, 1996
M.S., Bogazici University, 1998
Ph.D., University of Akron, 2003
Contact
515-294-5326
1025 Crop Genome Informatics Lab
Ames
IA
50011-