Theoretical and computational biophysical chemistry; developing new computational methods and models to study nucleic acids; drug design targeting RNA molecules causing genetic disease (such as Huntington Disease, Myotonic Dystrophy, and Fragile X-Syndrome); investigating properties of microRNA/AGO complex; force field development for modified RNA residues; interactions of transcription factors with DNA; DNA based nanomaterials.

Yildirim, I., Chakraborty, D., Disney, M. D., Wales, D. J., and Schatz, G. C., “Computational Investigation of RNA CUG repeats responsible for Myotonic Dystrophy 1”, J. Chem. Theory Comput. 11, 4943–4958, 2015 . http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00728 Philips, S. J., Hernandez, M. C., Yildirim, I., Schatz, G. C., Mondragón, A., O’Halloran, T. V., “Allosteric Transcriptional Regulation via Changes in the Overall Topology of the Core Promoter”, Science 349, 877-881, 2015. http://www.sciencemag.org/content/349/6250/877.short Yildirim, I., Kierzek, E., Kierzek, R., and Schatz, G. C., “Interplay of LNA and 2ʹ-O-methyl RNA in the structure and thermodynamics of RNA hybrid systems: A molecular dynamics study using revised AMBER force field and comparison to experimental results”, J. Phys. Chem. B 118, 14177–14187, 2014. http://pubs.acs.org/doi/abs/10.1021/jp506703g Yildirim, I., Eryazici, I., Nguyen, S. T., Schatz, G. C., “Hydrophobic Organic Linkers in the Self-assembly of Small Molecule-DNA hybrid Dimers: A Computational-Experimental Study of the Role of Linkage Direction in Product Distributions and Stabilities”, J. Phys. Chem. B 118, 2366–2376, 2014. http://pubs.acs.org/doi/abs/10.1021/jp501041m Childs-Disney, J. L., Stepniak-Konieczna E., Tran, T., Yildirim, I., Park, H., Chen., C. Z., Hoskins, J., Southall, N., Marugan, J. J., Patnaik, S., Zheng, W., Austin, C. P., Schatz, G. C., Sobczak, K., Thornton, C. A., Disney, M. D., “Induction and Reversal of Myotonic Dystrophy Type 1 Pre-mRNA Splicing Defects by Small Molecules”, Nat. Commun. 4, 2044, 2013. http://www.nature.com/ncomms/2013/130628/ncomms3044/full/ncomms3044.html