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Ivaylo Ivanov

Associate Professor

B.S. (1996): Sofia University "St. Kliment Ohridski", Sofia, Bulgaria
M.S. (1999) : Carnegie Mellon University, Pittsburgh, PA
Ph.D. (2004) : University of Pennsylvania, Philadelphia, PA
University of California, San Diego, Postdoctoral Research Fellow, 2005-2009


Computational biology and biophysics, Molecular modeling and simulations, Drug design, Computational chemistry, Biological assemblies and mechanisms of genome duplication and maintenance.


DNA replication is a major target for cancer therapies, while efficient DNA repair antagonizes those same therapies. Both replication and repair are critically dependent on the dynamics, coordinated access, and conformational switching of key proteins in the replication machinery. Research in our group is centered on the development and application of integrative or hybrid approaches for computational modeling of biological assemblies involved in these processes. We model and structurally characterize these dynamic assemblies to elucidate their roles in  maintaining genome stability. Success of this research could have impact on cancer etiology and interventions. Our computational work feeds back directly to collaborative experimental work,  forming strong contextual underpinnings for the multidisciplinary experiments designed to tackle the complex biology of DNA replication and DNA repair.


Recent publications:
1. Han, Y.; Yan, C.; Nguyen, K.; Jackobel, A.; Ivanov, I.; Knutson, B.A.; He, Y. Structural mechanism of ATP-independent transcription initiation by RNA polymerase I. eLife (2017) 6, e27414
2. He, Y., Yan, C., Inouye, C., Fang, J., Tjian, R., Ivanov, I. & Nogales E. Structural basis of transcription promoter opening using single particle cryo-EM. Nature (2016) 533, 359–365
3. Hudson, W.H., Kossmann, B., de Vera, I.M., Chuo, S.W., Weikum, E.A., Eick G., Thornton, J., Ivanov, I., Kojetin, D.J., & Ortlund, E.A Distal substitutions drive divergent DNA specificity among paralogous transcription factors through a subdivision of conformational space Proceedings of the National Academy of Sciences U.S.A (2016) 113, 326-331
4. Ivanov I. Enzyme cofactors: Double-edged sword for catalysis Nature Chemistry (2013) 5, 6-7
5. Querol-Audi J; Yan C.; Xu X.; Tsutakawa S.E.; Tsai M.S.; Tainer J.A.; Cooper P.K; Nogales E.; Ivanov I. Repair complexes of FEN1, DNA and Rad9-Hus1-Rad1 are distinguished from their PCNA counterparts by functionally important stability Proceedings of the National Academy of Sciences U.S.A. (2012) 109, 8528-8533
6. Tsutakawa, S.E.; Van Wynsberghe, A.; Freudenthal, B.D.; Weinacht, C.P.; Gakhar, L.; Washington, M.T.; Zhuang, Z.; Tainer, J. A.; Ivanov, I. Solution X-ray scattering combined with computational modeling reveals multiple conformations of covalently-bound ubiquitin on PCNA Proceedings of the National Academy of Sciences U.S.A. (2011) 108, 17672-176727.