Rod Sharp Professor in Microbiology
500 Aronoff Laboratory
318 W. 12th Avenue
Areas of Expertise
- Signal transduction
- Evolutionary genomics
- Computational biology
- B.S./M.S., Saratov State University, 1983
- Ph.D., St. Petersburg State University, 1988
- PostDoc, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 1988-1990
- PostDoc, University of Oxford, 1990-1991
- PostDoc, Loma Linda University School of Medicine, 1992-1996
We develop and apply computational genomics approaches to best characterized biological processes in order to reveal novel functional features that cannot be obtained by experimental techniques alone. In this work, we use an array of bioinformatics tools - from sensitive similarity searches to phylogenetics and structure prediction - and several tiers of hardware - from workstations and stand-alone servers to Linux clusters and supercomputers.
We are interested in fundamental biological questions, such as signal transduction, gene regulation and protein-protein interactions, which we study through the prism of molecular evolution. Our main focus is on prokaryotes, but we also apply approaches developed with bacterial systems to human genes that are implicated in diseases ranging from rare Mendelian disorders to cancer. Our credo is simple: Nature has already performed millions of genetic experiments; all we need to do is to carefully analyze the results. Most of our studies generate testable hypotheses that are often taken directly into experiment by our colleagues in "wet" laboratories.
- Ortega DR, Fleetwood AD, Krell T, Harwood CS, Jensen GJ, Zhulin IB. 2017. Assigning chemoreceptors to chemosensory pathways in Pseudomonas aeruginosa. Proc. Natl. Acad. Sci. USA 114: 12809-12814.
- Ortega Á, Zhulin IB, Krell T. 2017. Sensory repertoire of bacterial chemoreceptors. Microbiol. Mol. Biol. Rev. 81: e00033-17.
- Day CJ, King RM, Shewell LK, Tram G, Najnin T, Hartley-Tassell LE, Wilson JC, Fleetwood AD, Zhulin IB, Korolik V. 2016. A direct-sensing galactose chemoreceptor recently evolved in invasive strains of Campylobacter jejuni. Nat. Commun. 7: 13206.
- Upadhyay AA, Fleetwood AD, Adebali O, Finn RD, Zhulin IB. 2016. Cache domains that are homologous to, but different from PAS domains comprise the largest superfamily of extracellular sensors in prokaryotes. PLoS Comput. Biol. 12: e1004862.
- Adebali O, Reznik AO, Ory DS, Zhulin IB. 2016. Establishing the precise evolutionary history of a gene improves prediction of disease-causing missense mutations. Genet. Med. 18: 1029-1036.
- Ortega DR, Yang C, Ames P, Baudry J, Parkinson JS, Zhulin IB. 2013. A phenylalanine rotameric switch for signal-state control in bacterial chemoreceptors. Nat. Commun. 4: 2881.
- Wisniewski-Dyé F, Borziak K, Khalsa-Moyers G, Alexandre G, Sukharnikov LO, Wuichet K, Hurst GB, McDonald WH, Robertson JS, Barbe V, Calteau A, Rouy Z, Mangenot S, Prigent-Combaret C, Normand P, Boyer M, Siguier P, Dessaux Y, Elmerich C, Condemine G, Krishnen G, Kennedy I, Paterson AH, González V, Mavingui P, Zhulin IB. 2011. Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments. PLoS Genet. 7: e1002430.
- Wuichet K, Zhulin IB. 2010. Origins and diversification of a complex signal transduction system in prokaryotes. Sci. Signal. 3: ra50.
- Ulrich LE, Koonin EV, Zhulin IB. 2005. One-component systems dominate signal transduction in prokaryotes. Trends Microbiol. 13: 52-56.
- Taylor BL, Zhulin IB. 1999. PAS domains: internal sensors of oxygen, redox potential, and light. Microbiol. Mol. Biol. Rev. 63: 479-506.
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