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Reza Salavati - Publications

Link to lab webpage publications

Shateri Najafabadi, H., Salavati, R. (2010)
Functional genome annotation by combined analysis across microarray studies of Trypanosoma brucei. PLoS Negl Trop Dis 4
Salavati, R., Najafabadi, H. S. (2010)
Sequence-based functional annotation: what if most of the genes are unique to a genome? Trends Parasitol 26 225-229.
Moshiri, H., Salavati, R. (2010)
A fluorescence-based reporter substrate for monitoring RNA editing in trypanosomatid pathogens. Nucleic Acids Res 38 e138.
Kala, S., Salavati, R. (2010)
OB-fold domain of KREPA4 mediates high-affinity interaction with guide RNA and possesses annealing activity. RNA 16 1951-1967.
Shaneh, A., Salavati, R. (2009)
Kinetoplastid RNA editing ligases 1 and 2 exhibit different electrostatic properties. Journal of molecular modeling
Najafabadi, H. S., Goodarzi, H., Salavati, R. (2009)
Universal function-specificity of codon usage. Nucleic Acids Res 37 7014-7023.
Mao, Y., Najafabadi, H. S., Salavati, R. (2009)
Genome-wide computational identification of functional RNA elements in Trypanosoma brucei. BMC Genomics 10 355.
Najafabadi, H. S., Salavati, R. (2008)
Sequence-based prediction of protein-protein interactions by means of codon usage. Genome Biol 9 R87.
Salavati, R., Ernst, N. L., O'Rear, J., Gilliam, T., Tarun, S., Jr., Stuart, K. (2006)
KREPA4, an RNA binding protein essential for editosome integrity and survival of Trypanosoma brucei. RNA 12 819-831.
Panigrahi, A. K., Ernst, N. L., Domingo, G. J., Fleck, M., Salavati, R., Stuart, K. D. (2006)
Compositionally and functionally distinct editosomes in Trypanosoma brucei. RNA 12 1038-1049.
Mian, I. S., Worthey, E. A., Salavati, R. (2006)
Taking U out, with two nucleases? BMC Bioinformatics 7 305.
Stuart, K., Salavati, R., Igo, R. P., Lewis Ernst, N., Palazzo, S. S., Wang, B. (2004)
In vitro assays for kinetoplastid U insertion-deletion editing and associated activities. Methods in Molecular Biology 265 251-272.
Deng, J., Schnaufer, A., Salavati, R., Stuart, K. D., Hol, W. G. (2004)
High resolution crystal structure of a key editosome enzyme from Trypanosoma brucei: RNA editing ligase 1. Journal of Molecular Biology 343 601-613.

 

 

 

Najafabadi HS, Goodarzi H, Salavati R. (2009)Universal function-specificity of codon usage. Nucleic Acids Res. doi:10.1093/nar/gkp792Mao Y, Najafabadi HS, Salavati R. (2009)Genome-wide computational identification of functional RNA elements in Trypanosoma brucei. BMC Genomics. 2009;10(1):355Shaneh A and Salavati R. (2009)Kinetoplastid RNA editing ligases 1 and 2 exhibit different electrostatic properties. J Mol Model.Shateri N and Salavati R, (2008)Sequence-based prediction of protein-protein interactions by means of codon usage. Genome Biol. 9: R87.Mian IS, Worthey EA, and Salavati R, (2006)Taking U out, with two nucleases? BMC Bioinformatics. 7: 305.Panigrahi1 A K, Ernst N L, Domingo1 G J, Fleck M, Salavati R, and Kenneth D. Stuart K D, (2006)Compositionally and functionally distinct editosomes in Trypanosoma brucei RNA 12: 1038-1049Salavati, R, Ernst, N. L., O'Rear, J., Gilliam, T., Tarun S., Stuart K (2006)KREPA4, an RNA binding protein essential for editosome integrity and survival of Trypanosoma brucei. RNA 12: 819-831Deng J, Schnaufer A, Salavati, R, Stuart KD, Hol WG. (2004)High resolution crystal structure of a key editosome enzyme from Trypanosoma brucei: RNA editing ligase 1. J Mol Biol. 343(3):601-13.Worthey EA, Schnaufer, A., Mian, S., Stuart, K., Salavati, R. (2003)Comparative analysis of editosome proteins in trypanosomatids. Nucleic Acids Res. 31(22):6392-408.Schnaufer, A., Ernst, N. L., Palazzo, S., O'Rear, J., Salavati, R. Stuart, K. (2003)Separate insertion and deletion sub-complexes of the Trypanosoma brucei RNA editing complex. Mol Cell. 12(2):307-19.Ernst, N. L., Panicucci, B., Igo, R. P. Jr., Panigrahi AK, Salavati R, Stuart K. (2003)TbMP57 is a 3' terminal uridylyl transferase (TUTase) of the Trypanosoma brucei editosome. Mol Cell. 11(6):1525-36.Worthey EA, Martinez-Calvillo S, Schnaufer A, Aggarwal G, Cawthra J, Fazelinia G, Fong C, Fu G, Hassebrock M, Hixson G, Ivens AC, Kiser P, Marsolini F, Rickell E, Salavati R, Sisk E, Sunkin SM, Stuart KD, Myler PJ. (2003)Leishmania major chromosome 3 contains two long convergent polycistronic gene clusters separated by a tRNA gene. Nucleic Acids Res. 31(14):4201-10.Wang, B., Ernst, N. L., Palazzo, S., Panigrahi, A.K., Salavati, R., and Stuart, K. (2003)TbMP44 is a component of the editosome that is essential for editing and editosome structure in Trypanosoma brucei. Euk Cell. 2(3):578-87.Domingo, G. J., Palazzo, S., Wang, B., Panicucci, B., Salavati, R., and Stuart, K. (2003)Dyskinetoplastic contain functional editing complexes. Euk Cell. 2(3):569-77.Palazzo, S., Panigrahi, A.K., Igo, R. P. Jr., Salavati, R., and Stuart, K. (2003)Kinetoplastid RNA editing ligases: complex association, characterization, and substrate requirements. Mol Biochem Parasitol. 127(2):161-7.Panigrahi, A.K., Schnaufer, A., Ernst, N. L., Palazzo, S. S., Wang, B., Carmean, N., Salavati, R., Stuart, K.D. (2003)Identification of novel components of Trypanosoma brucei editosomes. RNA. 9(4):484-92.Igo, R. P. Jr., Weston, D.A., Ernst, N. L., Panigrahi, A.K., Salavati, R., and Stuart, K.D. (2002)Role of uridylate-specific exoribonuclease activity in Trypanosoma brucei RNA editing. Euk Cell. 1: 112-118.Stuart, K.D., Panigrahi, A.K., Schnaufer, A., Drozdz, M., Clayton, C., Salavati, R. (2002)Composition of the editing complex of Trypanosoma brucei. Philos Trans R Soc Lond B Biol Sci. 357(1417):71-9.Salavati, R., Panigrahi, A.K., Morach, B. A., Palazzo, S.S., Igo, R. P. Jr., and Stuart, K.D. (2002)Endoribonuclease activities of Trypanosoma brucei mitochondria. Mol Biochem Parasitol. 120(1):23-31.Drozdz, M., Palazzo, S., Salavati, R., Clayton, C., and Stuart, K. (2002)TbMP81 is associated with RNA editing in T. brucei. EMBO J 1;21(7):1791-9.Wang, B., Salavati, R., Heidman, S., and Stuart, K. (2002)A hammerhead ribozyme substrate and reporter for in vitro kinetoplastid RNA editing. RNA. 8(4):548-54.