Salavati Lab

– – – – – – 2020 – – – – – –

Aphasizheva I., Alfonzo J., Carnes J., Cestari I., Goringer U., Stephen H., Lukes J., Madison-Antenuccii S., Maslov D., McDermott S., Ochsenreiter T., Read L., Salavati R., Schnaufer A., Schneider A., Simpson L., Stuart K., Yurchenko V., Zhou Z., Zikova A., Zhang L., Ziimmer S.,   Aphasizhev R.  (2020). Lexis and Grammar of Mitochondrial RNA Processing in Trypanosomes. Trends in Parasitology Apr 36(4): 337-355.

Mehta V., Moshiri H., Srikanth A., Kala S., Lukeš J.,  Salavati R.  (2020). Sulfonated inhibitors of the RNA editing ligases validate the essential role of the MRP1/2 proteins in kinetoplastid RNA editing. RNA Jul 26(7): 827-835.

– – – – – – 2019 – – – – – –

Nikpour N.,  Salavati R.  (2019). The RNA binding activity of the first identified trypanosome protein with Z-DNA-binding domains. Sci Rep. Apr 11;9(1):5904.

– – – – – – 2018 – – – – – –

Salavati R.,  Gazestani VH.  (2018). Gene Function Discovery for Kinetoplastid Pathogens. Trends Parasitol. 2018;35: 8-12.

Gazestani VH., Hampton M., Shaw AK., Salavati R., Zimmer SL. (2018). Tail characteristics of Trypanosoma brucei mitochondrial transcripts are developmentally altered in a transcript-specific manner. Int J Parasitol. 2018 Feb;48: 179-189.

– – – – – – 2017 – – – – – –

Gazestani VH., Yip CW., Nikpour N., Berghuis N., Salavati R. (2017). TrypsNetDB: an integrated framework for the functional characterization of trypanosomatid proteins. PLoS Negl Trop Dis. 

Kala S., Mehta V., Yip CW., Moshiri H., Najafabadi HS., Ma R., Nikpour N., Zimmer SL.,  Salavati R. (2017). The interaction of a Trypanosoma brucei KH-domain protein with a ribonuclease is implicated in ribosome processing. Mol Bioiochem Parasitol. 2017. 211:94-103.

– – – – – – 2016 – – – – – –

Gazestani VH., Hampton M., Abrahante JE.,  Salavati R.*, Zimmer SL*. (2016). circTAIL-seq, a targeted method for deep analysis of RNA 3' tails, reveals transcript-specific differences by multiple metrics. RNA  2016. *(Co-corresponding authors).

Shaneh As., Purisima E.O.,  Salavati R., Sulea T. (2016). Structural studies of Trypanosoma brucei RNA editing ligases and their binding partner proteinss. Biochemistry. 2016. Mar 31 [epub ahead of print].

Gazestani VH, Nikpour N., Mehta V., Najafabadi H.S., Moshiri H, Jardim A., Salavati R. (2016). A Protein Complex Map of Trypanosoma brucei. PLos Negl. Trop. Dis. 2016. Mar 18; 10(3):e0004533.

– – – – – – 2015 – – – – – –

Gazestani VH., Salavati R. (2015). Deciphering RNA Regulatory Elements Involved in the Developmental and Environmental Gene Regulation of Trypanosoma brucei. PLoS One.  2015.

Bhaskar J., Gazestani VH., Yip CW., Salavati R. (2015). The DRBD13 RNA binding protein is involved in the insect-stage differentiation process of Trypanosoma brucei. FEBS Letters. . 589(15): 1966-74. 2015.

Mehta V., Sen R., Moshiri H., Salavati R. (2015). Mutational Analysis of Trypanosoma brucei RNA Editing Ligase Reveals Regions Critical for Interaction with KREPA2. PLoS One 10(3): e0120844. 2015.

– – – – – – 2014 – – – – – –

Moshiri H., Mehta V.,  Salavati R. (2014). RNA catalyst as a reporter for screening drugs against RNA editing in trypanosomes. Journal of visualized experiments : JoVE.  2014.

Moshiri H., Mehta V., Yipp CW., Salavati R. (2014). Pilot-Scale Compound Screening against RNA Editing Identifies Trypanocidal Agents. Journal of biomolecular screening. 2014.

Gazestani VH., Lu Z.,  Salavati R. (2014). Deciphering RNA regulatory elements in trypanosomatids: one piece at a time or genome-wide? Trends Parasitol.  2014; 30: 234-240.

– – – – – – 2013 – – – – – –

Najafabadi HS., Lu Z., Macpherson C., Mehta V., Adoue V., Pastinen T., Salavati R. (2013). Global identification of conserved post-transcriptional regulatory programs in trypanosomatids. Nucleic Acids Res. 2013; 41: 8591-8600.

– – – – – – 2012 – – – – – –

Kala S., Moshiri H., Mehta V., Yip CW., Salavati R. (2012). The Oligonucleotide Binding (OB)-Fold Domain of KREPA4 Is Essential for Stable Incorporation into Editosomes. PLoS One. 2012; doi: 10.1371/journal.pone.0046864.

Goodarzi H., Najafabadi HS., Oikonomou P., Greco TM., Fish L.,  Salavati R., Cristea IM., Tavazoie S. (2012). Systematic discovery of structural elements governing stability of mammalian messenger RNAs. Nature. 2012; doi: 10.1038/nature11013.

Salavati R., Moshiri H., Kala S., Najafabadi HS. (2012). Inhibitors of RNA editing as potential chemotherapeutics against trypanosomatid pathogens. Int J Parasitol Drugs Drug Resist. 2012; 2:36-46.

– – – – – – 2011 – – – – – –

Moshiri H., Acoca S., Kala S., Najafabadi HS., Hogues H., Purisima E.,  Salavati R. (2011). Naphthalene-based RNA editing inhibitor blocks RNA editing activities and editosome assembly in Trypanosoma brucei. J Biol Chem. 2011; 286(16):14178-89.

– – – – – – 2010 – – – – – –

Najafabadi HS., Salavati R. (2010). Functional genome annotation by combined analysis across microarray studies of Trypanosoma brucei. PLoS Negl Trop Dis. 2010; 4(8):e810.

Kala S., Salavati R. (2010). OB-fold domain of KREPA4 mediates high affinity interaction with guide RNA and also possesses annealing activity. RNA. 2010; 16(10):1951-1967.

Moshiri H., Salavati R. (2010). A fluorescence-based reporter substrate for monitoring RNA editing in trypanosomatid pathogens. Nucleic Acids Res.  2010; 38(13):e138.

Salavati R., Najafabadi HS. (2010). Sequence-based functional annotation: what if most of the genes are unique to a genome? Trends Parasitol.  2010; 26(5):225-229.

– – – – – – 2009 – – – – – –

Najafabadi HS., Goodarzi H., Salavati R. (2009). Universal function-specificity of codon usage. Nucleic Acids Res. 2009; 37(21):7014-7023.

Mao Y., Najafabadi HS., Salavati R. (2009). Genome-wide computational identification of functional RNA elements in Trypanosoma brucei. BMC Genomics. 2009; 10(1):355.

Shaneh A., Salavati R. (2009). Kinetoplastid RNA editing ligases 1 and 2 exhibit different electrostatic properties. J Mol Model. 2009 May 27.

– – – – – – 2008 – – – – – –

Najafabadi HS., Salavati R. (2008). Sequence-based prediction of protein-protein interactions by means of codon usage. Genome Biol. 2008; 9(5):R87. Epub 2008 May 23.

– – – – – – 2006 – – – – – –

Mian IS., Worthey EA., Salavati R. (2006). Taking U out, with two nucleases? BMC Bioinformatics. 2006; Jun 16;7:305.

Panigrahi AK., Ernst NL., Domingo GJ., Fleck M., Salavati R., Stuart KD. (2006). Compositionally and functionally distinct editosomes in Trypanosoma brucei.RNA.  2006 Jun; 12(6):1038-49. Epub 2006 Apr 12.

Salavati R., Ernst NL., O'Rear J., Gilliam T., Tarun S Jr., Stuart KD. (2006). KREPA4, an RNA binding protein essential for editosome integrity and survival of Trypanosoma brucei.RNA.  2006 May; 12(5):819-31. Epub 2006 Apr 6.

Panigrahi AK., Ernst NL., Domingo GJ., Fleck M., Salavati R., Stuart KD. (2006). Compositionally and functionally distinct editosomes in Trypanosoma brucei.RNA.  2006 Jun; 12(6):1038-49. Epub 2006 Apr 12.

– – – – – – 2004 – – – – – –

Deng 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. 2004 Oct 22; 343(3):601-13.

– – – – – – 2003 – – – – – –

Worthey EA., Schnaufer A., Mian IS., Stuart K., Salavati R. (2003). Comparative analysis of editosome proteins in trypanosomatids. J Nucleic Acids Res. 2003 May; 12(5): 819-31.

Schnaufer A., Ernst NL., Palazzo SS., O'Rear J., Salavati R., Stuart K. (2003). Separate insertion and deletion subcomplexes of the Trypanosoma brucei RNA editing complex. Mol Cell. 2003 Aug; 12(2): 307-19.

Ernst NL., Panicucci B., Igo RP Jr., Panigrahi AK., Salavati R., Stuart K. (2003). TbMP57 is a 3' terminal uridylyl transferase (TUTase) of the Trypanosoma brucei editosome. Mol Cell. 2003 Jun; 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., Rickel 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. 2003 Jul 15;31(14):4201-10.

Wang B., Ernst NL., Palazzo SS., Panigrahi AK., Salavati R., Stuart K. (2003). TbMP44 is essential for RNA editing and structural integrity of the editosome in Trypanosoma brucei. Eukaryot Cell.  2003 Jun;2(3):578-87.

Domingo GJ., Palazzo SS., Wang B., Pannicucci B., Salavati R., Stuart KD. (2003). Dyskinetoplastic Trypanosoma brucei contains functional editing complexes. Eukaryot Cell.  2003 Jun;2(3): 569-77.

Palazzo SS., Panigrahi AK., Igo RP., Salavati R., Stuart KD. (2003). Kinetoplastid RNA editing ligases: complex association, characterization, and substrate requirements. Mol Biochem Parasitol.  2003 Apr 3; 127(2): 161-7.

Panigrahi AK., Schnaufer A., Ernst NL., Wang B., Carmean N., Salavati R., Stuart KD. (2003). Identification of novel components of Trypanosoma brucei editosomes.RNA.  2003 Apr; 9(4): 484-92.

– – – – – – 2002 – – – – – –

Igo RP Jr., Weston DS., Ernst NL., Panigrahi AK., Salavati R., Stuart K. (2002). Role of uridylate-specific exoribonuclease activity in Trypanosoma brucei RNA editing. J Eukaryot Cell.  2002 Feb; 1(1): 112-8.

Salavati R., Panigrahi AK., Morach BA., Palazzo SS., Igo RP., Stuart KD. (2002). Endoribonuclease activities of Trypanosoma brucei mitochondria. Mol Biochem Parasitol.  2002 Mar; 120(1): 23-31.

Drozdz M., Palazzo SS.,  Salavati R., O'Rear J., Clayton C., Stuart KD. (2002). TbMP81 is required for RNA editing in Trypanosoma bruceis. EMBO J.  2002 Apr 2;21(7):1791-9.