·
Gazestani, VH., Yip, CW., Nikpour, N., Berghuis, N., Salavati, R.
TrypsNetDB: an integrated framework for the functional characterization of trypanosomatid proteins.
PLoS Negl Trop Dis. (accepted)
·
Kala, S., Mehta, V., Yip, CW., Moshiri, H., Najafabadi, HS., Ma, R., Nikpour, N., Zimmer, SL., Salavati, R.
The interaction of a Trypanosoma brucei KH-domain protein with a ribonuclease is implicated in ribosome processing.
Mol Biochem Parasitol. 2017. 211:94-103.
·
Gazestani, VH., Hampton, M., Abrahante, JE., Salavati, R.*, Zimmer, SL*.
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 A., Purisima E.O., Salavati R., Sulea T.
Structural studies of Trypanosoma brucei RNA editing ligases and their binding partner proteins.
Biochemistry. 2016 Mar 31. [Epub ahead of print]
·
Gazestani V.H., Nikpour N., Mehta V., Najafabadi H.S., Moshiri H, Jardim A., Reza Salavati R.
A Protein Complex Map of Trypanosoma brucei
PLoS Negl. Trop. Dis. 2016 Mar 18;10(3):e0004533
|||
Online Supplementary
Materials
|||
·
Gazestani VH, Salavati R.
Deciphering RNA Regulatory Elements Involved in the Developmental and Environmental Gene Regulation of Trypanosoma brucei
PLoS One. 2015
·
Jha Bhaskar, Gazestani VH, Yip CW, Salavati R.
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.
Mutational Analysis of Trypanosoma brucei RNA Editing Ligase Reveals Regions Critical for Interaction with KREPA2
PLoS One 10(3):e0120844. 2015
·
Moshiri H, Mehta V, Salavati R.
RNA catalyst as a reporter for screening drugs against RNA editing in trypanosomes
Journal of visualized experiments : JoVE 2014.
·
Moshiri H, Mehta V, Yip CW, Salavati R.
Pilot-Scale Compound Screening against RNA Editing Identifies Trypanocidal Agents
Journal of biomolecular screening 2014.
·
Gazestani VH, Lu Z, Salavati R.
Deciphering RNA regulatory elements in trypanosomatids: one piece at a time or genome-wide?
Trends Parasitol. 2014;30: 234-240
·
Najafabadi HS, Lu Z, Macpherson C, Mehta V, Adoue V, Pastinen T, Salavati R.
Global identification of conserved post-transcriptional regulatory programs in trypanosomatids.
Nucleic Acids Res. 2013;41: 8591-8600
·
Kala S, Moshiri H, Mehta V, Yip CW, Salavati R.
The Oligonucleotide Binding (OB)-Fold Domain of KREPA4 Is Essential for Stable Incorporation into Editosomes.
PLoS One;doi: 10.1371/journal.pone.0046864.
·
Goodarzi H,
Najafabadi HS, Oikonomou P, Greco TM, Fish L, Salavati R, Cristea IM,
Tavazoie S.
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.
Inhibitors of RNA
editing as potential chemotherapeutics against trypanosomatid pathogens
Int J Parasitol Drugs Drug Resist. 2012; 2:36-46.
·
Moshiri H, Acoca S,
Kala S, Najafabadi HS, Hogues H, Purisima E, Salavati R.
Naphthalene-based RNA
editing inhibitor blocks RNA editing activities and editosome assembly in Trypanosoma brucei
J Biol Chem. 2011; 286(16):14178-89.
·
Najafabadi HS,
Salavati R.
Functional genome
annotation by combined analysis across microarray studies of
Trypanosoma
brucei
PLoS Negl Trop Dis. 2010;
4(8):e810
|||Online
Supplementary Information|||
·
Kala S, Salavati R.
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.
A fluorescence-based reporter substrate for monitoring RNA editing in trypanosomatid pathogens.
Nucleic Acids Res. 2010; 38(13):e138
·
Salavati R,
Najafabadi HS.
Sequence-based functional annotation: what if most of the genes are unique to a genome?
Trends Parasitol. 2010; 26(5):225-229
·
Najafabadi HS,
Goodarzi H, Salavati R.
Universal
function-specificity of codon usage.
Nucleic Acids Res. 2009; 37(21):7014-7023
|||Software|||
·
Mao Y, Najafabadi HS, Salavati R. |||Highly accessed|||
Genome-wide
computational identification of functional RNA elements in Trypanosoma brucei.
BMC Genomics. 2009;10(1):355
·
Shaneh A, Salavati
R.
Kinetoplastid RNA
editing ligases 1 and 2 exhibit different electrostatic properties.
J Mol Model. 2009 May 27.
·
Najafabadi HS,
Salavati R. |||Highly accessed|||
Sequence-based
prediction of protein-protein interactions by means of codon usage.
Genome Biol. 2008;9(5):R87. Epub 2008 May 23.
|||Online Supplementary
Materials|||
·
Mian IS, Worthey
EA, Salavati R.
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.
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 K.
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.
·
Deng J, Schnaufer
A, Salavati R, Stuart KD, Hol WG.
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.
·
Worthey EA,
Schnaufer A, Mian IS, Stuart K, Salavati R.
Comparative
analysis of editosome proteins in trypanosomatids.
Nucleic Acids Res. 2003 Nov 15;31(22):6392-408.
·
Schnaufer A, Ernst
NL, Palazzo SS, O'Rear J, Salavati R, Stuart K.
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.
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.
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. Erratum in: Nucleic Acids Res.
2004 Dec;32(22):6716. Rickell, Erika [corrected to Rickel, Erika].
·
Wang B, Ernst NL,
Palazzo SS, Panigrahi AK, Salavati R, Stuart K.
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.
Dyskinetoplastic
Trypanosoma brucei contains
functional editing complexes.
Eukaryot Cell. 2003 Jun;2(3):569-77.
·
Palazzo SS,
Panigrahi AK, Igo RP, Salavati R, Stuart K.
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 K.
Identification
of novel components of Trypanosoma
brucei editosomes.
RNA. 2003 Apr;9(4):484-92.
·
Igo RP Jr, Weston
DS, Ernst NL, Panigrahi AK, Salavati R, Stuart K.
Role
of uridylate-specific exoribonuclease activity in Trypanosoma brucei RNA editing.
Eukaryot Cell. 2002 Feb;1(1):112-8.
·
Panigrahi AK, Ernst
NL, Domingo GJ, Fleck M, Salavati R, Stuart KD.
Compositionally
and functionally distinct editosomes in Trypanosoma
brucei.
RNA. 2006 Jun;12(6):1038-49. Epub 2006 Apr 12.
·
Salavati R,
Panigrahi AK, Morach BA, Palazzo SS, Igo RP, Stuart K.
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 K.
TbMP81
is required for RNA editing in Trypanosoma
brucei.
EMBO J. 2002 Apr 2;21(7):1791-9.
·
Wang B, Salavati R,
Heidmann S, Stuart K.
A
hammerhead ribozyme substrate and reporter for in vitro kinetoplastid RNA
editing.
RNA. 2002 Apr;8(4):548-54.