Sequence-based prediction of protein-protein interactions by means of codon usage (2008)
Najafabadi, Hamed, Salavati, Reza
Abstract We introduce a novel approach to predict interaction of two proteins solely by analyzing their coding sequences. We found that similarity in codon usage is a strong predictor of...
Taking U out, with two nucleases? (2006)
Mian, I Saira, Worthey, Elizabeth A, Salavati, Reza
Abstract Background REX1 and REX2 are protein components of the RNA editing complex (the editosome) and function as exouridylylases. The exact roles of REX1 and REX2 in the editosome are unclear and...
Thesis (Ph. D.)--Wesleyan University, 1996.
Phenotypic conversion of drug-resistant bacteria to drug sensitivity
Guerrier-Takada, Cecilia, Salavati, Reza, Altman, Sidney
Plasmids that contain synthetic genes coding for small oligoribonucleotides called external guide sequences (EGSs) have been introduced into strains of Escherichia coli harboring antibiotic...
Panigrahi, Aswini K., Gygi, Steven P., Ernst, Nancy L., Igo, Robert P., Palazzo, Setareh S., Schnaufer, Achim, ...
RNA editing in kinetoplastid mitochondria inserts and deletes uridylates at multiple sites in pre-mRNAs as directed by guide RNAs. This occurs by a series of steps that are catalyzed by...
Four Related Proteins of the Trypanosoma brucei RNA Editing Complex
Panigrahi, Aswini K., Schnaufer, Achim, Carmean, Nicole, Igo, Robert P., Gygi, Steven P., Ernst, Nancy L., ...
RNA editing in kinetoplastid mitochondria occurs by a series of enzymatic steps that is catalyzed by a macromolecular complex. Four novel proteins and their corresponding genes were identified by...
Role of Uridylate-Specific Exoribonuclease Activity in Trypanosoma brucei RNA Editing
Igo, Robert P., Weston, David S., Ernst, Nancy Lewis, Panigrahi, Aswini K., Salavati, Reza, Stuart, Kenneth
Editing of mitochondrial mRNAs in kinetoplastid protozoa occurs by a series of enzymatic steps that insert and delete uridylates (U's) as specified by guide RNAs (gRNAs). The characteristics of the...
TbMP81 is required for RNA editing in Trypanosoma brucei
Drozdz, Maciej, Palazzo, Setareh S., Salavati, Reza, O’Rear, Jeff, Clayton, Christine, Stuart, Kenneth
Most mitochondrial mRNAs are edited in Trypano soma brucei by a series of steps that are catalyzed by a multienzyme complex that is in its initial stages of characterization. RNA interference...
Dyskinetoplastic Trypanosoma brucei Contains Functional Editing Complexes
Domingo, Gonzalo J., Palazzo, Setareh S., Wang, Bingbing, Pannicucci, Brian, Salavati, Reza, Stuart, Kenneth D.
Mitochondrial pre-mRNAs undergo posttranscriptional RNA editing as directed by small guide RNAs (gRNAs) to produce functional mRNAs in kinetoplastid protozoa. The pre-mRNAs and gRNAs are encoded in...
TbMP44 Is Essential for RNA Editing and Structural Integrity of the Editosome in Trypanosoma brucei
Wang, Bingbing, Ernst, Nancy Lewis, Palazzo, Setareh S., Panigrahi, Aswini K., Salavati, Reza, Stuart, Kenneth
RNA editing produces mature mitochondrial mRNAs in trypanosomatids by the insertion and deletion of uridylates. It is catalyzed by a multiprotein complex, the editosome. We identified TbMP44 among...
Worthey, E. A., Martinez-Calvillo, Santiago, Schnaufer, Achim, Aggarwal, Gautam, Cawthra, Jason, Fazelinia, Gholam, ...
Leishmania parasites (order Kinetoplastida, family Trypanosomatidae) cause a spectrum of human diseases ranging from asymptomatic to lethal. The ∼33.6 Mb genome is distributed among 36 chromosome...
SURVEY AND SUMMARY: Comparative analysis of editosome proteins in trypanosomatids
Worthey, Elizabeth A., Schnaufer, Achim, Mian, I. Saira, Stuart, Kenneth, Salavati, Reza
Detailed comparisons of 16 editosome proteins from Trypanosoma brucei, Trypanosoma cruzi and Leishmania major identified protein motifs associated with catalysis and protein or nucleic acid...
A hammerhead ribozyme substrate and reporter for in vitro kinetoplastid RNA editing.
Wang, Bingbing, Salavati, Reza, Heidmann, Stefan, Stuart, Kenneth
Current in vitro assays for RNA editing in kinetoplastids directly examine the products generated by incubation of pre-mRNA substrate with guide RNA (gRNA) and mitochondrial (mt) extract. RNA editing...
Identification of novel components of Trypanosoma brucei editosomes
PANIGRAHI, ASWINI K., SCHNAUFER, ACHIM, ERNST, NANCY L., WANG, BINGBING, CARMEAN, NICOLE, SALAVATI, REZA, ...
The editosome is a multiprotein complex that catalyzes the insertion and deletion of uridylates that occurs during RNA editing in trypanosomatids. We report the identification of nine novel editosome...
KREPA4, an RNA binding protein essential for editosome integrity and survival of Trypanosoma brucei
Salavati, Reza, Ernst, Nancy Lewis, O'Rear, Jeff, Gilliam, Troy, Tarun, Salvador, Stuart, Kenneth
The 20S editosome, a multiprotein complex, catalyzes the editing of most mitochondrial mRNAs in trypanosomatids by uridylate insertion and deletion. RNAi mediated inactivation of expression of KREPA4...
Compositionally and functionally distinct editosomes in Trypanosoma brucei
Panigrahi, Aswini K., Ernst, Nancy Lewis, Domingo, Gonzalo J., Fleck, Michele, Salavati, Reza, Stuart, Kenneth D.
Uridylate insertion/deletion RNA editing in Trypanosoma brucei mitochondria is catalyzed by a multiprotein complex, the ∼20S editosome. Editosomes purified via three related tagged RNase III...
Phenotypic conversion of drug-resistant bacteria to drug sensitivity
Guerrier-Takada, Cecilia, Salavati, Reza, Altman, Sidney
Plasmids that contain synthetic genes coding for small oligoribonucleotides called external guide sequences (EGSs) have been introduced into strains of Escherichia coli harboring antibiotic...
Panigrahi, Aswini K., Gygi, Steven P., Ernst, Nancy L., Igo, Robert P., Palazzo, Setareh S., Schnaufer, Achim, ...
RNA editing in kinetoplastid mitochondria inserts and deletes uridylates at multiple sites in pre-mRNAs as directed by guide RNAs. This occurs by a series of steps that are catalyzed by...
Four Related Proteins of the Trypanosoma brucei RNA Editing Complex
Panigrahi, Aswini K., Schnaufer, Achim, Carmean, Nicole, Igo, Robert P., Gygi, Steven P., Ernst, Nancy L., ...
RNA editing in kinetoplastid mitochondria occurs by a series of enzymatic steps that is catalyzed by a macromolecular complex. Four novel proteins and their corresponding genes were identified by...
Role of Uridylate-Specific Exoribonuclease Activity in Trypanosoma brucei RNA Editing
Igo, Robert P., Weston, David S., Ernst, Nancy Lewis, Panigrahi, Aswini K., Salavati, Reza, Stuart, Kenneth
Editing of mitochondrial mRNAs in kinetoplastid protozoa occurs by a series of enzymatic steps that insert and delete uridylates (U's) as specified by guide RNAs (gRNAs). The characteristics of the...
TbMP81 is required for RNA editing in Trypanosoma brucei
Drozdz, Maciej, Palazzo, Setareh S., Salavati, Reza, O’Rear, Jeff, Clayton, Christine, Stuart, Kenneth
Most mitochondrial mRNAs are edited in Trypano soma brucei by a series of steps that are catalyzed by a multienzyme complex that is in its initial stages of characterization. RNA interference...
Dyskinetoplastic Trypanosoma brucei Contains Functional Editing Complexes
Domingo, Gonzalo J., Palazzo, Setareh S., Wang, Bingbing, Pannicucci, Brian, Salavati, Reza, Stuart, Kenneth D.
Mitochondrial pre-mRNAs undergo posttranscriptional RNA editing as directed by small guide RNAs (gRNAs) to produce functional mRNAs in kinetoplastid protozoa. The pre-mRNAs and gRNAs are encoded in...
TbMP44 Is Essential for RNA Editing and Structural Integrity of the Editosome in Trypanosoma brucei
Wang, Bingbing, Ernst, Nancy Lewis, Palazzo, Setareh S., Panigrahi, Aswini K., Salavati, Reza, Stuart, Kenneth
RNA editing produces mature mitochondrial mRNAs in trypanosomatids by the insertion and deletion of uridylates. It is catalyzed by a multiprotein complex, the editosome. We identified TbMP44 among...
Worthey, E. A., Martinez-Calvillo, Santiago, Schnaufer, Achim, Aggarwal, Gautam, Cawthra, Jason, Fazelinia, Gholam, ...
Leishmania parasites (order Kinetoplastida, family Trypanosomatidae) cause a spectrum of human diseases ranging from asymptomatic to lethal. The ∼33.6 Mb genome is distributed among 36 chromosome...
SURVEY AND SUMMARY: Comparative analysis of editosome proteins in trypanosomatids
Worthey, Elizabeth A., Schnaufer, Achim, Mian, I. Saira, Stuart, Kenneth, Salavati, Reza
Detailed comparisons of 16 editosome proteins from Trypanosoma brucei, Trypanosoma cruzi and Leishmania major identified protein motifs associated with catalysis and protein or nucleic acid...
A hammerhead ribozyme substrate and reporter for in vitro kinetoplastid RNA editing.
Wang, Bingbing, Salavati, Reza, Heidmann, Stefan, Stuart, Kenneth
Current in vitro assays for RNA editing in kinetoplastids directly examine the products generated by incubation of pre-mRNA substrate with guide RNA (gRNA) and mitochondrial (mt) extract. RNA editing...
Identification of novel components of Trypanosoma brucei editosomes
PANIGRAHI, ASWINI K., SCHNAUFER, ACHIM, ERNST, NANCY L., WANG, BINGBING, CARMEAN, NICOLE, SALAVATI, REZA, ...
The editosome is a multiprotein complex that catalyzes the insertion and deletion of uridylates that occurs during RNA editing in trypanosomatids. We report the identification of nine novel editosome...
KREPA4, an RNA binding protein essential for editosome integrity and survival of Trypanosoma brucei
Salavati, Reza, Ernst, Nancy Lewis, O'Rear, Jeff, Gilliam, Troy, Tarun, Salvador, Stuart, Kenneth
The 20S editosome, a multiprotein complex, catalyzes the editing of most mitochondrial mRNAs in trypanosomatids by uridylate insertion and deletion. RNAi mediated inactivation of expression of KREPA4...
Compositionally and functionally distinct editosomes in Trypanosoma brucei
Panigrahi, Aswini K., Ernst, Nancy Lewis, Domingo, Gonzalo J., Fleck, Michele, Salavati, Reza, Stuart, Kenneth D.
Uridylate insertion/deletion RNA editing in Trypanosoma brucei mitochondria is catalyzed by a multiprotein complex, the ∼20S editosome. Editosomes purified via three related tagged RNase III...
Sequence-based prediction of protein-protein interactions by means of codon usage
Najafabadi, Hamed Shateri, Salavati, Reza
A new approach based on similarity in codon usage is used to predict protein-protein interactions.