Predicting Consensus Structures for RNA Alignments Via Pseudo-Energy Minimization (2009)
Junilda Spirollari, Kaizhong Zhang, Vivian Bellofatto, Yongkyu Park, Bruce A. Shapiro
Thermodynamic processes with free energy parameters are often used in algorithms that solve the free energy minimization problem to predict secondary structures of single RNA sequences. While results...
Banerjee, Hiren, Palenchar, Jennifer B., Lukaszewicz, Maciej, Bojarska, Elzbieta, Stepinski, Janusz, Jemielity, Jacek, ...
A new member of the FHIT protein family, designated HIT-45, has been identified in the African trypanosome Trypanosoma brucei. Recombinant HIT-45 proteins were purified from trypanosomal and...
RADAR: a web server for RNA data analysis and research (2007)
Khaladkar, Mugdha, Bellofatto, Vivian, Wang, Jason T. L., Tian, Bin, Shapiro, Bruce A.
RADAR is a web server that provides a multitude of functionality for RNA data analysis and research. It can align structure-annotated RNA sequences so that both sequence and structure information are...
Tkacz, Itai Dov, Lustig, Yaniv, Stern, Michael Zeev, Biton, Moshe, Salmon-Divon, Mali, Das, Anish, ...
In eukaryotes the seven Sm core proteins bind to U1, U2, U4, and U5 snRNAs. In Trypanosoma brucei, Sm proteins have been implicated in binding both spliced leader (SL) and U snRNAs. In this study, we...
Tkacz, Itai Dov, Lustig, Yaniv, Stern, Michael Zeev, Biton, Moshe, Salmon-Divon, Mali, Das, Anish, ...
In eukaryotes the seven Sm core proteins bind to U1, U2, U4, and U5 snRNAs. In Trypanosoma brucei, Sm proteins have been implicated in binding both spliced leader (SL) and U snRNAs. In this study, we...
Tkacz, Itai Dov, Lustig, Yaniv, Stern, Michael Zeev, Biton, Moshe, Salmon-Divon, Mali, Das, Anish, ...
In eukaryotes the seven Sm core proteins bind to U1, U2, U4, and U5 snRNAs. In Trypanosoma brucei, Sm proteins have been implicated in binding both spliced leader (SL) and U snRNAs. In this study, we...
MILONE, JOSEPH, WILUSZ, JEFFREY, BELLOFATTO, VIVIAN
The stability of mRNAs is an important point in the regulation of gene expression in eukaryotes. The mRNA turnover pathways have been identified in yeast and mammals. However, mRNA turnover pathways...
Milone, Joseph, Wilusz, Jeffrey, Bellofatto, Vivian
mRNA turnover is a regulated process that contributes to the steady state level of cytoplasmic mRNA. The amount of each mRNA determines, to a large extent, the amount of protein produced by that...
Gilinger, Gwen, Bellofatto, Vivian
Typical general transcription factors, such as TATA binding protein and TFII B, have not yet been identified in any member of the Trypanosomatidae family of parasitic protozoa. Interestingly, mRNA...
Kapotas, Nikitas, Bellofatto, Vivian
In trypanosomatlds, nuclear pre-mRNA splicing is exclusively a trans-spliclng reaction in which a capped, 39 nt exon, the mini-exon, is positioned 5' to an open reading frame. Differential RNA...
Bellofatto, Vivian, Cooper, Robin, Cross, George A.M.
Mature mRNAs of trypanosomatid protozoa result from the joining of at least two exons, which are initially transcribed as separate RNAs. In all trypanosomatids examined to date, the first exon...
Gilinger, Gwen, Bellofatto, Vivian
Typical general transcription factors, such as TATA binding protein and TFII B, have not yet been identified in any member of the Trypanosomatidae family of parasitic protozoa. Interestingly, mRNA...
Milone, Joseph, Wilusz, Jeffrey, Bellofatto, Vivian
mRNA turnover is a regulated process that contributes to the steady state level of cytoplasmic mRNA. The amount of each mRNA determines, to a large extent, the amount of protein produced by that...
Das, Anish, Bellofatto, Vivian
Spliced leader RNA transcription is essential for cell viability in trypanosomes. The SL RNA genes are expressed from the only defined RNA polymerase II-dependent promoter identified to date in the...
Das, Anish, Zhang, Qing, Palenchar, Jennifer B., Chatterjee, Bithi, Cross, George A. M., Bellofatto, Vivian
Protein-coding genes of trypanosomes are mainly transcribed polycistronically and cleaved into functional mRNAs in a process that requires trans splicing of a capped 39-nucleotide RNA derived from a...
MILONE, JOSEPH, WILUSZ, JEFFREY, BELLOFATTO, VIVIAN
The stability of mRNAs is an important point in the regulation of gene expression in eukaryotes. The mRNA turnover pathways have been identified in yeast and mammals. However, mRNA turnover pathways...
Palenchar, Jennifer B., Liu, Wenzhe, Palenchar, Peter M., Bellofatto, Vivian
Transcription by RNA polymerase II in trypanosomes deviates from the standard eukaryotic paradigm. Genes are transcribed polycistronically and subsequently cleaved into functional mRNAs, requiring...
Gilinger, Gwen, Bellofatto, Vivian
Typical general transcription factors, such as TATA binding protein and TFII B, have not yet been identified in any member of the Trypanosomatidae family of parasitic protozoa. Interestingly, mRNA...
Milone, Joseph, Wilusz, Jeffrey, Bellofatto, Vivian
mRNA turnover is a regulated process that contributes to the steady state level of cytoplasmic mRNA. The amount of each mRNA determines, to a large extent, the amount of protein produced by that...
Das, Anish, Bellofatto, Vivian
Spliced leader RNA transcription is essential for cell viability in trypanosomes. The SL RNA genes are expressed from the only defined RNA polymerase II-dependent promoter identified to date in the...
Das, Anish, Zhang, Qing, Palenchar, Jennifer B., Chatterjee, Bithi, Cross, George A. M., Bellofatto, Vivian
Protein-coding genes of trypanosomes are mainly transcribed polycistronically and cleaved into functional mRNAs in a process that requires trans splicing of a capped 39-nucleotide RNA derived from a...
MILONE, JOSEPH, WILUSZ, JEFFREY, BELLOFATTO, VIVIAN
The stability of mRNAs is an important point in the regulation of gene expression in eukaryotes. The mRNA turnover pathways have been identified in yeast and mammals. However, mRNA turnover pathways...
Palenchar, Jennifer B., Liu, Wenzhe, Palenchar, Peter M., Bellofatto, Vivian
Transcription by RNA polymerase II in trypanosomes deviates from the standard eukaryotic paradigm. Genes are transcribed polycistronically and subsequently cleaved into functional mRNAs, requiring...
Tkacz, Itai Dov, Lustig, Yaniv, Stern, Michael Zeev, Biton, Moshe, Salmon-Divon, Mali, Das, Anish, ...
In eukaryotes the seven Sm core proteins bind to U1, U2, U4, and U5 snRNAs. In Trypanosoma brucei, Sm proteins have been implicated in binding both spliced leader (SL) and U snRNAs. In this study, we...
RADAR: a web server for RNA data analysis and research
Khaladkar, Mugdha, Bellofatto, Vivian, Wang, Jason T. L., Tian, Bin, Shapiro, Bruce A.
RADAR is a web server that provides a multitude of functionality for RNA data analysis and research. It can align structure-annotated RNA sequences so that both sequence and structure information are...
Spliced-leader RNA silencing: a novel stress-induced mechanism in Trypanosoma brucei
Lustig, Yaniv, Sheiner, Lilach, Vagima, Yaron, Goldshmidt, Hanoch, Das, Anish, Bellofatto, Vivian, ...
The signal-recognition particle (SRP) mediates the translocation of membrane and secretory proteins across the endoplasmic reticulum upon interaction with the SRP receptor. In trypanosomes, the main...
The Non-Canonical CTD of RNAP-II Is Essential for Productive RNA Synthesis in Trypanosoma brucei
Das, Anish, Bellofatto, Vivian
The carboxy-terminal domain (CTD) of the largest subunit (RPB1) of RNA polymerase II (RNAP-II) is essential for gene expression in metazoa and yeast. The canonical CTD is characterized by...