11 Result(s)
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Neelanjan Mukherjee
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Article
Open AccessGlobal identification of functional microRNA-mRNA interactions in Drosophila
MicroRNAs (miRNAs) are key mediators of post-transcriptional gene expression silencing. So far, no comprehensive experimental annotation of functional miRNA target sites exists in Drosophila. Here, we generated a...
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Article
Integrative classification of human coding and noncoding genes through RNA metabolism profiles
Quantitative assessment of transcription, splicing, degradation, localization and translation of coding and noncoding genes allows classification of RNAs on the basis of their metabolism and may aid in inferen...
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Article
Detecting actively translated open reading frames in ribosome profiling data
RiboTaper quantifies the three-nucleotide periodicity in Ribo-seq data to find translated open reading frames (ORFs). The de novo inferred set of ORFs comprehensively defines the cellular proteome across a wide e...
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Protocol
Identifying RBP Targets with RIP-seq
Throughout their lifetime RNA molecules interact with a variety of RNA-binding proteins (RBPs). RBPs control gene expression by regulating splicing, polyadenylation, editing, transport, stability, and translat...
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Article
Open AccessGlobal target mRNA specification and regulation by the RNA-binding protein ZFP36
ZFP36, also known as tristetraprolin or TTP, and ELAVL1, also known as HuR, are two disease-relevant RNA-binding proteins (RBPs) that both interact with AU-rich sequences but have antagonistic roles. While ELA...
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Article
MicroRNA target site identification by integrating sequence and binding information
The integration of microRNA target sequence features and data from cross-linking and immunoprecipitation of Argonaute proteins, implemented in the hidden Markov model–based framework MUMMIE, provides accurate ...
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Article
FMRP targets distinct mRNA sequence elements to regulate protein expression
Fragile X syndrome (FXS) is a multi-organ disease that leads to mental retardation, macro-orchidism in males and premature ovarian insufficiency in female carriers. FXS is also a prominent monogenic disease as...
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Article
Open AccessPARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data
Crosslinking and immunoprecipitation (CLIP) protocols have made it possible to identify transcriptome-wide RNA-protein interaction sites. In particular, PAR-CLIP utilizes a photoactivatable nucleoside for more...
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Article
A viral microRNA functions as an orthologue of cellular miR-155
Some viral microRNAs are known to bind host cell mRNAs to block translation or induce their degradation. Now a microRNA from the herpes virus associated with Kaposi's sarcoma has been found to mimic the ubiqui...
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Article
Radiation Enhances the Invasive Potential of Primary Glioblastoma Cells via Activation of the Rho Signaling Pathway
Glioblastoma multiforme (GBM) is among the most treatment-refractory of all human tumors. Radiation is effective at prolonging survival of GBM patients; however, the vast majority of GBM patients demonstrate p...
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Chapter and Conference Paper
Predicting Signal Peptides with Support Vector Machines
We examine using a Support Vector Machine to predict secretory signal peptides. We predict signal peptides for both prokaryotic and eukaryotic signal organisms. Signalling peptides versus non-signaling peptide...
