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Citations per year

Number of citations per year for the bioinformatics software tool RRS
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This map represents all the scientific publications referring to RRS per scientific context
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RRS specifications

Information


Unique identifier OMICS_20309
Name RRS
Alternative name Ribosome Release Score
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainers


  • person_outline Eric Lander
  • person_outline Mitchell Guttman

Publication for Ribosome Release Score

RRS citations

 (10)
library_books

Global analysis of ribosome associated noncoding RNAs unveils new modes of translational regulation

2017
Proc Natl Acad Sci U S A
PMCID: 5699049
PMID: 29087317
DOI: 10.1073/pnas.1708433114

[…] ribo-lncRNAs contained at least one sORF encoding ≥10 aa, but only 397 met the threshold of ≥1 rpkM for RFs on at least one sORF of ≥30 nt (). To seek evidence of sORF translation, we determined the ribosome release score (RRS) () (), which quantifies the decline in RF number (drop-off) seen after the termination codon (). Comparison of TE and RRS values of protein-coding and ribo-lncRNA ORFs ide […]

library_books

Dynamic transcriptome changes during adipose tissue energy expenditure reveal critical roles for long noncoding RNA regulators

2017
PLoS Biol
PMCID: 5538645
PMID: 28763438
DOI: 10.1371/journal.pbio.2002176

[…] For the lncRNA analysis, we employed the multiexonic lncRNA catalog (approximately 1,500 lncRNAs) established in our earlier work, which was stringently filtered by PhyloCSF score, CPC analysis, and ribosome release score []. Hierarchical clustering analysis of mRNA expression profiles demonstrated that samples within each condition tightly clustered with each other (). Notably, the clustering of […]

library_books

A lncRNA fine tunes the dynamics of a cell state transition involving Lin28, let 7 and de novo DNA methylation

2017
eLife
PMCID: 5562443
PMID: 28820723
DOI: 10.7554/eLife.23468.032

[…] e, we designated linc1281 as Ephemeron (Eprn). Ribosomal profiling analysis indicated that Eprn is indeed a non-coding RNA, with the longest predicted open reading frame (80 amino acids) possessing a ribosome release score typical of a non-coding sequence (). Eprn is located in a region of high transposable element (TE) content, with its exons comprised of 76.4% annotated TE sequences (including E […]

library_books

Role of lncRNAs in Cellular Aging

2016
PMCID: 5138193
PMID: 27999563
DOI: 10.3389/fendo.2016.00151

[…] howed that many lncRNAs were, in fact, ribosome-bound while high sensitivity mass spectrometry failed to identify those small peptides from supposed “lncRNA ORFs” (). With the help of bioinformatics, ribosome release score has been calculated for protein-coding and non-coding RNAs. Ribosome release score is produced by using ribosome dissociation and association values of given part of RNA. Using […]

library_books

Long Noncoding RNA Identification: Comparing Machine Learning Based Tools for Long Noncoding Transcripts Discrimination

2016
Biomed Res Int
PMCID: 5153550
PMID: 28042575
DOI: 10.1155/2016/8496165

[…] nslation terminates, the ribosomes will be released from protein-coding transcripts. Therefore, it is likely to capture a considerable drop of ribosome occupancy when ribosomes reach stop codons. The Ribosome Release Score to capture this change of ribosome occupancy is defined:(12)Ribosome  Release  Score=Ribosome  coverage  of  ORF/lengthORFRibosome  coverage  of  3′UTR/length3′UTR,and a protein […]

library_books

Incredible RNA: Dual Functions of Coding and Noncoding

2016
Mol Cells
PMCID: 4870183
PMID: 27137091
DOI: 10.14348/molcells.2016.0039

[…] neutrophil cells (). Intriguingly, the ribosome association is mostly restricted to sORFs, and this association rapidly decays at the location of ribosome release at the stop codon, estimated as the ribosome release score (RRS) (). For example, MALAT1 is highly expressed in the nucleus during cancer metastasis () and has a putative sORF that can encode about 71 amino acids. In fact, the sORFs are […]


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RRS institution(s)
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA; Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA, USA

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