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Estimation of ribosome profiling performance and reproducibility at various levels of resolution

Overview of attention for article published in Biology Direct, May 2016
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Title
Estimation of ribosome profiling performance and reproducibility at various levels of resolution
Published in
Biology Direct, May 2016
DOI 10.1186/s13062-016-0127-4
Pubmed ID
Authors

Alon Diament, Tamir Tuller

Abstract

Ribosome profiling (or Ribo-seq) is currently the most popular methodology for studying translation; it has been employed in recent years to decipher various fundamental gene expression regulation aspects. The main promise of the approach is its ability to detect ribosome densities over an entire transcriptome in high resolution of single codons. Indeed, dozens of ribo-seq studies have included results related to local ribosome densities in different parts of the transcript; nevertheless, the performance of Ribo-seq has yet to be quantitatively evaluated and reported in a large-scale multi-organismal and multi-protocol study of currently available datasets. Here we provide the first objective evaluation of Ribo-seq at the resolution of a single nucleotide(s) using clear, interpretable measures, based on the analysis of 15 experiments, 6 organisms, and a total of 612, 961 transcripts. Our major conclusion is that the ability to infer signals of ribosomal densities at nucleotide scale is considerably lower than previously thought, as signals at this level are not reproduced well in experimental replicates. In addition, we provide various quantitative measures that connect the expected error rate with Ribo-seq analysis resolution. The analysis of Ribo-seq data at the resolution of codons and nucleotides provides a challenging task, calls for task-specific statistical methods and further protocol improvements. We believe that our results are important for every researcher studying translation and specifically for researchers analyzing data generated by the Ribo-seq approach. This article was reviewed by Dmitrij Frishman, Eugene Koonin and Frank Eisenhaber.

Twitter Demographics

The data shown below were collected from the profiles of 2 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 80 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 2 3%
United Kingdom 1 1%
France 1 1%
Argentina 1 1%
Unknown 75 94%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 27 34%
Researcher 20 25%
Student > Master 10 13%
Student > Doctoral Student 5 6%
Student > Bachelor 3 4%
Other 5 6%
Unknown 10 13%
Readers by discipline Count As %
Agricultural and Biological Sciences 33 41%
Biochemistry, Genetics and Molecular Biology 30 38%
Computer Science 4 5%
Mathematics 1 1%
Immunology and Microbiology 1 1%
Other 2 3%
Unknown 9 11%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 11 May 2016.
All research outputs
#5,811,584
of 7,684,314 outputs
Outputs from Biology Direct
#499
of 521 outputs
Outputs of similar age
#187,517
of 267,934 outputs
Outputs of similar age from Biology Direct
#12
of 12 outputs
Altmetric has tracked 7,684,314 research outputs across all sources so far. This one is in the 13th percentile – i.e., 13% of other outputs scored the same or lower than it.
So far Altmetric has tracked 521 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.7. This one is in the 2nd percentile – i.e., 2% of its peers scored the same or lower than it.
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We're also able to compare this research output to 12 others from the same source and published within six weeks on either side of this one. This one is in the 1st percentile – i.e., 1% of its contemporaries scored the same or lower than it.