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The Repertoire Dissimilarity Index as a method to compare lymphocyte receptor repertoires

Overview of attention for article published in BMC Bioinformatics, March 2017
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Title
The Repertoire Dissimilarity Index as a method to compare lymphocyte receptor repertoires
Published in
BMC Bioinformatics, March 2017
DOI 10.1186/s12859-017-1556-5
Pubmed ID
Authors

Christopher R. Bolen, Florian Rubelt, Jason A. Vander Heiden, Mark M. Davis

Abstract

The B and T cells of the human adaptive immune system leverage a highly diverse repertoire of antigen-specific receptors to protect the human body from pathogens. The sequencing and analysis of immune repertoires is emerging as an important tool to understand immune responses, whether beneficial or harmful (in the case of autoimmunity). However, methods for studying these repertoires, and for directly comparing different immune repertoires, are lacking. In this paper, we present a non-parametric method for directly comparing sequencing repertoires, with the goal of rigorously quantifying differences in V, D, and J gene segment utilization. This method, referred to as the Repertoire Dissimilarity Index (RDI), uses a bootstrapped subsampling approach to account for variance in sequencing depth, and, coupled with a data simulation approach, allows for direct quantification of the average variation between repertoires. We use the RDI method to recapitulate known differences in the formation of the CD4(+) and CD8(+) T cell repertoires, and further show that antigen-driven activation of naïve CD8(+) T cells is more selective than in the CD4(+) repertoire, resulting in a more specialized CD8(+) memory repertoire. We prove that the RDI method is an accurate and versatile method for comparisons of immune repertoires. The RDI method has been implemented as an R package, and is available for download through Bitbucket.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 75 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 1%
Unknown 74 99%

Demographic breakdown

Readers by professional status Count As %
Researcher 22 29%
Student > Ph. D. Student 13 17%
Professor 6 8%
Student > Master 6 8%
Student > Bachelor 5 7%
Other 12 16%
Unknown 11 15%
Readers by discipline Count As %
Immunology and Microbiology 18 24%
Agricultural and Biological Sciences 15 20%
Biochemistry, Genetics and Molecular Biology 10 13%
Medicine and Dentistry 6 8%
Computer Science 4 5%
Other 10 13%
Unknown 12 16%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 2. 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 03 September 2017.
All research outputs
#13,313,060
of 23,577,654 outputs
Outputs from BMC Bioinformatics
#3,819
of 7,400 outputs
Outputs of similar age
#150,848
of 309,161 outputs
Outputs of similar age from BMC Bioinformatics
#53
of 129 outputs
Altmetric has tracked 23,577,654 research outputs across all sources so far. This one is in the 43rd percentile – i.e., 43% of other outputs scored the same or lower than it.
So far Altmetric has tracked 7,400 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.4. This one is in the 48th percentile – i.e., 48% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 309,161 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 50% of its contemporaries.
We're also able to compare this research output to 129 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 58% of its contemporaries.