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Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands

Overview of attention for article published in Proceedings of the National Academy of Sciences of the United States of America, October 2013
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (84th percentile)
  • Above-average Attention Score compared to outputs of the same age and source (51st percentile)

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5 X users
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16 patents
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2 Facebook pages

Citations

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162 Dimensions

Readers on

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284 Mendeley
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1 CiteULike
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Title
Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands
Published in
Proceedings of the National Academy of Sciences of the United States of America, October 2013
DOI 10.1073/pnas.1310615110
Pubmed ID
Authors

Jacob Schreiber, Zachary L. Wescoe, Robin Abu-Shumays, John T. Vivian, Baldandorj Baatar, Kevin Karplus, Mark Akeson

Abstract

Cytosine, 5-methylcytosine, and 5-hydroxymethylcytosine were identified during translocation of single DNA template strands through a modified Mycobacterium smegmatis porin A (M2MspA) nanopore under control of phi29 DNA polymerase. This identification was based on three consecutive ionic current states that correspond to passage of modified or unmodified CG dinucleotides and their immediate neighbors through the nanopore limiting aperture. To establish quality scores for these calls, we examined ~3,300 translocation events for 48 distinct DNA constructs. Each experiment analyzed a mixture of cytosine-, 5-methylcytosine-, and 5-hydroxymethylcytosine-bearing DNA strands that contained a marker that independently established the correct cytosine methylation status at the target CG of each molecule tested. To calculate error rates for these calls, we established decision boundaries using a variety of machine-learning methods. These error rates depended upon the identity of the bases immediately 5' and 3' of the targeted CG dinucleotide, and ranged from 1.7% to 12.2% for a single-pass read. We estimate that Q40 values (0.01% error rates) for methylation status calls could be achieved by reading single molecules 5-19 times depending upon sequence context.

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X Demographics

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 284 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 4 1%
Germany 3 1%
Spain 2 <1%
United Kingdom 2 <1%
Belgium 2 <1%
Czechia 1 <1%
Brazil 1 <1%
Netherlands 1 <1%
Korea, Republic of 1 <1%
Other 2 <1%
Unknown 265 93%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 73 26%
Researcher 64 23%
Student > Master 40 14%
Student > Bachelor 24 8%
Student > Doctoral Student 11 4%
Other 33 12%
Unknown 39 14%
Readers by discipline Count As %
Agricultural and Biological Sciences 95 33%
Biochemistry, Genetics and Molecular Biology 57 20%
Chemistry 21 7%
Engineering 19 7%
Physics and Astronomy 14 5%
Other 32 11%
Unknown 46 16%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 9. 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 16 January 2024.
All research outputs
#3,914,244
of 24,625,114 outputs
Outputs from Proceedings of the National Academy of Sciences of the United States of America
#36,641
of 101,438 outputs
Outputs of similar age
#33,008
of 218,725 outputs
Outputs of similar age from Proceedings of the National Academy of Sciences of the United States of America
#448
of 948 outputs
Altmetric has tracked 24,625,114 research outputs across all sources so far. Compared to these this one has done well and is in the 84th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 101,438 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 38.8. This one has gotten more attention than average, scoring higher than 59% of its peers.
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 218,725 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 84% of its contemporaries.
We're also able to compare this research output to 948 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 51% of its contemporaries.