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A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens

Overview of attention for article published in Genome Medicine, November 2014
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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 (93rd percentile)
  • High Attention Score compared to outputs of the same age and source (82nd percentile)

Mentioned by

blogs
1 blog
twitter
23 tweeters
facebook
1 Facebook page

Citations

dimensions_citation
28 Dimensions

Readers on

mendeley
130 Mendeley
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Title
A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens
Published in
Genome Medicine, November 2014
DOI 10.1186/s13073-014-0101-7
Pubmed ID
Authors

Maha R Farhat, B Jesse Shapiro, Samuel K Sheppard, Caroline Colijn, Megan Murray

Abstract

Whole genome sequencing is increasingly used to study phenotypic variation among infectious pathogens and to evaluate their relative transmissibility, virulence, and immunogenicity. To date, relatively little has been published on how and how many pathogen strains should be selected for studies associating phenotype and genotype. There are specific challenges when identifying genetic associations in bacteria which often comprise highly structured populations. Here we consider general methodological questions related to sampling and analysis focusing on clonal to moderately recombining pathogens. We propose that a matched sampling scheme constitutes an efficient study design, and provide a power calculator based on phylogenetic convergence. We demonstrate this approach by applying it to genomic datasets for two microbial pathogens: Mycobacterium tuberculosis and Campylobacter species.

Twitter Demographics

The data shown below were collected from the profiles of 23 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 130 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 3 2%
United Kingdom 1 <1%
Brazil 1 <1%
Spain 1 <1%
Netherlands 1 <1%
Unknown 123 95%

Demographic breakdown

Readers by professional status Count As %
Researcher 35 27%
Student > Ph. D. Student 21 16%
Student > Master 17 13%
Student > Bachelor 9 7%
Professor 6 5%
Other 23 18%
Unknown 19 15%
Readers by discipline Count As %
Agricultural and Biological Sciences 41 32%
Biochemistry, Genetics and Molecular Biology 29 22%
Medicine and Dentistry 12 9%
Immunology and Microbiology 11 8%
Computer Science 3 2%
Other 13 10%
Unknown 21 16%

Attention Score in Context

This research output has an Altmetric Attention Score of 24. 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 09 January 2015.
All research outputs
#887,110
of 16,027,726 outputs
Outputs from Genome Medicine
#193
of 1,078 outputs
Outputs of similar age
#12,587
of 192,027 outputs
Outputs of similar age from Genome Medicine
#9
of 52 outputs
Altmetric has tracked 16,027,726 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 94th percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 1,078 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 23.6. This one has done well, scoring higher than 82% 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 192,027 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 93% of its contemporaries.
We're also able to compare this research output to 52 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 82% of its contemporaries.