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Plasmodium copy number variation scan: gene copy numbers evaluation in haploid genomes

Overview of attention for article published in Malaria Journal, April 2016
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2 tweeters

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15 Dimensions

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54 Mendeley
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Title
Plasmodium copy number variation scan: gene copy numbers evaluation in haploid genomes
Published in
Malaria Journal, April 2016
DOI 10.1186/s12936-016-1258-x
Pubmed ID
Authors

Johann Beghain, Anne-Claire Langlois, Eric Legrand, Laura Grange, Nimol Khim, Benoit Witkowski, Valentine Duru, Laurence Ma, Christiane Bouchier, Didier Ménard, Richard E. Paul, Frédéric Ariey

Abstract

In eukaryotic genomes, deletion or amplification rates have been estimated to be a thousand more frequent than single nucleotide variation. In Plasmodium falciparum, relatively few transcription factors have been identified, and the regulation of transcription is seemingly largely influenced by gene amplification events. Thus copy number variation (CNV) is a major mechanism enabling parasite genomes to adapt to new environmental changes. Currently, the detection of CNVs is based on quantitative PCR (qPCR), which is significantly limited by the relatively small number of genes that can be analysed at any one time. Technological advances that facilitate whole-genome sequencing, such as next generation sequencing (NGS) enable deeper analyses of the genomic variation to be performed. Because the characteristics of Plasmodium CNVs need special consideration in algorithms and strategies for which classical CNV detection programs are not suited a dedicated algorithm to detect CNVs across the entire exome of P. falciparum was developed. This algorithm is based on a custom read depth strategy through NGS data and called PlasmoCNVScan. The analysis of CNV identification on three genes known to have different levels of amplification and which are located either in the nuclear, apicoplast or mitochondrial genomes is presented. The results are correlated with the qPCR experiments, usually used for identification of locus specific amplification/deletion. This tool will facilitate the study of P. falciparum genomic adaptation in response to ecological changes: drug pressure, decreased transmission, reduction of the parasite population size (transition to pre-elimination endemic area).

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 54 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 2%
Unknown 53 98%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 13 24%
Student > Master 10 19%
Researcher 7 13%
Student > Bachelor 5 9%
Student > Doctoral Student 2 4%
Other 6 11%
Unknown 11 20%
Readers by discipline Count As %
Agricultural and Biological Sciences 14 26%
Biochemistry, Genetics and Molecular Biology 11 20%
Pharmacology, Toxicology and Pharmaceutical Science 4 7%
Immunology and Microbiology 4 7%
Computer Science 3 6%
Other 5 9%
Unknown 13 24%

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 19 April 2016.
All research outputs
#3,463,004
of 7,571,218 outputs
Outputs from Malaria Journal
#1,453
of 2,502 outputs
Outputs of similar age
#123,748
of 270,094 outputs
Outputs of similar age from Malaria Journal
#116
of 174 outputs
Altmetric has tracked 7,571,218 research outputs across all sources so far. This one has received more attention than most of these and is in the 52nd percentile.
So far Altmetric has tracked 2,502 research outputs from this source. They receive a mean Attention Score of 4.8. This one is in the 37th percentile – i.e., 37% 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 270,094 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 174 others from the same source and published within six weeks on either side of this one. This one is in the 22nd percentile – i.e., 22% of its contemporaries scored the same or lower than it.