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HyLiTE: accurate and flexible analysis of gene expression in hybrid and allopolyploid species

Overview of attention for article published in BMC Bioinformatics, January 2015
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  • Above-average Attention Score compared to outputs of the same age (52nd percentile)
  • Average Attention Score compared to outputs of the same age and source

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1 Facebook page

Citations

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15 Dimensions

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51 Mendeley
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Title
HyLiTE: accurate and flexible analysis of gene expression in hybrid and allopolyploid species
Published in
BMC Bioinformatics, January 2015
DOI 10.1186/s12859-014-0433-8
Pubmed ID
Authors

Wandrille Duchemin, Pierre-Yves Dupont, Matthew A Campbell, Austen RD Ganley, Murray P Cox

Abstract

BackgroundForming a new species through the merger of two or more divergent parent species is increasingly seen as a key phenomenon in the evolution of many biological systems. However, little is known about how expression of parental gene copies (homeologs) responds following genome merger. High throughput RNA sequencing now makes this analysis technically feasible, but tools to determine homeolog expression are still in their infancy.ResultsHere we present HyLiTE ¿ a single-step analysis to obtain tables of homeolog expression in a hybrid or allopolyploid and its parent species directly from raw mRNA sequence files. By implementing on-the-fly detection of diagnostic parental polymorphisms, HyLiTE can perform SNP calling and read classification simultaneously, thus allowing HyLiTE to be run as parallelized code. HyLiTE accommodates any number of parent species, multiple data sources (including genomic DNA reads to improve SNP detection), and implements a statistical framework optimized for genes with low to moderate expression.ConclusionsHyLiTE is a flexible and easy-to-use program designed for bench biologists to explore patterns of gene expression following genome merger. HyLiTE offers practical advantages over manual methods and existing programs, has been designed to accommodate a wide range of genome merger systems, can identify SNPs that arose following genome merger, and offers accurate performance on non-model organisms.

Twitter Demographics

The data shown below were collected from the profiles of 3 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 51 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Spain 2 4%
United States 2 4%
Netherlands 1 2%
Sweden 1 2%
Unknown 45 88%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 18 35%
Researcher 13 25%
Student > Doctoral Student 3 6%
Student > Bachelor 3 6%
Student > Master 2 4%
Other 6 12%
Unknown 6 12%
Readers by discipline Count As %
Agricultural and Biological Sciences 28 55%
Biochemistry, Genetics and Molecular Biology 15 29%
Computer Science 1 2%
Mathematics 1 2%
Unknown 6 12%

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 02 December 2015.
All research outputs
#8,825,560
of 15,047,368 outputs
Outputs from BMC Bioinformatics
#3,403
of 5,549 outputs
Outputs of similar age
#127,284
of 283,530 outputs
Outputs of similar age from BMC Bioinformatics
#18
of 41 outputs
Altmetric has tracked 15,047,368 research outputs across all sources so far. This one is in the 39th percentile – i.e., 39% of other outputs scored the same or lower than it.
So far Altmetric has tracked 5,549 research outputs from this source. They receive a mean Attention Score of 5.0. This one is in the 35th percentile – i.e., 35% 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 283,530 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 52% of its contemporaries.
We're also able to compare this research output to 41 others from the same source and published within six weeks on either side of this one. This one is in the 46th percentile – i.e., 46% of its contemporaries scored the same or lower than it.