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Transposable Elements

Overview of attention for book
Cover of 'Transposable Elements'

Table of Contents

  1. Altmetric Badge
    Book Overview
  2. Altmetric Badge
    Chapter 1 An Overview of Best Practices for Transposable Element Identification, Classification, and Annotation in Eukaryotic Genomes
  3. Altmetric Badge
    Chapter 2 Assembly-Free Detection and Quantification of Transposable Elements with dnaPipeTE
  4. Altmetric Badge
    Chapter 3 Detecting Horizontal Transfer of Transposons
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    Chapter 4 Genotyping of Transposable Element Insertions Segregating in Human Populations Using Short-Read Realignments
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    Chapter 5 A Pangenome Approach to Detect and Genotype TE Insertion Polymorphisms.
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    Chapter 6 Experimental Validation of Transposable Element Insertions Using the Polymerase Chain Reaction (PCR).
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    Chapter 7 Quantification of LINE-1 RNA Expression from Bulk RNA-seq Using L1EM
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    Chapter 8 Genome-Wide Young L1 Methylation Profiling by bs-ATLAS-seq
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    Chapter 9 Nanopore Sequencing to Identify Transposable Element Insertions and Their Epigenetic Modifications
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    Chapter 10 Targeted Nanopore Resequencing and Methylation Analysis of LINE-1 Retrotransposons
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    Chapter 11 Inferring Protein-DNA Binding Profiles at Interspersed Repeats Using HiChIP and PAtChER
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    Chapter 12 Affinity-Based Interactome Analysis of Endogenous LINE-1 Macromolecules
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    Chapter 13 LINE-1 Retrotransposition Assays in Embryonic Stem Cells
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    Chapter 14 Experimental Approaches to Study Somatic Transposition in Drosophila Using Whole-Genome DNA Sequencing.
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    Chapter 15 Precise and Scarless Insertion of Transposable Elements by Cas9-Mediated Genome Engineering
  17. Altmetric Badge
    Chapter 16 Epigenetic Manipulation of Transposable and Repetitive Elements
  18. Altmetric Badge
    Chapter 17 Genetic Knockout of TE Insertions by CRISPR-Cas9
Attention for Chapter 5: A Pangenome Approach to Detect and Genotype TE Insertion Polymorphisms.
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About this Attention Score

  • Good Attention Score compared to outputs of the same age (72nd percentile)
  • High Attention Score compared to outputs of the same age and source (91st percentile)

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Chapter title
A Pangenome Approach to Detect and Genotype TE Insertion Polymorphisms.
Chapter number 5
Book title
Transposable Elements
Published in
Methods in molecular biology, January 2023
DOI 10.1007/978-1-0716-2883-6_5
Pubmed ID
36449159
Book ISBNs
978-1-07-162882-9, 978-1-07-162883-6
Authors

Groza, Cristian, Bourque, Guillaume, Goubert, Clément, Cristian Groza, Guillaume Bourque, Clément Goubert

Abstract

Pangenome graphs are flexible data structures that contain the genetic variation that exists in a population of genomes and describe the sequences of the many possible ensuing haplotypes. Here, we use such a pangenome graph to represent and genotype transposable element (TE) polymorphisms. By combining the transposable element annotation (Alus, L1s, and SVAs) of the human genome reference with novel transposable element insertions observed in two high-quality assemblies (HG002 and HG00733), we show how to create a transposable element pangenome that consists of ~1.2 million reference and 2939 non-reference transposable elements. We then demonstrate this approach by aligning short-read sequencing data and genotyping transposable element deletions and insertions with reasonable specificity and sensitivity (0.85 F1-score).

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X Demographics

The data shown below were collected from the profiles of 9 X users who shared this research output. Click here to find out more about how the information was compiled.
 Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 6 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 6 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 3 50%
Unspecified 1 17%
Researcher 1 17%
Unknown 1 17%
Readers by discipline Count As %
Agricultural and Biological Sciences 3 50%
Unspecified 1 17%
Unknown 2 33%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 5. 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 2022.
All research outputs
#7,037,089
of 24,929,945 outputs
Outputs from Methods in molecular biology
#2,089
of 14,000 outputs
Outputs of similar age
#130,612
of 469,621 outputs
Outputs of similar age from Methods in molecular biology
#59
of 720 outputs
Altmetric has tracked 24,929,945 research outputs across all sources so far. This one has received more attention than most of these and is in the 71st percentile.
So far Altmetric has tracked 14,000 research outputs from this source. They receive a mean Attention Score of 3.5. This one has done well, scoring higher than 84% 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 469,621 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 72% of its contemporaries.
We're also able to compare this research output to 720 others from the same source and published within six weeks on either side of this one. This one has done particularly well, scoring higher than 91% of its contemporaries.

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