References

Genome-Wide Estimates of Transposable Element Insertion and Deletion Rates in Drosophila Melanogaster

10.1093/gbe/evx050 · 2017 · External reference

Discovering and detecting transposable elements in genome sequences

10.1093/bib/bbm048 · 2007 · External reference

T-lex3: an accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data

10.1093/bioinformatics/btz727 · 2020 · External reference

On the Base Composition of Transposable Elements

10.3390/ijms23094755 · 2022 · External reference

Ten things you should know about transposable elements

10.1186/s13059-018-1577-z · 2018 · External reference

A new simulation pipeline enhances benchmarking of transposon polymorphism detection tools

10.24072/pci.genomics.100418 · 2025 · External reference

RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing

10.7717/peerj.2942 · 2017 · External reference

Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast

10.1186/s13100-023-00296-4 · 2023 · External reference

The impact of retrotransposons on human genome evolution

10.1038/nrg2640 · 2009 · External reference

Transcription-related mutations and GC content drive variation in nucleotide substitution rates across the genomes of Arabidopsis thaliana and Arabidopsis lyrata

10.1186/1471-2148-7-66 · 2007 · External reference

All Quiet on the TE Front? The Role of Chromatin in Transposable Element Silencing

10.3390/cells11162501 · 2022 · External reference

New evaluation methods of read mapping by 17 aligners on simulated and empirical NGS data: an updated comparison of DNA- and RNA-Seq data from Illumina and Ion Torrent technologies

10.1007/s00521-021-06188-z · 2021 · External reference

Transposable element detection from whole genome sequence data

10.1186/s13100-015-0055-3 · 2015 · External reference

YAHA: fast and flexible long-read alignment with optimal breakpoint detection

10.1093/bioinformatics/bts456 · 2012 · External reference

Transposable element profiles reveal cell line identity and loss of heterozygosity in Drosophila cell culture

10.1093/genetics/iyab113 · 2021 · External reference

ART: a next-generation sequencing read simulator

10.1093/bioinformatics/btr708 · 2012 · External reference

Jitterbug: somatic and germline transposon insertion detection at single-nucleotide resolution

10.1186/s12864-015-1975-5 · 2015 · External reference

RetroSeq: transposable element discovery from next-generation sequencing data

10.1093/bioinformatics/bts697 · 2013 · External reference

An ancient retrotransposal insertion causes Fukuyama-type congenital muscular dystrophy

10.1038/28653 · 1998 · External reference

Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Complex Dynamics of Transposable Element Insertions in Drosophila melanogaster

10.1371/journal.pgen.1002487 · 2012 · External reference

PoPoolationTE2: Comparative Population Genomics of Transposable Elements Using Pool-Seq

10.1093/molbev/msw137 · 2016 · External reference

Fast gapped-read alignment with Bowtie 2

10.1038/nmeth.1923 · 2012 · External reference

e-lerat/replicaTE

10.5281/zenodo.15519958 · 2025 · External reference

Repeat in Genomes: How and Why You Should Consider Them in Genome Analyses?

10.1016/b978-0-12-809633-8.20227-6 · 2019 · External reference

10.1007/s00239-001-0059-0 · 2002 · Admitted local publication

Population-specific dynamics and selection patterns of transposable element insertions in European natural populations

10.1111/mec.14963 · 2019 · External reference

Fast and accurate short read alignment with Burrows-Wheeler transform

10.1093/bioinformatics/btp324 · 2009 · External reference

Whole Genome Resequencing Reveals Natural Target Site Preferences of Transposable Elements in Drosophila melanogaster

10.1371/journal.pone.0030008 · 2012 · External reference

Conserved Noncoding Elements Influence the Transposable Element Landscape in Drosophila

10.1093/gbe/evy104 · 2018 · External reference

McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data

10.1534/g3.117.043893 · 2017 · External reference

R: A Language and Environment for Statistical Computing

2017 · External reference

Benchmarking computational tools for polymorphic transposable element detection

10.1093/bib/bbw072 · 2017 · External reference

The Use of RelocaTE and Unassembled Short Reads to Produce High-Resolution Snapshots of Transposable Element Generated Diversity in Rice

10.1534/g3.112.005348 · 2013 · External reference

L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis

10.1101/gr.226993.117 · 2018 · External reference

The B73 Maize Genome: Complexity, Diversity, and Dynamics

10.1126/science.1178534 · 2009 · External reference

Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation

10.7554/elife.20777 · 2016 · External reference

A benchmark of transposon insertion detection tools using real data

10.1186/s13100-019-0197-9 · 2019 · External reference

Supplementary data and figures for "Particular sequence characteristics induce bias in the detection of polymorphic transposable element insertions"

10.5281/zenodo.15576566 · 2025 · External reference

Variation in mutation, recombination, and transposition rates in Drosophila melanogaster and Drosophila simulans

10.1101/gr.277383.122 · 2023 · External reference

Insights into social insects from the genome of the honeybee Apis mellifera

10.1038/nature05260 · 2006 · External reference

A unified classification system for eukaryotic transposable elements

10.1038/nrg2165 · 2007 · External reference

A benchmark and an algorithm for detecting germline transposon insertions and measuring de novo transposon insertion frequencies

10.1093/nar/gkab010 · 2021 · External reference

Transposable Elements: Distribution, Polymorphism, and Climate Adaptation in Populus

10.3389/fpls.2022.814718 · 2022 · External reference

TEMP: a computational method for analyzing transposable element polymorphism in populations

10.1093/nar/gku323 · 2014 · External reference