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References from Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues. Local targets link to admitted publications; unresolved targets remain external evidence.
Genome-Wide Estimates of Transposable Element Insertion and Deletion Rates in Drosophila Melanogaster
10.1093/gbe/evx050 · 2017 · External reference
Basic local alignment search tool
10.1016/s0022-2836(05)80360-2 · 1990 · External reference
Transposable element sequence fragments incorporated into coding and noncoding transcripts modulate the transcriptome of human pluripotent stem cells
10.1093/nar/gkab710 · 2021 · External reference
LINE-1 RNA splicing and influences on mammalian gene expression
10.1093/nar/gkl027 · 2006 · External reference
Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression
10.1371/journal.pcbi.1006453 · 2019 · External reference
Locus-specific expression of transposable elements in single cells with CELLO-seq
10.1038/s41587-021-01093-1 · 2021 · External reference
Ten things you should know about transposable elements
10.1186/s13059-018-1577-z · 2018 · External reference
The retrotransposon copia controls the relative levels of its gene products post-transcriptionally by differential expression from its two major mRNAs
10.1093/nar/18.10.2947 · 1990 · External reference
HeT-A and TART, two Drosophila retrotransposons with a bona fide role in chromosome structure for more than 60 million years
10.1159/000084947 · 2005 · External reference
The Landscapes of Full-Length Transcripts and Splice Isoforms as Well as Transposons Exonization in the Lepidopteran Model System, Bombyx mori
10.3389/fgene.2021.704162 · 2021 · External reference
NanoPack: visualizing and processing long-read sequencing data
10.1093/bioinformatics/bty149 · 2018 · External reference
STAR: ultrafast universal RNA-seq aligner
10.1093/bioinformatics/bts635 · 2013 · External reference
Nanopore Sequencing Enables Comprehensive Transposable Element Epigenomic Profiling
10.1016/j.molcel.2020.10.024 · 2020 · External reference
A Quantitative, Genome-Wide Analysis in Drosophila Reveals Transposable Elements’ Influence on Gene Expression Is Species-Specific
10.1093/gbe/evad160 · 2023 · External reference
Maternally inherited piRNAs direct transient heterochromatin formation at active transposons during early Drosophila embryogenesis
10.7554/elife.68573 · 2021 · External reference
Long-read direct RNA sequencing by 5'-Cap capturing reveals the impact of Piwi on the widespread exonization of transposable elements in locusts
10.1080/15476286.2019.1602437 · 2019 · External reference
Analysis of RNA-Seq Data Using TEtranscripts
10.1007/978-1-4939-7710-9_11 · 2018 · External reference
TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets
10.1093/bioinformatics/btv422 · 2015 · External reference
Measuring and interpreting transposable element expression
10.1038/s41576-020-0251-y · 2020 · External reference
Tissue specificity of Drosophila P element transposition is regulated at the level of mRNA splicing
10.1016/0092-8674(86)90480-0 · 1986 · External reference
TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes
10.1093/nar/gkw953 · 2017 · External reference
Minimap2: pairwise alignment for nucleotide sequences
10.1093/bioinformatics/bty191 · 2018 · External reference
Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly
10.1126/science.abk2432 · 2022 · External reference
The nucleotide sequence of Drosophila melanogaster copia-specific 2.1-kb mRNA
10.1093/nar/17.5.2134 · 1989 · External reference
A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore
10.3390/cells9081776 · 2020 · External reference
Long-Read cDNA Sequencing Enables a “Gene-Like” Transcript Annotation of Transposable Elements
10.1105/tpc.20.00115 · 2020 · External reference
Unveiling transposon dynamics: Advancing TE expression analysis in *Drosophila* with long-read sequencing
10.24072/pci.genomics.100250 · 2024 · External reference
Gypsy transposition correlates with the production of a retroviral envelope-like protein under the tissue-specific control of the Drosophila flamenco gene
10.1002/j.1460-2075.1994.tb06760.x · 1994 · External reference
Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues - Processed Data, Scripts & Supplementary Material [Data set].
10.5281/zenodo.10277511 · 2023 · External reference
Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila
10.1038/s41467-022-29518-8 · 2022 · External reference
Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules
10.1038/s41598-019-51470-9 · 2019 · External reference
DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update)
10.1093/nar/gkac194 · 2022 · External reference
Liftoff: accurate mapping of gene annotations
10.1093/bioinformatics/btaa1016 · 2021 · External reference
Transposable elements and the epigenetic regulation of the genome
10.1038/nrg2072 · 2007 · External reference
piRNA-mediated regulation of transposon alternative splicing in the soma and germ line
10.1038/nature25018 · 2017 · External reference
The pogo transposable element family of Drosophila melanogaster
10.1007/bf00299145 · 1992 · External reference
Investigation of chimeric reads using the MinION
10.12688/f1000research.11547.2 · 2017 · External reference
A unified classification system for eukaryotic transposable elements
10.1038/nrg2165 · 2007 · External reference
RepeatCraft: a meta-pipeline for repetitive element de-fragmentation and annotation
10.1093/bioinformatics/bty745 · 2019 · External reference
SQuIRE reveals locus-specific regulation of interspersed repeat expression
10.1093/nar/gky1301 · 2019 · External reference
Virus-like particle formation of Drosophila copia through autocatalytic processing
10.1002/j.1460-2075.1990.tb08140.x · 1990 · External reference
