ArticlePLoS computational biology2019
Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression.
Article in PLoS computational biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 136 papers.
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Who cites it
136 citing papers in PubMed.
- Epigenetic priming enhances antitumor immunity in platinum-resistant ovarian cancer.The Journal of clinical investigation · 2022Trial
- Review
- Active Human Transposable Elements: Long-Read Sequencing Technologies, Computational Analysis, and Implications for Human Disease.Biomolecules · 2026Review
- Chronic interferon signaling at baseline is associated with acquired resistance to immunotherapy in metastatic melanoma.Cell reports. Medicine · 2026Article
- Transposable Element Activation: A Hallmark of Cancer.Cancer discovery · 2026Review
- Fertility Gene Introns Harbor Transposable Elements that Shape Y-Loop Architecture.bioRxiv : the preprint server for biology · 2026Article
- Differential gene expression of retrotransposons (LTR and non-LTR) in peripheral blood leukocytes of people with gout.Arthritis research & therapy · 2026Article
- LINE-1 retrotransposons: Multifaceted functions and regulatory mechanisms in health and disease.Molecular therapy. Nucleic acids · 2026Review
- A phylogeny-guided framework for decoding mechanisms of human endogenous retrovirus regulation in health and disease.bioRxiv : the preprint server for biology · 2026Article
- Locus-specific LINE-1 mRNA expression reflects cell-type- and stimulus-specific senescence states.Nucleic acids research · 2026Article
- Characterization of Cellular Senescence in Primary Human Astrocytes.bioRxiv : the preprint server for biology · 2026Article
- HERV-K HML-2 transcriptional profiling and splicing pattern unveiled by direct single-molecule long-read RNA sequencing.Mobile DNA · 2026Article
- Pluripotency Factors Modulate Interferon Signaling in Embryonic Stem Cells.bioRxiv : the preprint server for biology · 2026Article
- Smoking-induced dysregulation of transposable elements in the small airway epithelium.Respiratory research · 2026Article
- A comprehensive annotation of conserved protein domains in human endogenous retroviruses.NAR genomics and bioinformatics · 2026Article
- Male sterility in Drosophila hybrids revealed by a multi-generational transcriptomic analysis of genes and transposable elements in testes.BMC biology · 2026Article
- Analysis of HERV-K (HML2) Expression in Colorectal Cancer Samples.Epigenomes · 2026Article
- CDK9 Inhibition with enitociclib reveals influence on HERV and LINE RNA abundances in whole blood, T-, and B-Cell lines.BMC medical genomics · 2026Article
- An expression signature of 19 human endogenous retroviruses identifies immunogenic luminal breast cancers likely to respond to immunotherapy.Frontiers in oncology · 2026Article
- Transposable Element Dysregulation in Hepatocellular Carcinoma: Epigenetic Mechanisms, Immune Remodeling, and Translational Opportunities.Journal of hepatocellular carcinoma · 2026Review
76 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors.
Funding
Abstract
Characterization of Human Endogenous Retrovirus (HERV) expression within the transcriptomic landscape using RNA-seq is complicated by uncertainty in fragment assignment because of sequence similarity. We present Telescope, a computational software tool that provides accurate estimation of transposable element expression (retrotranscriptome) resolved to specific genomic locations. Telescope directly addresses uncertainty in fragment assignment by reassigning ambiguously mapped fragments to the most probable source transcript as determined within a Bayesian statistical model. We demonstrate the utility of our approach through single locus analysis of HERV expression in 13 ENCODE cell types. When examined at this resolution, we find that the magnitude and breadth of the retrotranscriptome can be vastly different among cell types. Furthermore, our approach is robust to differences in sequencing technology and demonstrates that the retrotranscriptome has potential to be used for cell type identification. We compared our tool with other approaches for quantifying transposable element (TE) expression, and found that Telescope has the greatest resolution, as it estimates expression at specific TE insertions rather than at the TE subfamily level. Telescope performs highly accurate quantification of the retrotranscriptomic landscape in RNA-seq experiments, revealing a differential complexity in the transposable element biology of complex systems not previously observed. Telescope is available at https://github.com/mlbendall/telescope.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.