- Home
- Publications
- Publication Search
- Publication Details
Title
Measuring and interpreting transposable element expression
Authors
Keywords
-
Journal
NATURE REVIEWS GENETICS
Volume -, Issue -, Pages -
Publisher
Springer Science and Business Media LLC
Online
2020-06-23
DOI
10.1038/s41576-020-0251-y
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition
- (2020) Bernardo Rodriguez-Martin et al. NATURE GENETICS
- Pan-genomics in the human genome era
- (2020) Rachel M. Sherman et al. NATURE REVIEWS GENETICS
- Mobile genomics: tools and techniques for tackling transposons
- (2020) Kathryn O'Neill et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- Comparative analysis on the expression of L1 loci using various RNA-Seq preparations
- (2020) Tiffany Kaul et al. Mobile DNA
- Genome-wide DNA methylation and transcriptomic profiles in the lifestyle strategies and asexual development of the forest fungal pathogen Heterobasidion parviporum
- (2019) Zhen Zeng et al. Epigenetics
- Fast and accurate genomic analyses using genome graphs
- (2019) Goran Rakocevic et al. NATURE GENETICS
- SQuIRE reveals locus-specific regulation of interspersed repeat expression
- (2019) Wan R Yang et al. NUCLEIC ACIDS RESEARCH
- RepetDB: a unified resource for transposable element references
- (2019) Joëlle Amselem et al. Mobile DNA
- LINE-2 transposable elements are a source of functional human microRNAs and target sites
- (2019) Rebecca Petri et al. PLoS Genetics
- Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila
- (2019) Gabriel E. Rech et al. PLoS Genetics
- Transposable elements drive widespread expression of oncogenes in human cancers
- (2019) Hyo Sik Jang et al. NATURE GENETICS
- L1 drives IFN in senescent cells and promotes age-associated inflammation
- (2019) Marco De Cecco et al. NATURE
- LIONS: Analysis Suite for Detecting and Quantifying Transposable Element Initiated Transcription from RNA-seq
- (2019) Artem Babaian et al. BIOINFORMATICS
- Long-read direct RNA sequencing by 5’-Cap capturing reveals the impact of Piwi on the widespread exonization of transposable elements in locusts
- (2019) Feng Jiang et al. RNA Biology
- LINE-1 Evasion of Epigenetic Repression in Humans
- (2019) Francisco J. Sanchez-Luque et al. MOLECULAR CELL
- Paired-end mappability of transposable elements in the human genome
- (2019) Corinne E. Sexton et al. Mobile DNA
- On the Population Dynamics of Junk: A Review on the Population Genomics of Transposable Elements
- (2019) Yann Bourgeois et al. Genes
- Rapid evolution of piRNA pathway and its transposon targets in Japanese flounder (Paralichthys olivaceus)
- (2019) Haofei Song et al. Comparative Biochemistry and Physiology D-Genomics & Proteomics
- LTR retroelement expansion of the human cancer transcriptome and immunopeptidome revealed by de novo transcript assembly
- (2019) Jan Attig et al. GENOME RESEARCH
- Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
- (2019) Daehwan Kim et al. NATURE BIOTECHNOLOGY
- Transposable elements in human genetic disease
- (2019) Lindsay M. Payer et al. NATURE REVIEWS GENETICS
- Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression
- (2019) Matthew L. Bendall et al. PLoS Computational Biology
- TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements
- (2019) Fabio CP Navarro et al. PLoS Computational Biology
- Exploratory analysis of transposable elements expression in the C. elegans early embryo
- (2019) Federico Ansaloni et al. BMC BIOINFORMATICS
- Pedigree-based estimation of human mobile element retrotransposition rates
- (2019) Julie Feusier et al. GENOME RESEARCH
- dsRNA-Seq: Identification of Viral Infection by Purifying and Sequencing dsRNA
- (2019) Carolyn J. Decker et al. Viruses-Basel
- Long Noncoding RNAs and Repetitive Elements: Junk or Intimate Evolutionary Partners?
- (2019) Hyunmin Lee et al. TRENDS IN GENETICS
- Tools and best practices for retrotransposon analysis using high-throughput sequencing data
- (2019) Aurélie Teissandier et al. Mobile DNA
- A benchmark of transposon insertion detection tools using real data
- (2019) Pol Vendrell-Mir et al. Mobile DNA
- LINE-1 ORF2p expression is nearly imperceptible in human cancers
- (2019) Daniel Ardeljan et al. Mobile DNA
- TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model
- (2019) Gökhan Karakülah et al. PeerJ
- TEcandidates: prediction of genomic origin of expressed transposable elements using RNA-seq data
- (2018) Braulio Valdebenito-Maturana et al. BIOINFORMATICS
- A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity
- (2018) Michelle Percharde et al. CELL
- Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations
- (2018) Jesse J. Salk et al. NATURE REVIEWS GENETICS
- Spliced integrated retrotransposed element (SpIRE) formation in the human genome
- (2018) Peter A. Larson et al. PLOS BIOLOGY
- The case for not masking away repetitive DNA
- (2018) R. Keith Slotkin Mobile DNA
- Variation graph toolkit improves read mapping by representing genetic variation in the reference
- (2018) Erik Garrison et al. NATURE BIOTECHNOLOGY
- Computational tools to unmask transposable elements
- (2018) Patricia Goerner-Potvin et al. NATURE REVIEWS GENETICS
- ERVmap analysis reveals genome-wide transcription of human endogenous retroviruses
- (2018) Maria Tokuyama et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Bridging gaps in transposable element research with single-molecule and single-cell technologies
- (2018) Claudia Kutter et al. Mobile DNA
- Transposable Element Misregulation Is Linked to the Divergence between Parental piRNA Pathways in Drosophila Hybrids
- (2017) Valèria Romero-Soriano et al. Genome Biology and Evolution
- LTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes
- (2017) Rosa Maria Cossu et al. Genome Biology and Evolution
- Evolution and Diversity of Transposable Elements in Vertebrate Genomes
- (2017) Cibele G. Sotero-Caio et al. Genome Biology and Evolution
- Heritable L1 retrotransposition in the mouse primordial germline and early embryo
- (2017) Sandra R. Richardson et al. GENOME RESEARCH
- The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology
- (2017) Eugene J. Gardner et al. GENOME RESEARCH
- piRNA-mediated regulation of transposon alternative splicing in the soma and germ line
- (2017) Felipe Karam Teixeira et al. NATURE
- KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks
- (2017) Michaël Imbeault et al. NATURE
- DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats
- (2017) David Brocks et al. NATURE GENETICS
- LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo
- (2017) Joanna W Jachowicz et al. NATURE GENETICS
- Detecting DNA cytosine methylation using nanopore sequencing
- (2017) Jared T Simpson et al. NATURE METHODS
- Salmon provides fast and bias-aware quantification of transcript expression
- (2017) Rob Patro et al. NATURE METHODS
- Mobile DNA in Health and Disease
- (2017) Haig H. Kazazian et al. NEW ENGLAND JOURNAL OF MEDICINE
- The SIN3A histone deacetylase complex is required for a complete transcriptional response to hypoxia
- (2017) Maria Tiana et al. NUCLEIC ACIDS RESEARCH
- Structural variants caused byAluinsertions are associated with risks for many human diseases
- (2017) Lindsay M. Payer et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Dynamics of genome size evolution in birds and mammals
- (2017) Aurélie Kapusta et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- L1 Mosaicism in Mammals: Extent, Effects, and Evolution
- (2017) Geoffrey J. Faulkner et al. TRENDS IN GENETICS
- TRIM28 Controls a Gene Regulatory Network Based on Endogenous Retroviruses in Human Neural Progenitor Cells
- (2017) Per Ludvik Brattås et al. Cell Reports
- Considerations and complications of mapping small RNA high-throughput data to transposable elements
- (2017) Alexandros Bousios et al. Mobile DNA
- Genome-wide characterization of human L1 antisense promoter-driven transcripts
- (2016) Steven W. Criscione et al. BMC GENOMICS
- Bioinformatic analyses of sense and antisense expression from terminal inverted repeat transposons inDrosophilasomatic cells
- (2016) Andrew W. Harrington et al. FLY
- A hot L1 retrotransposon evades somatic repression and initiates human colorectal cancer
- (2016) Emma C. Scott et al. GENOME RESEARCH
- Long Terminal Repeats: From Parasitic Elements to Building Blocks of the Transcriptional Regulatory Repertoire
- (2016) Peter J. Thompson et al. MOLECULAR CELL
- DNA methylation on N6-adenine in mammalian embryonic stem cells
- (2016) Tao P. Wu et al. NATURE
- Near-optimal probabilistic RNA-seq quantification
- (2016) Nicolas L Bray et al. NATURE BIOTECHNOLOGY
- Regulatory activities of transposable elements: from conflicts to benefits
- (2016) Edward B. Chuong et al. NATURE REVIEWS GENETICS
- A comprehensive approach to expression of L1 loci
- (2016) Prescott Deininger et al. NUCLEIC ACIDS RESEARCH
- Division of labor amongMycobacterium smegmatisRNase H enzymes: RNase H1 activity of RnhA or RnhC is essential for growth whereas RnhB and RnhA guard against killing by hydrogen peroxide in stationary phase
- (2016) Richa Gupta et al. NUCLEIC ACIDS RESEARCH
- L1Base 2: more retrotransposition-active LINE-1s, more mammalian genomes
- (2016) Tobias Penzkofer et al. NUCLEIC ACIDS RESEARCH
- A Novel Analytical Strategy to Identify Fusion Transcripts between Repetitive Elements and Protein Coding-Exons Using RNA-Seq
- (2016) Tianyuan Wang et al. PLoS One
- The DNA methyltransferase DNMT3C protects male germ cells from transposon activity
- (2016) Joan Barau et al. SCIENCE
- Improved Placement of Multi-mapping Small RNAs
- (2016) Nathan R. Johnson et al. G3-Genes Genomes Genetics
- The Arabidopsis thaliana mobilome and its impact at the species level
- (2016) Leandro Quadrana et al. eLife
- Activation of individual L1 retrotransposon instances is restricted to cell-type dependent permissive loci
- (2016) Claude Philippe et al. eLife
- Restricting retrotransposons: a review
- (2016) John L. Goodier Mobile DNA
- Pluripotency and the endogenous retrovirus HERVH: Conflict or serendipity?
- (2015) Zsuzsanna Izsvák et al. BIOESSAYS
- TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets
- (2015) Ying Jin et al. BIOINFORMATICS
- DNA-Demethylating Agents Target Colorectal Cancer Cells by Inducing Viral Mimicry by Endogenous Transcripts
- (2015) David Roulois et al. CELL
- Inhibiting DNA Methylation Causes an Interferon Response in Cancer via dsRNA Including Endogenous Retroviruses
- (2015) Katherine B. Chiappinelli et al. CELL
- Primate-Specific ORF0 Contributes to Retrotransposon-Mediated Diversity
- (2015) Ahmet M. Denli et al. CELL
- Antisense Transcription of Retrotransposons in Drosophila: An Origin of Endogenous Small Interfering RNA Precursors
- (2015) J. Russo et al. GENETICS
- Comparative Analysis of Transposable Elements Highlights Mobilome Diversity and Evolution in Vertebrates
- (2015) Domitille Chalopin et al. Genome Biology and Evolution
- Atrans-Dominant Form of Gag Restricts Ty1 Retrotransposition and Mediates Copy Number Control
- (2015) Agniva Saha et al. JOURNAL OF VIROLOGY
- A survey of transposable element classification systems – A call for a fundamental update to meet the challenge of their diversity and complexity
- (2015) Benoît Piégu et al. MOLECULAR PHYLOGENETICS AND EVOLUTION
- Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells
- (2015) Edward J. Grow et al. NATURE
- Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm
- (2015) Meilina Ong-Abdullah et al. NATURE
- An integrated map of structural variation in 2,504 human genomes
- (2015) Peter H. Sudmant et al. NATURE
- The Dfam database of repetitive DNA families
- (2015) Robert Hubley et al. NUCLEIC ACIDS RESEARCH
- Enhancer RNAs: A Class of Long Noncoding RNAs Synthesized at Enhancers: Figure 1.
- (2015) Tae-Kyung Kim et al. Cold Spring Harbor Perspectives in Biology
- Transposable element detection from whole genome sequence data
- (2015) Adam D. Ewing Mobile DNA
- Transcriptional landscape of repetitive elements in normal and cancer human cells
- (2014) Steven W Criscione et al. BMC GENOMICS
- An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons
- (2014) Frank M. J. Jacobs et al. NATURE
- Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells
- (2014) Jichang Wang et al. NATURE
- The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity
- (2014) Xinyi Lu et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- An antisense promoter in mouse L1 retrotransposon open reading frame-1 initiates expression of diverse fusion transcripts and limits retrotransposition
- (2014) Jingfeng Li et al. NUCLEIC ACIDS RESEARCH
- Potential for genomic instability associated with retrotranspositionally-incompetent L1 loci
- (2014) Kristine J. Kines et al. NUCLEIC ACIDS RESEARCH
- Identification of RNA polymerase III-transcribed Alu loci by computational screening of RNA-Seq data
- (2014) Anastasia Conti et al. NUCLEIC ACIDS RESEARCH
- euL1db: the European database of L1HS retrotransposon insertions in humans
- (2014) Ashfaq A. Mir et al. NUCLEIC ACIDS RESEARCH
- Distinct isoform of FABP7 revealed by screening for retroelement-activated genes in diffuse large B-cell lymphoma
- (2014) F. E. Lock et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes
- (2014) J. M. C. Tubio et al. SCIENCE
- TE-array—a high throughput tool to study transposon transcription
- (2013) Veena P Gnanakkan et al. BMC GENOMICS
- Dealing with Pervasive Transcription
- (2013) Torben Heick Jensen et al. MOLECULAR CELL
- RNA-mediated interference and reverse transcription control the persistence of RNA viruses in the insect model Drosophila
- (2013) Bertsy Goic et al. NATURE IMMUNOLOGY
- RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond
- (2013) Stephane E. Castel et al. NATURE REVIEWS GENETICS
- Trim24-repressed VL30 retrotransposons regulate gene expression by producing noncoding RNA
- (2013) Benjamin Herquel et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA
- (2013) Anas Fadloun et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- mRNA–mRNA duplexes that autoelicit Staufen1-mediated mRNA decay
- (2013) Chenguang Gong et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- The Microprocessor controls the activity of mammalian retrotransposons
- (2013) Sara R Heras et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs
- (2013) Aurélie Kapusta et al. PLoS Genetics
- Active Transposition in Genomes
- (2012) Cheng Ran Lisa Huang et al. Annual Review of Genetics
- STAR: ultrafast universal RNA-seq aligner
- (2012) Alexander Dobin et al. BIOINFORMATICS
- Single-Neuron Sequencing Analysis of L1 Retrotransposition and Somatic Mutation in the Human Brain
- (2012) Gilad D. Evrony et al. CELL
- The impact of transposable elements on eukaryotic genomes: From genome size increase to genetic adaptation to stressful environments
- (2012) Benoît Chénais et al. GENE
- Identification and characterization of transposable element-mediated chimeric transcripts from porcine Refseq and EST databases
- (2012) Hong-Seok Ha et al. Genes & Genomics
- High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression
- (2012) P. Batut et al. GENOME RESEARCH
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- How important are transposons for plant evolution?
- (2012) Damon Lisch NATURE REVIEWS GENETICS
- Retrotransposons Control Fruit-Specific, Cold-Dependent Accumulation of Anthocyanins in Blood Oranges
- (2012) E. Butelli et al. PLANT CELL
- Fast Computation and Applications of Genome Mappability
- (2012) Thomas Derrien et al. PLoS One
- Microarray Analysis of LTR Retrotransposon Silencing Identifies Hdac1 as a Regulator of Retrotransposon Expression in Mouse Embryonic Stem Cells
- (2012) Judith Reichmann et al. PLoS Computational Biology
- The genomic landscape shaped by selection on transposable elements across 18 mouse strains
- (2012) Christoffer Nellåker et al. GENOME BIOLOGY
- Transposable elements reveal a stem cell-specific class of long noncoding RNAs
- (2012) David Kelley et al. GENOME BIOLOGY
- C-GATE - catalogue of genes affected by transposable elements
- (2012) Rita Rebollo et al. Mobile DNA
- Widespread establishment and regulatory impact of Alu exons in human genes
- (2011) S. Shen et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- LINE-1 Retrotransposition Activity in Human Genomes
- (2010) Christine R. Beck et al. CELL
- Global analysis of DNA methylation and transcription of human repetitive sequences.
- (2010) Béatrice Horard et al. Epigenetics
- High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes
- (2010) A. D. Ewing et al. GENOME RESEARCH
- R2 Retrotransposons Encode a Self-Cleaving Ribozyme for Processing from an rRNA Cotranscript
- (2010) D. G. Eickbush et al. MOLECULAR AND CELLULAR BIOLOGY
- Epigenetic Control of Retrotransposon Expression in Human Embryonic Stem Cells
- (2010) A. Macia et al. MOLECULAR AND CELLULAR BIOLOGY
- Somatic expression of LINE-1 elements in human tissues
- (2010) Victoria P. Belancio et al. NUCLEIC ACIDS RESEARCH
- Demethylation of a LINE-1 antisense promoter in the cMet locus impairs Met signalling through induction of illegitimate transcription
- (2010) B Weber et al. ONCOGENE
- Genome-Wide Patterns of Adaptation to Temperate Environments Associated with Transposable Elements in Drosophila
- (2010) Josefa González et al. PLoS Genetics
- TopHat: discovering splice junctions with RNA-Seq
- (2009) Cole Trapnell et al. BIOINFORMATICS
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen
- (2009) R. Keith Slotkin et al. CELL
- Exon-trapping mediated by the human retrotransposon SVA
- (2009) D. C. Hancks et al. GENOME RESEARCH
- 5'-Transducing SVA retrotransposon groups spread efficiently throughout the human genome
- (2009) A. Damert et al. GENOME RESEARCH
- Isolation of cancer-specific chimeric transcripts induced by hypomethylation of the LINE-1 antisense promoter
- (2009) Hazel A. Cruickshanks et al. GENOMICS
- The regulated retrotransposon transcriptome of mammalian cells
- (2009) Geoffrey J Faulkner et al. NATURE GENETICS
- Identification of an active LTR retrotransposon in rice
- (2009) Nathalie Picault et al. PLANT JOURNAL
- Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants
- (2009) J. S. Hawkins et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Genetic Evidence That the Non-Homologous End-Joining Repair Pathway Is Involved in LINE Retrotransposition
- (2009) Jun Suzuki et al. PLoS Genetics
- Many LINE1 elements contribute to the transcriptome of human somatic cells
- (2009) Sanjida H Rangwala et al. GENOME BIOLOGY
- Trex1 Prevents Cell-Intrinsic Initiation of Autoimmunity
- (2008) Daniel B. Stetson et al. CELL
- A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE
- (2008) Geoffrey J. Faulkner et al. GENOMICS
- Genome-Wide Assessments Reveal Extremely High Levels of Polymorphism of Two Active Families of Mouse Endogenous Retroviral Elements
- (2008) Ying Zhang et al. PLoS Genetics
Become a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get StartedAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started