TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets

Transposable elements become active and mobile in the genomes of aging mammalian somatic tissues

(2016) Marco De Cecco et al.   Aging-US

A tumor-promoting mechanism mediated by retrotransposon-encoded reverse transcriptase is active in human transformed cell lines

(2015) Ilaria Sciamanna et al.   Oncotarget

Regulatory roles of LINE-1-encoded reverse transcriptase in cancer onset and progression

(2015) Ilaria Sciamanna et al.   Oncotarget

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing

(2014) Bo W. Han et al.   BIOINFORMATICS

Transcriptional landscape of repetitive elements in normal and cancer human cells

(2014) Steven W Criscione et al.   BMC GENOMICS

Two waves of de novo methylation during mouse germ cell development

(2014) A. Molaro et al.   GENES & DEVELOPMENT

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

Increased L1 Retrotransposition in the Neuronal Genome in Schizophrenia

(2014) Miki Bundo et al.   NEURON

Dynamic regulation of human endogenous retroviruses mediates factor-induced reprogramming and differentiation potential

(2014) M. Ohnuki 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

Death by transposition - the enemy within?

(2013) John M. Sedivy et al.   BIOESSAYS

TE-array—a high throughput tool to study transposon transcription

(2013) Veena P Gnanakkan et al.   BMC GENOMICS

Endogenous Retrotransposition Activates Oncogenic Pathways in Hepatocellular Carcinoma

(2013) Ruchi Shukla et al.   CELL

Multiple roles for Piwi in silencing Drosophila transposons

(2013) N. V. Rozhkov et al.   GENES & DEVELOPMENT

DmGTSF1 is necessary for Piwi-piRISC-mediated transcriptional transposon silencing in the Drosophila ovary

(2013) H. Ohtani et al.   GENES & DEVELOPMENT

The Role of Transposable Elements in Health and Diseases of the Central Nervous System

(2013) M. T. Reilly et al.   JOURNAL OF NEUROSCIENCE

Activation of transposable elements during aging and neuronal decline in Drosophila

(2013) Wanhe Li et al.   NATURE NEUROSCIENCE

Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA

(2013) Anas Fadloun et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transposition-Driven Genomic Heterogeneity in the Drosophila Brain

(2013) P. N. Perrat et al.   SCIENCE

LINE-1 Retrotransposition in the Nervous System

(2012) Charles A. Thomas et al.   Annual Review of Cell and Developmental Biology

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

Active human retrotransposons: variation and disease

(2012) Dustin C Hancks et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Modelling and simulating generic RNA-Seq experiments with the flux simulator

(2012) Thasso Griebel et al.   NUCLEIC ACIDS RESEARCH

MIPS PlantsDB: a database framework for comparative plant genome research

(2012) Thomas Nussbaumer et al.   NUCLEIC ACIDS RESEARCH

Transposable Elements in TDP-43-Mediated Neurodegenerative Disorders

(2012) Wanhe Li et al.   PLoS One

Landscape of Somatic Retrotransposition in Human Cancers

(2012) E. Lee et al.   SCIENCE

Transposable elements reveal a stem cell-specific class of long noncoding RNAs

(2012) David Kelley et al.   GENOME BIOLOGY

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Ataxia telangiectasia mutated (ATM) modulates long interspersed element-1 (L1) retrotransposition in human neural stem cells

(2011) N. G. Coufal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exome sequencing and analysis of induced pluripotent stem cells identify the cilia-related gene male germ cell-associated kinase (MAK) as a cause of retinitis pigmentosa

(2011) B. A. Tucker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data

(2011) Dongjun Chung et al.   PLoS Computational Biology

A Gibbs sampling strategy applied to the mapping of ambiguous short-sequence tags

(2010) Jianrong Wang et al.   BIOINFORMATICS

LINE-1 Retrotransposition Activity in Human Genomes

(2010) Christine R. Beck et al.   CELL

Investigating repetitively matching short sequencing reads: The enigmatic nature of H3K9me3

(2010) Jeffrey A. Rosenfeld et al.   Epigenetics

Epigenetic Control of Retrotransposon Expression in Human Embryonic Stem Cells

(2010) A. Macia et al.   MOLECULAR AND CELLULAR BIOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Derepression of an endogenous long terminal repeat activates the CSF1R proto-oncogene in human lymphoma

(2010) Björn Lamprecht et al.   NATURE MEDICINE

Estimating enrichment of repetitive elements from high-throughput sequence data

(2010) Daniel S Day et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

L1 retrotransposition occurs mainly in embryogenesis and creates somatic mosaicism

(2009) H. Kano et al.   GENES & DEVELOPMENT

L1 retrotransposition in human neural progenitor cells

(2009) Nicole G. Coufal et al.   NATURE

The regulated retrotransposon transcriptome of mammalian cells

(2009) Geoffrey J Faulkner et al.   NATURE GENETICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Active Alu retrotransposons in the human genome

(2008) E. A. Bennett et al.   GENOME RESEARCH

Simple and Globally Convergent Methods for Accelerating the Convergence of Any EM Algorithm

(2008) RAVI VARADHAN et al.   SCANDINAVIAN JOURNAL OF STATISTICS