Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression

Bioconda: sustainable and comprehensive software distribution for the life sciences

(2018) Björn Grüning et al.   NATURE METHODS

Tau Activates Transposable Elements in Alzheimer’s Disease

(2018) Caiwei Guo et al.   Cell Reports

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Human transposon insertion profiling: Analysis, visualization and identification of somatic LINE-1 insertions in ovarian cancer

(2017) Zuojian Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HERV-K(HML-2), a seemingly silent subtenant - but still waters run deep

(2016) Kirsten Hanke et al.   APMIS

The role of human endogenous retroviruses in brain development and function

(2016) Kristien Mortelmans et al.   APMIS

Human endogenous retroviruses: friend or foe?

(2016) Robin A. Weiss   APMIS

Human endogenous retroviruses in neurologic disease

(2016) Tove Christensen   APMIS

MMR: a tool for read multi-mapper resolution

(2015) André Kahles et al.   BIOINFORMATICS

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

(2015) Ying Jin et al.   BIOINFORMATICS

Differential expression analysis of human endogenous retroviruses based on ENCODE RNA-seq data

(2015) Kerstin Haase et al.   BMC Medical Genomics

Dynamic Transcription of Distinct Classes of Endogenous Retroviral Elements Marks Specific Populations of Early Human Embryonic Cells

(2015) Jonathan Göke et al.   Cell Stem Cell

Are human endogenous retroviruses triggers of autoimmune diseases? Unveiling associations of three diseases and viral loci

(2015) Bjørn A. Nexø et al.   IMMUNOLOGIC RESEARCH

Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells

(2015) Edward J. Grow et al.   NATURE

Retrotransposon insertions in the clonal evolution of pancreatic ductal adenocarcinoma

(2015) Nemanja Rodić et al.   NATURE MEDICINE

Human endogenous retrovirus-K contributes to motor neuron disease

(2015) Wenxue Li et al.   Science Translational Medicine

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

(2014) S. Anders et al.   BIOINFORMATICS

Transcriptional landscape of repetitive elements in normal and cancer human cells

(2014) Steven W Criscione et al.   BMC GENOMICS

Regulation of the Human Endogenous Retrovirus K (HML-2) Transcriptome by the HIV-1 Tat Protein

(2014) M. J. Gonzalez-Hernandez et al.   JOURNAL OF VIROLOGY

The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity

(2014) Xinyi Lu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Defining functional DNA elements in the human genome

(2014) M. Kellis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microarray analysis reveals global modulation of endogenous retroelement transcription by microbes

(2014) George R Young et al.   Retrovirology

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

(2013) Veena P Gnanakkan et al.   BMC GENOMICS

Pathoscope: Species identification and strain attribution with unassembled sequencing data

(2013) O. E. Francis et al.   GENOME RESEARCH

'There and back again': revisiting the pathophysiological roles of human endogenous retroviruses in the post-genomic era

(2013) G. Magiorkinis et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

HERV-K(HML-2), the Best Preserved Family of HERVs: Endogenization, Expression, and Implications in Health and Disease

(2013) Oliver Hohn et al.   Frontiers in Oncology

Identifying differentially expressed transcripts from RNA-seq data with biological variation

(2012) Peter Glaus et al.   BIOINFORMATICS

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Cole Trapnell et al.   Nature Protocols

Dfam: a database of repetitive DNA based on profile hidden Markov models

(2012) Travis J. Wheeler et al.   NUCLEIC ACIDS RESEARCH

Microarray-Based Sketches of the HERV Transcriptome Landscape

(2012) Philippe Pérot et al.   PLoS One

Human Endogenous Retrovirus Expression Is Inversely Associated with Chronic Immune Activation in HIV-1 Infection

(2012) Christopher E. Ormsby et al.   PLoS One

HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency

(2012) Federico A Santoni et al.   Retrovirology

What Makes Each Brain Unique

(2012) Fred H. Gage et al.   SCIENTIFIC AMERICAN

Molecular characteristics of Human Endogenous Retrovirus type-W in schizophrenia and bipolar disorder

(2012) H Perron et al.   Translational Psychiatry

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Human Endogenous Retrovirus K(HML-2) Gag- and Env-Specific T-Cell Responses Are Infrequently Detected in HIV-1-Infected Subjects Using Standard Peptide Matrix-Based Screening

(2011) R. Brad Jones et al.   Clinical and Vaccine Immunology

Characterization of Human Endogenous Retroviral Elements in the Blood of HIV-1-Infected Individuals

(2011) R. Contreras-Galindo et al.   JOURNAL OF VIROLOGY

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

Repetitive DNA and next-generation sequencing: computational challenges and solutions

(2011) Todd J. Treangen et al.   NATURE REVIEWS GENETICS

Identification, characterization, and comparative genomic distribution of the HERV-K (HML-2) group of human endogenous retroviruses

(2011) Ravi P Subramanian et al.   Retrovirology

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads

(2011) Ernest Turro et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

L1 retrotransposition in neurons is modulated by MeCP2

(2010) Alysson R. Muotri et al.   NATURE

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Estimating enrichment of repetitive elements from high-throughput sequence data

(2010) Daniel S Day et al.   GENOME BIOLOGY

RNA-Seq gene expression estimation with read mapping uncertainty

(2009) Bo Li et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Many LINE1 elements contribute to the transcriptome of human somatic cells

(2009) Sanjida H Rangwala et al.   GENOME BIOLOGY

Expression patterns of transcribed human endogenous retrovirus HERV-K(HML-2) loci in human tissues and the need for a HERV Transcriptome Project

(2008) Aline Flockerzi et al.   BMC GENOMICS

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Regression of human kidney cancer following allogeneic stem cell transplantation is associated with recognition of an HERV-E antigen by T cells

(2008) Yoshiyuki Takahashi et al.   JOURNAL OF CLINICAL INVESTIGATION

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS