Transcription start site signal profiling improves transposable element RNA expression analysis at locus-level

Transposable Element Regulation and Expression in Cancer

(2021) Erin E. Grundy et al.   FEBS Journal

The role of retrotransposable elements in ageing and age-associated diseases

(2021) Vera Gorbunova et al.   NATURE

Locus-specific expression analysis of transposable elements

(2021) Robert Schwarz et al.   BRIEFINGS IN BIOINFORMATICS

Mobile genomics: tools and techniques for tackling transposons

(2020) Kathryn O'Neill et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Measuring and interpreting transposable element expression

(2020) Sophie Lanciano et al.   NATURE REVIEWS GENETICS

Nanopore Sequencing Enables Comprehensive Transposable Element Epigenomic Profiling

(2020) Adam D. Ewing et al.   MOLECULAR CELL

SQuIRE reveals locus-specific regulation of interspersed repeat expression

(2019) Wan R Yang et al.   NUCLEIC ACIDS RESEARCH

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

(2019) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Transposable elements drive widespread expression of oncogenes in human cancers

(2019) Hyo Sik Jang et al.   NATURE GENETICS

Safety and tolerability of Triumeq in amyotrophic lateral sclerosis: the Lighthouse trial

(2019) Julian Gold et al.   Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration

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

(2019) Matthew L. Bendall et al.   PLoS Computational Biology

Transposable element expression in tumors is associated with immune infiltration and increased antigenicity

(2019) Yu Kong et al.   Nature Communications

Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia

(2019) Oliver H. Tam et al.   Cell Reports

The role of transposable elements activity in aging and their possible involvement in laminopathic diseases

(2019) Davide Andrenacci et al.   AGEING RESEARCH REVIEWS

Tools and best practices for retrotransposon analysis using high-throughput sequencing data

(2019) Aurélie Teissandier et al.   Mobile DNA

Whole-genome sequencing reveals principles of brain retrotransposition in neurodevelopmental disorders

(2018) Jasmine Jacob-Hirsch et al.   CELL RESEARCH

The Retrotransposon storm and the dangers of a Collyer's genome

(2018) Josh Dubnau   CURRENT OPINION IN GENETICS & DEVELOPMENT

Tau Activates Transposable Elements in Alzheimer’s Disease

(2018) Caiwei Guo et al.   Cell Reports

Retrotransposons in the development and progression of amyotrophic lateral sclerosis

(2018) Abigail L Savage et al.   JOURNAL OF NEUROLOGY NEUROSURGERY AND PSYCHIATRY

Exonization of an Intronic LINE-1 Element Causing Becker Muscular Dystrophy as a Novel Mutational Mechanism in Dystrophin Gene

(2017) Ana Gonçalves et al.   Genes

Muscle-relevant genes marked by stable H3K4me2/3 profiles and enriched MyoD binding during myogenic differentiation

(2017) Huanhuan Cui et al.   PLoS One

A comprehensive approach to expression of L1 loci

(2016) Prescott Deininger et al.   NUCLEIC ACIDS RESEARCH

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Ying Jin et al.   BIOINFORMATICS

Polyester: simulating RNA-seq datasets with differential transcript expression

(2015) Alyssa C. Frazee et al.   BIOINFORMATICS

Onco-exaptation of an endogenous retroviral LTR drives IRF5 expression in Hodgkin lymphoma

(2015) A Babaian et al.   ONCOGENE

Transcriptional landscape of repetitive elements in normal and cancer human cells

(2014) Steven W Criscione et al.   BMC GENOMICS

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Intron Retention and TE Exonization Events inZRANB2

(2012) Sang-Je Park et al.   COMPARATIVE AND FUNCTIONAL GENOMICS

Exonization of transposed elements: A challenge and opportunity for evolution

(2011) Jürgen Schmitz et al.   BIOCHIMIE

Diverse Splicing Patterns of Exonized Alu Elements in Human Tissues

(2008) Lan Lin et al.   PLoS Genetics