Transcriptome analyses of tumor-adjacent somatic tissues reveal genes co-expressed with transposable elements

SQuIRE reveals locus-specific regulation of interspersed repeat expression

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

Paired-end mappability of transposable elements in the human genome

(2019) Corinne E. Sexton et al.   Mobile DNA

A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity

(2018) Michelle Percharde et al.   CELL

Interplay between RNASEH2 and MOV10 controls LINE-1 retrotransposition

(2018) Jongsu Choi et al.   NUCLEIC ACIDS RESEARCH

Transcription factor profiling reveals molecular choreography and key regulators of human retrotransposon expression

(2018) Xiaoji Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Cancer Transcriptome Quantifies Repeat Element Polarization between Immunotherapy Responsive and T Cell Suppressive Classes

(2018) Alexander Solovyov et al.   Cell Reports

LINE-1 protein localization and functional dynamics during the cell cycle

(2018) Paolo Mita et al.   eLife

Dissection of affinity captured LINE-1 macromolecular complexes

(2018) Martin S Taylor et al.   eLife

The case for not masking away repetitive DNA

(2018) R. Keith Slotkin   Mobile DNA

Hypomethylation, endogenous retrovirus expression, and interferon signaling in testicular germ cell tumors

(2018) Michael C. Haffner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators

(2017) Nian Liu et al.   NATURE

KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks

(2017) Michaël Imbeault et al.   NATURE

LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo

(2017) Joanna W Jachowicz et al.   NATURE GENETICS

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

A hot L1 retrotransposon evades somatic repression and initiates human colorectal cancer

(2016) Emma C. Scott et al.   GENOME RESEARCH

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

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

The aspartyl protease DDI2 activates Nrf1 to compensate for proteasome dysfunction

(2016) Shun Koizumi et al.   eLife

Activation of individual L1 retrotransposon instances is restricted to cell-type dependent permissive loci

(2016) Claude Philippe et al.   eLife

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

Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells

(2015) Edward J. Grow et al.   NATURE

C2H2 zinc finger proteins greatly expand the human regulatory lexicon

(2015) Hamed S Najafabadi et al.   NATURE BIOTECHNOLOGY

LINE-1 expression and retrotransposition in Barrett’s esophagus and esophageal carcinoma

(2015) Tara T. Doucet-O'Hare et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Zinc-Finger Antiviral Protein ZAP Inhibits LINE and Alu Retrotransposition

(2015) John B. Moldovan et al.   PLoS Genetics

Long Interspersed Element-1 Protein Expression Is a Hallmark of Many Human Cancers

(2014) Nemanja Rodić et al.   AMERICAN JOURNAL OF PATHOLOGY

Widespread contribution of transposable elements to the innovation of gene regulatory networks

(2014) Vasavi Sundaram et al.   GENOME RESEARCH

Comprehensive molecular characterization of gastric adenocarcinoma

(2014) Adam J. Bass et al.   NATURE

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons

(2014) Frank M. J. Jacobs et al.   NATURE

DNA methylation dynamics of the human preimplantation embryo

(2014) Zachary D. Smith et al.   NATURE

SIRT6 represses LINE1 retrotransposons by ribosylating KAP1 but this repression fails with stress and age

(2014) Michael Van Meter et al.   Nature Communications

In Vitro Screening for Compounds That Enhance Human L1 Mobilization

(2013) Natsuko Terasaki et al.   PLoS One

Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs

(2013) Aurélie Kapusta et al.   PLoS Genetics

A normalization strategy for comparing tag count data

(2012) Koji Kadota et al.   Algorithms for Molecular Biology

LINE-1 Retrotransposition Events Regulate Gene Expression After X-Ray Irradiation

(2012) Ferya Banaz-Yaşar et al.   DNA AND CELL BIOLOGY

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Comprehensive genomic characterization of squamous cell lung cancers

(2012)   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

LINE-1 retrotransposition in human neuroblastoma cells is affected by oxidative stress

(2011) Gianfranco Giorgi et al.   CELL AND TISSUE RESEARCH

Dynamic control of endogenous retroviruses during development

(2011) Helen M. Rowe et al.   VIROLOGY

Transposable elements have rewired the core regulatory network of human embryonic stem cells

(2010) Galih Kunarso et al.   NATURE GENETICS

Somatic expression of LINE-1 elements in human tissues

(2010) Victoria P. Belancio et al.   NUCLEIC ACIDS RESEARCH

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

Induction of long interspersed nucleotide element-1 (L1) retrotransposition by 6-formylindolo[3,2-b]carbazole (FICZ), a tryptophan photoproduct

(2010) N. Okudaira et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Embryonic stem cells use ZFP809 to silence retroviral DNAs

(2009) Daniel Wolf et al.   NATURE

The regulated retrotransposon transcriptome of mammalian cells

(2009) Geoffrey J Faulkner et al.   NATURE GENETICS

Many LINE1 elements contribute to the transcriptome of human somatic cells

(2009) Sanjida H Rangwala et al.   GENOME BIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS