Activation of neuronal genes via LINE-1 elements upon global DNA demethylation in human neural progenitors

High-throughput ChIPmentation: freely scalable, single day ChIPseq data generation from very low cell-numbers

(2019) Charlotte Gustafsson et al.   BMC GENOMICS

Pathogenic tau-induced piRNA depletion promotes neuronal death through transposable element dysregulation in neurodegenerative tauopathies

(2018) Wenyan Sun et al.   NATURE NEUROSCIENCE

Tau Activates Transposable Elements in Alzheimer’s Disease

(2018) Caiwei Guo et al.   Cell Reports

KAP1 regulates endogenous retroviruses in adult human cells and contributes to innate immune control

(2018) Christopher HC Tie et al.   EMBO REPORTS

TRIM28 Controls a Gene Regulatory Network Based on Endogenous Retroviruses in Human Neural Progenitor Cells

(2017) Per Ludvik Brattås et al.   Cell Reports

Retrotransposon activation contributes to neurodegeneration in a Drosophila TDP-43 model of ALS

(2017) Lisa Krug et al.   PLoS Genetics

Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia

(2016) Elizabeth J. Bhoj et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genome-wide characterization of human L1 antisense promoter-driven transcripts

(2016) Steven W. Criscione et al.   BMC GENOMICS

Transposable Elements and Their KRAB-ZFP Controllers Regulate Gene Expression in Adult Tissues

(2016) Gabriela Ecco et al.   DEVELOPMENTAL CELL

Loss of Uhrf1 in neural stem cells leads to activation of retroviral elements and delayed neurodegeneration

(2016) Vidya Ramesh et al.   GENES & DEVELOPMENT

L1-associated genomic regions are deleted in somatic cells of the healthy human brain

(2016) Jennifer A Erwin et al.   NATURE NEUROSCIENCE

Regulatory activities of transposable elements: from conflicts to benefits

(2016) Edward B. Chuong et al.   NATURE REVIEWS GENETICS

The landscape of DNA methylation amid a perfect storm of autism aetiologies

(2016) Annie Vogel Ciernia et al.   NATURE REVIEWS NEUROSCIENCE

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

L1Base 2: more retrotransposition-active LINE-1s, more mammalian genomes

(2016) Tobias Penzkofer et al.   NUCLEIC ACIDS RESEARCH

Resolving rates of mutation in the brain using single-neuron genomics

(2016) Gilad D Evrony et al.   eLife

The Developmental Control of Transposable Elements and the Evolution of Higher Species

(2015) Marc Friedli et al.   Annual Review of Cell and Developmental Biology

Defects of mutant DNMT1 are linked to a spectrum of neurological disorders

(2015) Jonathan Baets et al.   BRAIN

Ubiquitous L1 Mosaicism in Hippocampal Neurons

(2015) Kyle R. Upton et al.   CELL

Primate-Specific ORF0 Contributes to Retrotransposon-Mediated Diversity

(2015) Ahmet M. Denli et al.   CELL

Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells

(2015) Jing Liao et al.   NATURE GENETICS

Altered epigenetic regulation in early development associated with schizophrenia

(2015) Hemi Malkki   Nature Reviews Neurology

Cell Lineage Analysis in Human Brain Using Endogenous Retroelements

(2015) Gilad D. Evrony et al.   NEURON

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Human endogenous retrovirus-K contributes to motor neuron disease

(2015) Wenxue Li et al.   Science Translational Medicine

TRIM28 Represses Transcription of Endogenous Retroviruses in Neural Progenitor Cells

(2015) Liana Fasching et al.   Cell Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Severe infantile epileptic encephalopathy due to mutations inPLCB1: expansion of the genotypic and phenotypic disease spectrum

(2014) Adeline Ngoh et al.   DEVELOPMENTAL MEDICINE AND CHILD NEUROLOGY

Evolutionally dynamic L1 regulation in embryonic stem cells

(2014) N. Castro-Diaz et al.   GENES & DEVELOPMENT

Interplay of TRIM28 and DNA methylation in controlling human endogenous retroelements

(2014) Priscilla Turelli et al.   GENOME RESEARCH

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

(2013) Y. Liao et al.   BIOINFORMATICS

Neurodevelopmental disorders among individuals with duplication of 4p13 to 4p12 containing a GABAA receptor subunit gene cluster

(2013) Michelle B Polan et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Stem Cells Expanded from the Human Embryonic Hindbrain Stably Retain Regional Specification and High Neurogenic Potency

(2013) J. Tailor et al.   JOURNAL OF NEUROSCIENCE

Differential L1 regulation in pluripotent stem cells of humans and apes

(2013) Maria C. N. Marchetto et al.   NATURE

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

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

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

(2012) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Capture of Neuroepithelial-Like Stem Cells from Pluripotent Stem Cells Provides a Versatile System for In Vitro Production of Human Neurons

(2012) Anna Falk et al.   PLoS One

LINE-1 Elements in Structural Variation and Disease

(2011) Christine R. Beck et al.   Annual Review of Genomics and Human Genetics

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

In Embryonic Stem Cells, ZFP57/KAP1 Recognize a Methylated Hexanucleotide to Affect Chromatin and DNA Methylation of Imprinting Control Regions

(2011) Simon Quenneville et al.   MOLECULAR CELL

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Rare familial 16q21 microdeletions under a linkage peak implicate cadherin 8 (CDH8) in susceptibility to autism and learning disability

(2010) A. T. Pagnamenta et al.   JOURNAL OF MEDICAL GENETICS

KAP1 controls endogenous retroviruses in embryonic stem cells

(2010) Helen M. Rowe et al.   NATURE

Epigenetic Reprogramming in Plant and Animal Development

(2010) Suhua Feng et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

L1 retrotransposition in human neural progenitor cells

(2009) Nicole G. Coufal et al.   NATURE

Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics

(2009) Paul J Boersema et al.   Nature Protocols

Effects of Retroviruses on Host Genome Function

(2008) Patric Jern et al.   Annual Review of Genetics

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY