Epigenomic analysis of Parkinson’s disease neurons identifies Tet2 loss as neuroprotective

TET2-mediated Cdkn2A DNA hydroxymethylation in midbrain dopaminergic neuron injury of Parkinson’s disease

(2020) Ting-Ting Wu et al.   HUMAN MOLECULAR GENETICS

DNA methylation disruption reshapes the hematopoietic differentiation landscape

(2020) Franco Izzo et al.   NATURE GENETICS

Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap

(2019) Jüri Reimand et al.   Nature Protocols

Parkinson’s disease-linkedD620N VPS35knockin mice manifest tau neuropathology and dopaminergic neurodegeneration

(2019) Xi Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global modulation in DNA epigenetics during pro-inflammatory macrophage activation

(2019) Nikhil Jain et al.   Epigenetics

Transcriptome and proteome profiling of neural stem cells from the human subventricular zone in Parkinson’s disease

(2019) Vanessa Donega et al.   Acta Neuropathologica Communications

TET2 Regulates the Neuroinflammatory Response in Microglia

(2019) Alejandro Carrillo-Jimenez et al.   Cell Reports

Identification of novel risk loci, causal insights, and heritable risk for Parkinson's disease: a meta-analysis of genome-wide association studies

(2019) Mike A Nalls et al.   LANCET NEUROLOGY

Transcription factor Pebbled/RREB1 regulates injury-induced axon degeneration

(2018) Jonathan E. Farley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CellProfiler 3.0: Next-generation image processing for biology

(2018) Claire McQuin et al.   PLOS BIOLOGY

Anti–Tumor Necrosis Factor Therapy and Incidence of Parkinson Disease Among Patients With Inflammatory Bowel Disease

(2018) Inga Peter et al.   JAMA Neurology

Enhancers active in dopamine neurons are a primary link between genetic variation and neuropsychiatric disease

(2018) Xianjun Dong et al.   NATURE NEUROSCIENCE

A unique role for DNA (hydroxy)methylation in epigenetic regulation of human inhibitory neurons

(2018) Alexey Kozlenkov et al.   Science Advances

Global, regional, and national burden of Parkinson's disease, 1990–2016: a systematic analysis for the Global Burden of Disease Study 2016

(2018) E. Ray Dorsey et al.   LANCET NEUROLOGY

Triggers, Facilitators, and Aggravators: Redefining Parkinson’s Disease Pathogenesis

(2018) Michaela E. Johnson et al.   TRENDS IN NEUROSCIENCES

Multiregional analysis of global 5-methylcytosine and 5-hydroxymethylcytosine throughout the progression of Alzheimer's disease

(2017) Elizabeth M. Ellison et al.   JOURNAL OF NEUROCHEMISTRY

Genome-wide characterization of mammalian promoters with distal enhancer functions

(2017) Lan T M Dao et al.   NATURE GENETICS

Comparison of computational methods for Hi-C data analysis

(2017) Mattia Forcato et al.   NATURE METHODS

Chromatin-state discovery and genome annotation with ChromHMM

(2017) Jason Ernst et al.   Nature Protocols

Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex

(2017) Chongyuan Luo et al.   SCIENCE

Three-dimensional genome architecture and emerging technologies: looping in disease

(2017) Arpit Mishra et al.   Genome Medicine

Epigenetic Biomarkers for Parkinson’s Disease: From Diagnostics to Therapeutics

(2017) Jennifer L. Jakubowski et al.   Journal of Parkinsons Disease

Epigenetic regulation in Parkinson’s disease

(2016) Catherine Labbé et al.   ACTA NEUROPATHOLOGICA

Dynamic DNA Methylation Regulates Levodopa-Induced Dyskinesia

(2016) David A. Figge et al.   JOURNAL OF NEUROSCIENCE

Parkinson-associated risk variant in distal enhancer of α-synuclein modulates target gene expression

(2016) Frank Soldner et al.   NATURE

Lactase nonpersistence is directed by DNA-variation-dependent epigenetic aging

(2016) Viviane Labrie et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Lactase nonpersistence is directed by DNA-variation-dependent epigenetic aging

(2016) Viviane Labrie et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome

(2016) Anthony D. Schmitt et al.   Cell Reports

Aberrant epigenome in iPSC-derived dopaminergic neurons from Parkinson's disease patients

(2015) R. Fernandez-Santiago et al.   EMBO Molecular Medicine

The Methylcytosine Dioxygenase Tet2 Promotes DNA Demethylation and Activation of Cytokine Gene Expression in T Cells

(2015) Kenji Ichiyama et al.   IMMUNITY

Tet2 is required to resolve inflammation by recruiting Hdac2 to specifically repress IL-6

(2015) Qian Zhang et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Identification of neurodegenerative factors using translatome–regulatory network analysis

(2015) Lars Brichta et al.   NATURE NEUROSCIENCE

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

(2015) Alisa Mo et al.   NEURON

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Two-dimensional segmentation for analyzing Hi-C data

(2014) C. Levy-Leduc et al.   BIOINFORMATICS

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

5mC Oxidation by Tet2 Modulates Enhancer Activity and Timing of Transcriptome Reprogramming during Differentiation

(2014) Gary C. Hon et al.   MOLECULAR CELL

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

Semiautomated correlative 3D electron microscopy of in vivo–imaged axons and dendrites

(2014) Bohumil Maco et al.   Nature Protocols

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Disease duration and the integrity of the nigrostriatal system in Parkinson’s disease

(2013) Jeffrey H. Kordower et al.   BRAIN

Distinctive patterns of DNA methylation associated with Parkinson disease

(2013) Eliezer Masliah et al.   Epigenetics

Prefrontal dopamine signaling and cognitive symptoms of Parkinson’s disease

(2013) Nandakumar S. Narayanan et al.   REVIEWS IN THE NEUROSCIENCES

Global Epigenomic Reconfiguration During Mammalian Brain Development

(2013) R. Lister et al.   SCIENCE

oPOSSUM-3: Advanced Analysis of Regulatory Motif Over-Representation Across Genes or ChIP-Seq Datasets

(2013) Andrew T. Kwon et al.   G3-Genes Genomes Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Library-free methylation sequencing with bisulfite padlock probes

(2012) Dinh Diep et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Genome-scale methylation analysis of Parkinson's disease patients' brains reveals DNA hypomethylation and increased mRNA expression of cytochrome P450 2E1

(2012) Oliver Kaut et al.   NEUROGENETICS

Normalization, bias correction, and peak calling for ChIP-seq

(2012) Aaron Diaz et al.   Statistical Applications in Genetics and Molecular Biology

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

Neurodegeneration Across Stages of Cognitive Decline in Parkinson Disease

(2011) Daniel Weintraub   ARCHIVES OF NEUROLOGY

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

(2011) Felix Krueger et al.   BIOINFORMATICS

Inhibition of TET2-mediated conversion of 5-methylcytosine to 5-hydroxymethylcytosine disturbs erythroid and granulomonocytic differentiation of human hematopoietic progenitors

(2011) E. Pronier et al.   BLOOD

Direct generation of functional dopaminergic neurons from mouse and human fibroblasts

(2011) Massimiliano Caiazzo et al.   NATURE

Neuronal activity modifies the DNA methylation landscape in the adult brain

(2011) Junjie U Guo et al.   NATURE NEUROSCIENCE

5-hmC–mediated epigenetic dynamics during postnatal neurodevelopment and aging

(2011) Keith E Szulwach et al.   NATURE NEUROSCIENCE

Heritability of Parkinson disease in Swedish twins: a longitudinal study

(2011) Karin Wirdefeldt et al.   NEUROBIOLOGY OF AGING

Factors influencing the symmetry of Parkinson's disease symptoms

(2010) Juan Carlos Gómez-Esteban et al.   CLINICAL NEUROLOGY AND NEUROSURGERY

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons

(2010) Jian Feng et al.   NATURE NEUROSCIENCE

Anti-inflammatory drugs and risk of Parkinson disease: A meta-analysis

(2010) J. J. Gagne et al.   NEUROLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain

(2009) S. Kriaucionis et al.   SCIENCE