Transcriptional alterations in glioma result primarily from DNA methylation–independent mechanisms

Targeting glioma stem-like cell survival and chemoresistance through inhibition of lysine-specific histone demethylase KDM2B

(2018) Mikkel Staberg et al.   Molecular Oncology

DNA methylation profiling reveals a pathological signature that contributes to transcriptional defects of CD34+ CD15− cells in early chronic-phase chronic myeloid leukemia

(2018) Stéphanie Maupetit-Mehouas et al.   Molecular Oncology

Targeting TWIST1 through loss of function inhibits tumorigenicity of human glioblastoma

(2018) Andrei M. Mikheev et al.   Molecular Oncology

SALL4 suppresses PTEN expression to promote glioma cell proliferation via PI3K/AKT signaling pathway

(2017) Chuanjin Liu et al.   JOURNAL OF NEURO-ONCOLOGY

Blocking MIR155HG/miR-155 axis inhibits mesenchymal transition in glioma

(2017) Xuechao Wu et al.   NEURO-ONCOLOGY

Knockdown of Collagen Triple Helix Repeat Containing 1 (CTHRC1) Inhibits Epithelial‐Mesenchymal Transition and Cellular Migration in Glioblastoma Cells

(2017) Jianpeng Liu et al.   ONCOLOGY RESEARCH

Epigenetic plasticity and the hallmarks of cancer

(2017) William A. Flavahan et al.   SCIENCE

The cancer epigenome: Concepts, challenges, and therapeutic opportunities

(2017) Mark A. Dawson   SCIENCE

The 2016 World Health Organization Classification of Tumors of the Central Nervous System: a summary

(2016) David N. Louis et al.   ACTA NEUROPATHOLOGICA

Identification of DNA Methylation–Independent Epigenetic Events Underlying Clear Cell Renal Cell Carcinoma

(2016) Elinne Becket et al.   CANCER RESEARCH

Acquired Tissue-Specific Promoter Bivalency Is a Basis for PRC2 Necessity in Adult Cells

(2016) Unmesh Jadhav et al.   CELL

Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma

(2016) Michele Ceccarelli et al.   CELL

Comprehensive characterization, annotation and innovative use of Infinium DNA methylation BeadChip probes

(2016) Wanding Zhou et al.   NUCLEIC ACIDS RESEARCH

Epigenetic Determinants of Cancer

(2016) Stephen B. Baylin et al.   Cold Spring Harbor Perspectives in Biology

5-Hydroxymethylcytosine localizes to enhancer elements and is associated with survival in glioblastoma patients

(2016) Kevin C. Johnson et al.   Nature Communications

An annotated list of bivalent chromatin regions in human ES cells: a new tool for cancer epigenetic research

(2016) Franck Court et al.   Oncotarget

The tumoral A genotype of the MGMT rs34180180 single-nucleotide polymorphism in aggressive gliomas is associated with shorter patients’ survival

(2015) Anne Fogli et al.   CARCINOGENESIS

Downregulation of HTATIP2 expression is associated with promoter methylation and poor prognosis in glioma

(2015) Xingyu Dong et al.   EXPERIMENTAL AND MOLECULAR PATHOLOGY

Imprinting control regions (ICRs) are marked by mono-allelic bivalent chromatin when transcriptionally inactive

(2015) Stéphanie Maupetit-Méhouas et al.   NUCLEIC ACIDS RESEARCH

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

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

FactoMineR: AnRPackage for Multivariate Analysis

(2015) Sébastien Lê et al.   Journal of Statistical Software

Biological significance of the CpG island methylator phenotype

(2014) Hiromu Suzuki et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

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

(2014) S. Anders et al.   BIOINFORMATICS

Loss of the Polycomb Mark from Bivalent Promoters Leads to Activation of Cancer-Promoting Genes in Colorectal Tumors

(2014) M. A. Hahn et al.   CANCER RESEARCH

Variant PRC1 Complex-Dependent H2A Ubiquitylation Drives PRC2 Recruitment and Polycomb Domain Formation

(2014) Neil P. Blackledge et al.   CELL

Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment

(2014) F. Court et al.   GENOME RESEARCH

Gene Silencing Triggers Polycomb Repressive Complex 2 Recruitment to CpG Islands Genome Wide

(2014) Eva Madi Riising et al.   MOLECULAR CELL

Genomic insights into cancer-associated aberrant CpG island hypermethylation

(2013) D. Sproul et al.   Briefings in Functional Genomics

The Somatic Genomic Landscape of Glioblastoma

(2013) Cameron W. Brennan et al.   CELL

IDH1 and IDH2 Mutations in Gliomas

(2013) Adam L. Cohen et al.   Current Neurology and Neuroscience Reports

Fbxl10/Kdm2b Recruits Polycomb Repressive Complex 1 to CpG Islands and Regulates H2A Ubiquitylation

(2013) Xudong Wu et al.   MOLECULAR CELL

Epigenetic Reprogramming in Cancer

(2013) M. L. Suva et al.   SCIENCE

Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

(2013) J. Gao et al.   Science Signaling

Chromatin Sampling—An Emerging Perspective on Targeting Polycomb Repressor Proteins

(2013) Robert J. Klose et al.   PLoS Genetics

Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb target genes

(2013) James P Reddington et al.   GENOME BIOLOGY

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Regional Activation of the Cancer Genome by Long-Range Epigenetic Remodeling

(2012) Saul A. Bert et al.   CANCER CELL

A Tumorigenic MLL-Homeobox Network in Human Glioblastoma Stem Cells

(2012) M. Gallo et al.   CANCER RESEARCH

Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA

(2012) Aaron L. Statham et al.   GENOME RESEARCH

Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk

(2012) Arie B. Brinkman et al.   GENOME RESEARCH

IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype

(2012) Sevin Turcan et al.   NATURE

i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules

(2012) Carl Herrmann et al.   NUCLEIC ACIDS RESEARCH

Integrated Epigenome Profiling of Repressive Histone Modifications, DNA Methylation and Gene Expression in Normal and Malignant Urothelial Cells

(2012) Ewa Dudziec et al.   PLoS One

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands

(2012) Anca M Farcas et al.   eLife

Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns

(2012) Duncan Sproul et al.   GENOME BIOLOGY

Prognostic DNA methylation patterns in cytogenetically normal acute myeloid leukemia are predefined by stem cell chromatin marks

(2011) S. Deneberg et al.   BLOOD

DNA Hypermethylation and Histone Modifications Downregulate the Candidate Tumor Suppressor Gene RRP22 on 22q12 in Human Gliomas

(2011) Natalie Schmidt et al.   BRAIN PATHOLOGY

CpG islands and the regulation of transcription

(2011) A. M. Deaton et al.   GENES & DEVELOPMENT

Genome-scale analysis of aberrant DNA methylation in colorectal cancer

(2011) T. Hinoue et al.   GENOME RESEARCH

Transcriptionally repressed genes become aberrantly methylated and distinguish tumors of different lineages in breast cancer

(2011) D. Sproul et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Breast Cancer Methylomes Establish an Epigenomic Foundation for Metastasis

(2011) F. Fang et al.   Science Translational Medicine

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

Identification of a CpG Island Methylator Phenotype that Defines a Distinct Subgroup of Glioma

(2010) Houtan Noushmehr et al.   CANCER CELL

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

GC-Rich Sequence Elements Recruit PRC2 in Mammalian ES Cells

(2010) Eric M. Mendenhall et al.   PLoS Genetics

Bmi1 deficient neural stem cells have increased Integrin dependent adhesion to self-secreted matrix

(2009) Sophia W.M. Bruggeman et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

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

EZH2 Is Essential for Glioblastoma Cancer Stem Cell Maintenance

(2009) M.-L. Suva et al.   CANCER RESEARCH

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Copy number alterations of the polycomb gene BMI1 in gliomas

(2008) Valtteri Häyry et al.   ACTA NEUROPATHOLOGICA

Gene silencing in cancer by histone H3 lysine 27 trimethylation independent of promoter DNA methylation

(2008) Yutaka Kondo et al.   NATURE GENETICS

Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line

(2008) E. N. Gal-Yam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Integrated Genomic Analysis of Human Glioblastoma Multiforme

(2008) D. W. Parsons et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY