DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma

Atypical Teratoid/Rhabdoid Tumors Are Comprised of Three Epigenetic Subgroups with Distinct Enhancer Landscapes

(2016) Pascal D. Johann et al.   CANCER CELL

Intratumoral Heterogeneity of the Epigenome

(2016) Tali Mazor et al.   CANCER CELL

Quantitative comparison of DNA methylation assays for biomarker development and clinical applications

(2016) Christoph Bock et al.   NATURE BIOTECHNOLOGY

Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia

(2016) Sheng Li et al.   NATURE MEDICINE

LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor

(2015) Nathan C. Sheffield et al.   BIOINFORMATICS

DNA Methylation and Somatic Mutations Converge on the Cell Cycle and Define Similar Evolutionary Histories in Brain Tumors

(2015) Tali Mazor et al.   CANCER CELL

Leukemia-Associated Cohesin Mutants Dominantly Enforce Stem Cell Programs and Impair Human Hematopoietic Progenitor Differentiation

(2015) Claire Mazumdar et al.   Cell Stem Cell

Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers

(2015) Xabier Agirre et al.   GENOME RESEARCH

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Toward understanding and exploiting tumor heterogeneity

(2015) Ash A Alizadeh et al.   NATURE MEDICINE

The UCSC Genome Browser database: 2016 update

(2015) Matthew L. Speir et al.   NUCLEIC ACIDS RESEARCH

Differential DNA Methylation Analysis without a Reference Genome

(2015) Johanna Klughammer et al.   Cell Reports

Epigenome Mapping Reveals Distinct Modes of Gene Regulation and Widespread Enhancer Reprogramming by the Oncogenic Fusion Protein EWS-FLI1

(2015) Eleni M. Tomazou et al.   Cell Reports

Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics

(2015) Matthias Farlik et al.   Cell Reports

Epigenetic and in vivo comparison of diverse MSC sources reveals an endochondral signature for human hematopoietic niche formation

(2014) A. Reinisch et al.   BLOOD

Locally Disordered Methylation Forms the Basis of Intratumor Methylome Variation in Chronic Lymphocytic Leukemia

(2014) Dan A. Landau et al.   CANCER CELL

EWS-FLI1 Utilizes Divergent Chromatin Remodeling Mechanisms to Directly Activate or Repress Enhancer Elements in Ewing Sarcoma

(2014) Nicolò Riggi et al.   CANCER CELL

Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing

(2014) Volker Hovestadt et al.   NATURE

CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities

(2014) Manuel Sánchez-Castillo et al.   NUCLEIC ACIDS RESEARCH

Characterization of Human Mesenchymal Stem Cells from Ewing Sarcoma Patients. Pathogenetic Implications

(2014) Ana Teresa Amaral et al.   PLoS One

The Genomic Landscape of Pediatric Ewing Sarcoma

(2014) B. D. Crompton et al.   Cancer Discovery

Genomic Landscape of Ewing Sarcoma Defines an Aggressive Subtype with Co-Association of STAG2 and TP53 Mutations

(2014) F. Tirode et al.   Cancer Discovery

The Genomic Landscape of the Ewing Sarcoma Family of Tumors Reveals Recurrent STAG2 Mutation

(2014) Andrew S. Brohl et al.   PLoS Genetics

Unmasking risk loci: DNA methylation illuminates the biology of cancer predisposition

(2013) Dvir Aran et al.   BIOESSAYS

Targeting Oxidative Stress in Embryonal Rhabdomyosarcoma

(2013) Xiang Chen et al.   CANCER CELL

Dynamic DNA methylation across diverse human cell lines and tissues

(2013) K. E. Varley et al.   GENOME RESEARCH

Oncogenic ETS fusions deregulate E2F3 target genes in Ewing sarcoma and prostate cancer

(2013) Sven Bilke et al.   GENOME RESEARCH

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions

(2013) N. C. Sheffield et al.   GENOME RESEARCH

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues

(2013) Gary C Hon et al.   NATURE GENETICS

Identification of active regulatory regions from DNA methylation data

(2013) Lukas Burger et al.   NUCLEIC ACIDS RESEARCH

DNA Methylation Dynamics during In Vivo Differentiation of Blood and Skin Stem Cells

(2012) Christoph Bock et al.   MOLECULAR CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia

(2012) Marta Kulis et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

DNA methylation profiling in the clinic: applications and challenges

(2012) Holger Heyn et al.   NATURE REVIEWS GENETICS

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

(2011) Felix Krueger et al.   BIOINFORMATICS

RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing

(2011) Yuanxin Xi et al.   BIOINFORMATICS

Cistrome: an integrative platform for transcriptional regulation studies

(2011) Tao Liu et al.   GENOME BIOLOGY

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC BIOINFORMATICS

Primary Disseminated Multifocal Ewing Sarcoma: Results of the Euro-EWING 99 Trial

(2010) Ruth Ladenstein et al.   JOURNAL OF CLINICAL ONCOLOGY

Quantitative comparison of genome-wide DNA methylation mapping technologies

(2010) Christoph Bock et al.   NATURE BIOTECHNOLOGY

Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution

(2010) Hongcang Gu et al.   NATURE METHODS

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BSMAP: whole genome bisulfite sequence MAPping program

(2009) Yuanxin Xi et al.   BMC BIOINFORMATICS

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY