Therapeutic targeting of ependymoma as informed by oncogenic enhancer profiling

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

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

Models of human core transcriptional regulatory circuitries

(2016) Violaine Saint-André et al.   GENOME RESEARCH

Decreased FOXJ1 expression and its ciliogenesis programme in aggressive ependymoma and choroid plexus tumours

(2016) Malak S Abedalthagafi et al.   JOURNAL OF PATHOLOGY

Active medulloblastoma enhancers reveal subgroup-specific cellular origins

(2016) Charles Y. Lin et al.   NATURE

QSEA—modelling of genome-wide DNA methylation from sequencing enrichment experiments

(2016) Matthias Lienhard et al.   NUCLEIC ACIDS RESEARCH

COSMIC: somatic cancer genetics at high-resolution

(2016) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

InFusion: Advancing Discovery of Fusion Genes and Chimeric Transcripts from Deep RNA-Sequencing Data

(2016) Konstantin Okonechnikov et al.   PLoS One

Molecular Classification of Ependymal Tumors across All CNS Compartments, Histopathological Grades, and Age Groups

(2015) Kristian W. Pajtler et al.   CANCER CELL

Convergence of Developmental and Oncogenic Signaling Pathways at Transcriptional Super-Enhancers

(2015) Denes Hnisz et al.   MOLECULAR CELL

Data analysis: Create a cloud commons

(2015) Lincoln D. Stein et al.   NATURE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers

(2015) Xiaoyang Zhang et al.   NATURE GENETICS

An in vivo screen identifies ependymoma oncogenes and tumor-suppressor genes

(2015) Kumarasamypet M Mohankumar et al.   NATURE GENETICS

Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing

(2014) Volker Hovestadt et al.   NATURE

Epigenomic alterations define lethal CIMP-positive ependymomas of infancy

(2014) S. C. Mack et al.   NATURE

Topologically associating domains are stable units of replication-timing regulation

(2014) Benjamin D. Pope et al.   NATURE

C11orf95–RELA fusions drive oncogenic NF-κB signalling in ependymoma

(2014) Matthew Parker et al.   NATURE

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

DGIdb: mining the druggable genome

(2013) Malachi Griffith et al.   NATURE METHODS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Delineation of Two Clinically and Molecularly Distinct Subgroups of Posterior Fossa Ependymoma

(2011) Hendrik Witt et al.   CANCER CELL

Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites

(2010) Stephen A. Ramsey et al.   BIOINFORMATICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Cross-species genomics matches driver mutations and cell compartments to model ependymoma

(2010) Robert A. Johnson et al.   NATURE