Epigenetic activation of a RAS/MYC axis in H3.3K27M-driven cancer

SuperFreq: Integrated mutation detection and clonal tracking in cancer

(2020) Christoffer Flensburg et al.   PLoS Computational Biology

The expanding landscape of ‘oncohistone’ mutations in human cancers

(2019) Benjamin A. Nacev et al.   NATURE

H3.3 K27M depletion increases differentiation and extends latency of diffuse intrinsic pontine glioma growth in vivo

(2019) André B. Silveira et al.   ACTA NEUROPATHOLOGICA

Pervasive H3K27 Acetylation Leads to ERV Expression and a Therapeutic Vulnerability in H3K27M Gliomas

(2019) Brian Krug et al.   CANCER CELL

Identification of novel RAS signaling therapeutic vulnerabilities in Diffuse Intrinsic Pontine Gliomas

(2019) Robert F Koncar et al.   CANCER RESEARCH

Mutant H3 histones drive human pre-leukemic hematopoietic stem cell expansion and promote leukemic aggressiveness

(2019) Meaghan Boileau et al.   Nature Communications

Dynamic Incorporation of Histone H3 Variants into Chromatin Is Essential for Acquisition of Aggressive Traits and Metastatic Colonization

(2019) Ana P. Gomes et al.   CANCER CELL

SOX2 protein biochemistry in stemness, reprogramming, and cancer: the PI3K/AKT/SOX2 axis and beyond

(2019) Thorsten Schaefer et al.   ONCOGENE

Histone Variant and Cell Context Determine H3K27M Reprogramming of the Enhancer Landscape and Oncogenic State

(2019) Surya Nagaraja et al.   MOLECULAR CELL

Impaired oligodendrogenesis and myelination by elevated S100B levels during neurodevelopment

(2018) Gisela Santos et al.   NEUROPHARMACOLOGY

SOX10 Single Transcription Factor-Based Fast and Efficient Generation of Oligodendrocytes from Human Pluripotent Stem Cells

(2018) Juan Antonio García-León et al.   Stem Cell Reports

Histone H3.3 K27M Accelerates Spontaneous Brainstem Glioma and Drives Restricted Changes in Bivalent Gene Expression

(2018) Jon D. Larson et al.   CANCER CELL

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

The mouse Gene Expression Database (GXD): 2019 update

(2018) Constance M Smith et al.   NUCLEIC ACIDS RESEARCH

Histone H3.3K27M Represses p16 to Accelerate Gliomagenesis in a Murine Model of DIPG

(2017) Francisco J. Cordero et al.   MOLECULAR CANCER RESEARCH

EZH2 is a potential therapeutic target for H3K27M-mutant pediatric gliomas

(2017) Faizaan Mohammad et al.   NATURE MEDICINE

Therapeutic targeting of polycomb and BET bromodomain proteins in diffuse intrinsic pontine gliomas

(2017) Andrea Piunti et al.   NATURE MEDICINE

Overview of the Use of Murine Models in Leukemia and Lymphoma Research

(2017) Rebecca Kohnken et al.   Frontiers in Oncology

A Comprehensive Mouse Transcriptomic BodyMap across 17 Tissues by RNA-seq

(2017) Bin Li et al.   Scientific Reports

Epigenetics of hematopoiesis and hematological malignancies

(2016) Deqing Hu et al.   GENES & DEVELOPMENT

Greater Than the Sum of Parts: Complexity of the Dynamic Epigenome

(2016) Alexey A. Soshnev et al.   MOLECULAR CELL

A predictive computational framework for direct reprogramming between human cell types

(2016) Owen J L Rackham et al.   NATURE GENETICS

COSMIC: somatic cancer genetics at high-resolution

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

Reactive Oxygen Species Derived from NOX3 and NOX5 Drive Differentiation of Human Oligodendrocytes

(2016) Roberta Accetta et al.   Frontiers in Cellular Neuroscience

Spatial and temporal homogeneity of driver mutations in diffuse intrinsic pontine glioma

(2016) Hamid Nikbakht et al.   Nature Communications

The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins

(2016) Andrew D. Rouillard et al.   Database-The Journal of Biological Databases and Curation

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing

(2016) Eric Talevich et al.   PLoS Computational Biology

Spatial genomic heterogeneity in diffuse intrinsic pontine and midline high-grade glioma: implications for diagnostic biopsy and targeted therapeutics

(2016) Lindsey M. Hoffman et al.   Acta Neuropathologica Communications

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Fatty Acid Binding Protein 7 Regulates Phagocytosis and Cytokine Production in Kupffer Cells during Liver Injury

(2014) Hirofumi Miyazaki et al.   AMERICAN JOURNAL OF PATHOLOGY

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

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs

(2014) P. J. Balwierz et al.   GENOME RESEARCH

PRC2 loss amplifies Ras-driven transcription and confers sensitivity to BRD4-based therapies

(2014) Thomas De Raedt et al.   NATURE

Genomic analysis of diffuse intrinsic pontine gliomas identifies three molecular subgroups and recurrent activating ACVR1 mutations

(2014) Pawel Buczkowicz et al.   NATURE GENETICS

Reduced H3K27me3 and DNA Hypomethylation Are Major Drivers of Gene Expression in K27M Mutant Pediatric High-Grade Gliomas

(2013) Sebastian Bender et al.   CANCER CELL

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Differential transformation capacity of neuro-glial progenitors during development

(2013) D. M. Munoz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inhibition of PRC2 Activity by a Gain-of-Function H3 Mutation Found in Pediatric Glioblastoma

(2013) P. W. Lewis et al.   SCIENCE

Comprehensive Analysis of Transcriptome Variation Uncovers Known and Novel Driver Events in T-Cell Acute Lymphoblastic Leukemia

(2013) Zeynep Kalender Atak et al.   PLoS Genetics

The Transcription Factors Sox10 and Myrf Define an Essential Regulatory Network Module in Differentiating Oligodendrocytes

(2013) Julia Hornig et al.   PLoS Genetics

K27M mutation in histone H3.3 defines clinically and biologically distinct subgroups of pediatric diffuse intrinsic pontine gliomas

(2012) Dong-Anh Khuong-Quang et al.   ACTA NEUROPATHOLOGICA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma

(2012) Jeremy Schwartzentruber et al.   NATURE

Genome-wide analysis of EGR2/SOX10 binding in myelinating peripheral nerve

(2012) Rajini Srinivasan et al.   NUCLEIC ACIDS RESEARCH

Dynamic Distribution of Linker Histone H1.5 in Cellular Differentiation

(2012) Jing-Yu Li et al.   PLoS Genetics

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Epigenetics and B-cell lymphoma

(2011) Rita Shaknovich et al.   CURRENT OPINION IN HEMATOLOGY

The Polycomb complex PRC2 and its mark in life

(2011) Raphaël Margueron et al.   NATURE

Hedgehog-responsive candidate cell of origin for diffuse intrinsic pontine glioma

(2011) M. Monje et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Mutational Landscape of Head and Neck Squamous Cell Carcinoma

(2011) N. Stransky et al.   SCIENCE

Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1

(2010) Roel G.W. Verhaak et al.   CANCER CELL

Identification of FABP7 in fibroblastic reticular cells of mouse lymph nodes

(2010) Nobuko Tokuda et al.   HISTOCHEMISTRY AND CELL BIOLOGY

Whole-Genome Profiling of Pediatric Diffuse Intrinsic Pontine Gliomas Highlights Platelet-Derived Growth Factor Receptor α and Poly (ADP-ribose) Polymerase As Potential Therapeutic Targets

(2010) Maryam Zarghooni et al.   JOURNAL OF CLINICAL ONCOLOGY

Sox10 directs neural stem cells toward the oligodendrocyte lineage by decreasing Suppressor of Fused expression

(2010) C. D. Pozniak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast and accurate short read alignment with Burrows-Wheeler transform

(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

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

(2009) Da Wei Huang et al.   Nature Protocols

Genetic Analysis of Congenital Cystic Adenomatoid Malformation Reveals a Novel Pulmonary Gene: Fatty Acid Binding Protein-7 (Brain Type)

(2009) Amy J Wagner et al.   PEDIATRIC RESEARCH

Sox9 and Sox10 influence survival and migration of oligodendrocyte precursors in the spinal cord by regulating PDGF receptor   expression

(2008) M. Finzsch et al.   DEVELOPMENT

A Transcriptome Database for Astrocytes, Neurons, and Oligodendrocytes: A New Resource for Understanding Brain Development and Function

(2008) J. D. Cahoy et al.   JOURNAL OF NEUROSCIENCE