Mutant-IDH1-dependent chromatin state reprogramming, reversibility, and persistence

Inhibiting DNA Methylation Causes an Interferon Response in Cancer via dsRNA Including Endogenous Retroviruses

(2016) Katherine B. Chiappinelli et al.   CELL

Epiproteomics: quantitative analysis of histone marks and codes by mass spectrometry

(2016) Yupeng Zheng et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Extreme Vulnerability of IDH1 Mutant Cancers to NAD+ Depletion

(2015) Kensuke Tateishi et al.   CANCER CELL

Molecular and Genetic Properties of Tumors Associated with Local Immune Cytolytic Activity

(2015) Michael S. Rooney et al.   CELL

DNA-Demethylating Agents Target Colorectal Cancer Cells by Inducing Viral Mimicry by Endogenous Transcripts

(2015) David Roulois et al.   CELL

Insulator dysfunction and oncogene activation in IDH mutant gliomas

(2015) William A. Flavahan et al.   NATURE

Integrated genomic characterization of IDH1-mutant glioma malignant progression

(2015) Hanwen Bai et al.   NATURE GENETICS

Mapping Social Behavior-Induced Brain Activation at Cellular Resolution in the Mouse

(2015) Yongsoo Kim et al.   Cell Reports

ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters

(2015) Swneke D. Bailey et al.   Nature Communications

Efficient induction of differentiation and growth inhibition in IDH1 mutant glioma cells by the DNMT Inhibitor Decitabine.

(2015) Sevin Turcan et al.   Oncotarget

Transcriptional landscape of the prenatal human brain

(2014) Jeremy A. Miller et al.   NATURE

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Site-specific human histone H3 methylation stability: fast K4me3 turnover

(2014) Yupeng Zheng et al.   PROTEOMICS

Using high-density DNA methylation arrays to profile copy number alterations

(2014) Andrew Feber et al.   GENOME BIOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

ChAMP: 450k Chip Analysis Methylation Pipeline

(2013) Tiffany J. Morris et al.   BIOINFORMATICS

Molecular Biomarkers of Cancer Stem/Progenitor Cells Associated with Progression, Metastases, and Treatment Resistance of Aggressive Cancers

(2013) M. Mimeault et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Systematic evaluation of spliced alignment programs for RNA-seq data

(2013) Pär G Engström et al.   NATURE METHODS

An Inhibitor of Mutant IDH1 Delays Growth and Promotes Differentiation of Glioma Cells

(2013) D. Rohle et al.   SCIENCE

L1CAM stimulates glioma cell motility and proliferation through the fibroblast growth factor receptor

(2012) Vishnu Mohanan et al.   CLINICAL & EXPERIMENTAL METASTASIS

A heterozygous IDH1R132H/WT mutation induces genome-wide alterations in DNA methylation

(2012) C. G. Duncan et al.   GENOME RESEARCH

IDH mutation impairs histone demethylation and results in a block to cell differentiation

(2012) Chao Lu et al.   NATURE

Transformation by the (R)-enantiomer of 2-hydroxyglutarate linked to EGLN activation

(2012) Peppi Koivunen et al.   NATURE

IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype

(2012) Sevin Turcan et al.   NATURE

Serial two-photon tomography for automated ex vivo mouse brain imaging

(2012) Timothy Ragan et al.   NATURE METHODS

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system

(2012) Susan M. Sunkin et al.   NUCLEIC ACIDS RESEARCH

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

miR-34a Repression in Proneural Malignant Gliomas Upregulates Expression of Its Target PDGFRA and Promotes Tumorigenesis

(2012) Joachim Silber et al.   PLoS One

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Prognostic variables in oligodendroglial tumors: a single-institution study of 95 cases

(2011) David Scheie et al.   NEURO-ONCOLOGY

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

(2011) Craig H Mermel et al.   GENOME BIOLOGY

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

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

CD24: from A to Z

(2010) Xianfeng Fang et al.   Cellular & Molecular Immunology

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

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

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Visualization of genomic data with the Hilbert curve

(2009) S. Anders   BIOINFORMATICS

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

(2009) Chongzhi Zang et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

elastix: A Toolbox for Intensity-Based Medical Image Registration

(2009) S. Klein et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

Cancer-associated IDH1 mutations produce 2-hydroxyglutarate

(2009) Lenny Dang et al.   NATURE

Convolutional Networks Can Learn to Generate Affinity Graphs for Image Segmentation

(2009) Srinivas C. Turaga et al.   NEURAL COMPUTATION

IDH1andIDH2Mutations in Gliomas

(2009) Hai Yan et al.   NEW ENGLAND JOURNAL OF MEDICINE

Targeting Cancer Stem Cells through L1CAM Suppresses Glioma Growth

(2008) S. Bao et al.   CANCER RESEARCH

Anaplastic oligodendrogliomas with 1p19q codeletion have a proneural gene expression profile

(2008) Francois Ducray et al.   Molecular Cancer

An Integrated Genomic Analysis of Human Glioblastoma Multiforme

(2008) D. W. Parsons et al.   SCIENCE