Recurrent somatic mutations in POLR2A define a distinct subset of meningiomas

Oncogenic PI3K mutations are as common asAKT1andSMOmutations in meningioma

(2016) Malak Abedalthagafi et al.   NEURO-ONCOLOGY

Stromal contribution to the colorectal cancer transcriptome

(2015) Claudio Isella et al.   NATURE GENETICS

CDK7 Inhibition Suppresses Super-Enhancer-Linked Oncogenic Transcription in MYCN-Driven Cancer

(2014) Edmond Chipumuro et al.   CELL

Neural Crest-Derived Mesenchymal Cells Require Wnt Signaling for Their Development and Drive Invagination of the Telencephalic Midline

(2014) Youngshik Choe et al.   PLoS One

Secretory meningiomas are defined by combined KLF4 K409Q and TRAF7 mutations

(2013) David E. Reuss et al.   ACTA NEUROPATHOLOGICA

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Genomic sequencing of meningiomas identifies oncogenic SMO and AKT1 mutations

(2013) Priscilla K Brastianos et al.   NATURE GENETICS

Poor-prognosis colon cancer is defined by a molecularly distinct subtype and develops from serrated precursor lesions

(2013) Felipe De Sousa E Melo et al.   NATURE MEDICINE

A colorectal cancer classification system that associates cellular phenotype and responses to therapy

(2013) Anguraj Sadanandam et al.   NATURE MEDICINE

CBTRUS Statistical Report: Primary Brain and Central Nervous System Tumors Diagnosed in the United States in 2006-2010

(2013) Q. T. Ostrom et al.   NEURO-ONCOLOGY

Genomic Analysis of Non-NF2 Meningiomas Reveals Mutations in TRAF7, KLF4, AKT1, and SMO

(2013) V. E. Clark et al.   SCIENCE

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Loss of SUFU Function in Familial Multiple Meningioma

(2012) Mervi Aavikko et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Somatic MED12 mutations in uterine leiomyosarcoma and colorectal cancer

(2012) K Kämpjärvi et al.   BRITISH JOURNAL OF CANCER

Revisiting Global Gene Expression Analysis

(2012) Jakob Lovén et al.   CELL

Transcriptional Amplification in Tumor Cells with Elevated c-Myc

(2012) Charles Y. Lin et al.   CELL

Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb

(2012) Justin Cotney et al.   GENOME RESEARCH

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

(2012) Jeremy Schwartzentruber et al.   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Identifying the Hotspots on the Top Faces of WD40-Repeat Proteins from Their Primary Sequences by β-Bulges and DHSW Tetrads

(2012) Xian-Hui Wu et al.   PLoS One

Multiplex Targeted Sequencing Identifies Recurrently Mutated Genes in Autism Spectrum Disorders

(2012) B. J. O'Roak et al.   SCIENCE

Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV

(2011) Jarupon Fah Sathirapongsasuti et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking

(2010) Matthew D. Wilkerson et al.   BIOINFORMATICS

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC 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

Regional neural tube closure defined by the Grainy head-like transcription factors

(2010) Yeliz Rifat et al.   DEVELOPMENTAL BIOLOGY

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

Whole-exome sequencing identifies recessive WDR62 mutations in severe brain malformations

(2010) Kaya Bilgüvar et al.   NATURE

A Network of Cancer Genes with Co-Occurring and Anti-Co-Occurring Mutations

(2010) Qinghua Cui   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

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

(2009) Da Wei Huang et al.   Nature Protocols

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

A novel AKT3 mutation in melanoma tumours and cell lines

(2008) M A Davies et al.   BRITISH JOURNAL OF CANCER

Zic Deficiency in the Cortical Marginal Zone and Meninges Results in Cortical Lamination Defects Resembling Those in Type II Lissencephaly

(2008) T. Inoue et al.   JOURNAL OF NEUROSCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY