Gastrointestinal stromal tumor enhancers support a transcription factor network predictive of clinical outcome

ChAsE: chromatin analysis and exploration tool

(2016) Hamid Younesy et al.   BIOINFORMATICS

Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis

(2016) Jialiang Huang et al.   DEVELOPMENTAL CELL

RNA sequencing validation of the Complexity INdex in SARComas prognostic signature

(2016) Tom Lesluyes et al.   EUROPEAN JOURNAL OF CANCER

Models of human core transcriptional regulatory circuitries

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

Active medulloblastoma enhancers reveal subgroup-specific cellular origins

(2016) Charles Y. Lin et al.   NATURE

Management of Gastrointestinal Stromal Tumors

(2016) Margaret von Mehren   SURGICAL CLINICS OF NORTH AMERICA

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

(2015) Denes Hnisz et al.   MOLECULAR CELL

Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains

(2015) Junwei Shi et al.   NATURE BIOTECHNOLOGY

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

(2015) Xiaoyang Zhang et al.   NATURE GENETICS

Combined Inhibition of MAP Kinase and KIT Signaling Synergistically Destabilizes ETV1 and Suppresses GIST Tumor Growth

(2015) L. Ran et al.   Cancer Discovery

Ponatinib Inhibits Polyclonal Drug-Resistant KIT Oncoproteins and Shows Therapeutic Potential in Heavily Pretreated Gastrointestinal Stromal Tumor (GIST) Patients

(2014) A. P. Garner et al.   CLINICAL CANCER RESEARCH

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

(2014) Paul A. Northcott et al.   NATURE

An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element

(2014) M. R. Mansour et al.   SCIENCE

Discovery and Characterization of Super-Enhancer-Associated Dependencies in Diffuse Large B Cell Lymphoma

(2013) Bjoern Chapuy et al.   CANCER CELL

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

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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Transcriptional Amplification in Tumor Cells with Elevated c-Myc

(2012) Charles Y. Lin et al.   CELL

Efficacy and Safety of Regorafenib in Patients With Metastatic and/or Unresectable GI Stromal Tumor After Failure of Imatinib and Sunitinib: A Multicenter Phase II Trial

(2012) Suzanne George et al.   JOURNAL OF CLINICAL ONCOLOGY

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Mitotic Checkpoints and Chromosome Instability Are Strong Predictors of Clinical Outcome in Gastrointestinal Stromal Tumors

(2011) P. Lagarde et al.   CLINICAL CANCER RESEARCH

The phosphatidyl inositol 3-kinase pathway is central to the pathogenesis of Kit-activated melanoma

(2011) Ruixia Liang et al.   Pigment Cell & Melanoma Research

ETV1 is a lineage survival factor that cooperates with KIT in gastrointestinal stromal tumours

(2010) Ping Chi et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Proteomic Profiling of γ-Secretase Substrates and Mapping of Substrate Requirements

(2008) Matthew L Hemming et al.   PLOS BIOLOGY