A Pan-Cancer Analysis of Transcriptome Changes Associated with Somatic Mutations in U2AF1 Reveals Commonly Altered Splicing Events

Short telomere length is associated withNOTCH1/SF3B1/TP53aberrations and poor outcome in newly diagnosed chronic lymphocytic leukemia patients

(2013) Larry Mansouri et al.   AMERICAN JOURNAL OF HEMATOLOGY

Integrated genomic characterization of endometrial carcinoma

(2013) Gad Getz et al.   NATURE

Recurrent mutations at codon 625 of the splicing factor SF3B1 in uveal melanoma

(2013) J William Harbour et al.   NATURE GENETICS

Pan-cancer patterns of somatic copy number alteration

(2013) Travis I Zack et al.   NATURE GENETICS

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Mapping the Hallmarks of Lung Adenocarcinoma with Massively Parallel Sequencing

(2012) Marcin Imielinski et al.   CELL

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

hnRNP A1 Proofreads 3′ Splice Site Recognition by U2AF

(2012) Joao Paulo Tavanez et al.   MOLECULAR CELL

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Frequent pathway mutations of splicing machinery in myelodysplasia

(2011) Kenichi Yoshida et al.   NATURE

Conservation of an RNA regulatory map between Drosophila and mammals

(2010) A. N. Brooks et al.   GENOME RESEARCH

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Identification of genes that regulate epithelial cell migration using an siRNA screening approach

(2008) Kaylene J. Simpson et al.   NATURE CELL BIOLOGY