Widespread intron retention diversifies most cancer transcriptomes

SRSF2 Mutations Contribute to Myelodysplasia by Mutant-Specific Effects on Exon Recognition

(2015) Eunhee Kim et al.   CANCER CELL

U2AF1mutations alter splice site recognition in hematological malignancies

(2014) Janine O. Ilagan et al.   GENOME RESEARCH

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

Whole Transcriptome Sequencing Reveals Extensive Unspliced mRNA in Metastatic Castration-Resistant Prostate Cancer

(2014) Adam G. Sowalsky et al.   MOLECULAR CANCER RESEARCH

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

(2014) Angela N. Brooks et al.   PLoS One

Sample processing obscures cancer-specific alterations in leukemic transcriptomes

(2014) Heidi Dvinge et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Patterns of missplicing due to somatic U2AF1 mutations in myeloid neoplasms

(2013) B. Przychodzen et al.   BLOOD

Genome-wide RNAi screens in human brain tumor isolates reveal a novel viability requirement for PHF5A

(2013) C. G. Hubert et al.   GENES & DEVELOPMENT

DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon-intron structure

(2013) S. Gelfman et al.   GENOME RESEARCH

Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects

(2013) J. M. Simon et al.   GENOME RESEARCH

Recurrent mutations, including NPM1c, activate a BRD4-dependent core transcriptional program in acute myeloid leukemia

(2013) M A Dawson et al.   LEUKEMIA

Exome sequencing identifies recurrent somatic mutations in EIF1AX and SF3B1 in uveal melanoma with disomy 3

(2013) Marcel Martin et al.   NATURE GENETICS

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

(2013) J William Harbour et al.   NATURE GENETICS

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

Hallmarks of alternative splicing in cancer

(2013) S Oltean et al.   ONCOGENE

Modeling precision treatment of breast cancer

(2013) Anneleen Daemen et al.   GENOME BIOLOGY

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Mapping the Hallmarks of Lung Adenocarcinoma with Massively Parallel Sequencing

(2012) Marcin Imielinski et al.   CELL

Validation of ITD mutations in FLT3 as a therapeutic target in human acute myeloid leukaemia

(2012) Catherine C. Smith et al.   NATURE

Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes

(2012) Andrew V. Biankin et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

The spliceosome as a target of novel antitumour drugs

(2012) Sophie Bonnal et al.   NATURE REVIEWS DRUG DISCOVERY

The UCSC Genome Browser database: extensions and updates 2013

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

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Alternative splicing of CD44 mRNA by ESRP1 enhances lung colonization of metastatic cancer cell

(2012) Toshifumi Yae et al.   Nature Communications

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Alternatively spliced androgen receptor variants

(2011) Scott M Dehm et al.   ENDOCRINE-RELATED CANCER

Increased levels of noisy splicing in cancers, but not for oncogene-derived transcripts

(2011) Lu Chen et al.   HUMAN MOLECULAR GENETICS

SF3B1, a splicing factor is frequently mutated in refractory anemia with ring sideroblasts

(2011) V Visconte et al.   LEUKEMIA

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

(2011) Sanjeev Shukla et al.   NATURE

Frequent pathway mutations of splicing machinery in myelodysplasia

(2011) Kenichi Yoshida et al.   NATURE

Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes

(2011) Timothy A Graubert et al.   NATURE GENETICS

Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia

(2011) Víctor Quesada et al.   NATURE GENETICS

SomaticSF3B1Mutation in Myelodysplasia with Ring Sideroblasts

(2011) E. Papaemmanuil et al.   NEW ENGLAND JOURNAL OF MEDICINE

An EMT–Driven Alternative Splicing Program Occurs in Human Breast Cancer and Modulates Cellular Phenotype

(2011) Irina M. Shapiro et al.   PLoS Genetics

Bayesian hypothesis testing for psychologists: A tutorial on the Savage–Dickey method

(2010) Eric-Jan Wagenmakers et al.   COGNITIVE PSYCHOLOGY

Fast stable restricted maximum likelihood and marginal likelihood estimation of semiparametric generalized linear models

(2010) Simon N. Wood   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Relationship between nucleosome positioning and DNA methylation

(2010) Ramakrishna K. Chodavarapu et al.   NATURE

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

The Honey Bee Epigenomes: Differential Methylation of Brain DNA in Queens and Workers

(2010) Frank Lyko et al.   PLOS BIOLOGY

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing

(2009) E. Hodges et al.   GENOME RESEARCH

Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes

(2009) Joel S. Parker et al.   JOURNAL OF CLINICAL ONCOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

The Biflavonoid Isoginkgetin Is a General Inhibitor of Pre-mRNA Splicing

(2008) Kristine O'Brien et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Proliferating Cells Express mRNAs with Shortened 3' Untranslated Regions and Fewer MicroRNA Target Sites

(2008) R. Sandberg et al.   SCIENCE