SURVIV for survival analysis of mRNA isoform variation

Integration of somatic mutation, expression and functional data reveals potential driver genes predictive of breast cancer survival

(2015) Chen Suo et al.   BIOINFORMATICS

Detection of recurrent alternative splicing switches in tumor samples reveals novel signatures of cancer

(2015) Endre Sebestyén et al.   NUCLEIC ACIDS RESEARCH

Identification of recurrent regulated alternative splicing events across human solid tumors

(2015) Miri Danan-Gotthold et al.   NUCLEIC ACIDS RESEARCH

Transcriptome-wide identification and study of cancer-specific splicing events across multiple tumors

(2015) Yihsuan S. Tsai et al.   Oncotarget

Widespread intron retention diversifies most cancer transcriptomes

(2015) Heidi Dvinge et al.   Genome Medicine

An N-terminal splice variant of human Stat5a that interacts with different transcription factors is the dominant form expressed in invasive ductal carcinoma

(2014) Dunyong Tan et al.   CANCER LETTERS

Assessing the clinical utility of cancer genomic and proteomic data across tumor types

(2014) Yuan Yuan et al.   NATURE BIOTECHNOLOGY

Isoform-level gene signature improves prognostic stratification and accurately classifies glioblastoma subtypes

(2014) Sharmistha Pal et al.   NUCLEIC ACIDS RESEARCH

Alternative splicing in cancer: implications for biology and therapy

(2014) J Chen et al.   ONCOGENE

rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

(2014) Shihao Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human Tra2 proteins jointly control a CHEK1 splicing switch among alternative and constitutive target exons

(2014) Andrew Best et al.   Nature Communications

Splicing mutation analysis reveals previously unrecognized pathways in lymph node-invasive breast cancer

(2014) Stephanie N. Dorman et al.   Scientific Reports

RNA-seq differential expression studies: more sequence or more replication?

(2013) Yuwen Liu et al.   BIOINFORMATICS

Regulation and function of pyruvate kinase M2 in cancer

(2013) Weiwei Yang et al.   CANCER LETTERS

Tumor-Specific Isoform Switch of the Fibroblast Growth Factor Receptor 2 Underlies the Mesenchymal and Malignant Phenotypes of Clear Cell Renal Cell Carcinomas

(2013) Q. Zhao et al.   CLINICAL CANCER RESEARCH

Comprehensive molecular characterization of clear cell renal cell carcinoma

(2013)   NATURE

Hallmarks of alternative splicing in cancer

(2013) S Oltean et al.   ONCOGENE

Prognostic microRNA/mRNA signature from the integrated analysis of patients with invasive breast cancer

(2013) S. Volinia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Alternative RNA splicing and cancer

(2013) Sali Liu et al.   Wiley Interdisciplinary Reviews-RNA

GLiMMPS: Robust statistical model for regulatory variation of alternative splicing using RNA-seq data

(2013) Keyan Zhao et al.   GENOME BIOLOGY

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Comprehensive genomic characterization of squamous cell lung cancers

(2012)   NATURE

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data

(2012) Shihao Shen et al.   NUCLEIC ACIDS RESEARCH

Identification of Evolutionarily Conserved Exons as Regulated Targets for the Splicing Activator Tra2β in Development

(2011) Sushma Grellscheid et al.   PLoS Genetics

Heterogeneous Nuclear Ribonucleoprotein H Blocks MST2-Mediated Apoptosis in Cancer Cells by Regulating a-raf Transcription

(2010) J. Rauch et al.   CANCER RESEARCH

An Alternative Splicing Network Links Cell-Cycle Control to Apoptosis

(2010) Michael J. Moore et al.   CELL

An ESRP-regulated splicing programme is abrogated during the epithelial–mesenchymal transition

(2010) Claude C Warzecha et al.   EMBO JOURNAL

Expansion of the eukaryotic proteome by alternative splicing

(2010) Timothy W. Nilsen et al.   NATURE

Alternative expression analysis by RNA sequencing

(2010) Malachi Griffith et al.   NATURE METHODS

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

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

(2009) Da Wei Huang et al.   Nature Protocols

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS

Insights into the connection between cancer and alternative splicing

(2007) Eddo Kim et al.   TRENDS IN GENETICS