Deep-learning augmented RNA-seq analysis of transcript splicing

The Expanding Landscape of Alternative Splicing Variation in Human Populations

(2018) Eddie Park et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Cancer transcriptome profiling at the juncture of clinical translation

(2017) Marcin Cieślik et al.   NATURE REVIEWS GENETICS

Determination of a Comprehensive Alternative Splicing Regulatory Network and Combinatorial Regulation by Key Factors during the Epithelial-to-Mesenchymal Transition

(2016) Yueqin Yang et al.   MOLECULAR AND CELLULAR BIOLOGY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Deep learning of the tissue-regulated splicing code

(2014) Michael K. K. Leung et al.   BIOINFORMATICS

Transcriptome-wide Landscape of Pre-mRNA Alternative Splicing Associated with Metastatic Colonization

(2014) Zhi-xiang Lu et al.   MOLECULAR CANCER RESEARCH

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

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

The human splicing code reveals new insights into the genetic determinants of disease

(2014) H. Y. Xiong et al.   SCIENCE

Genome-Wide Determination of a Broad ESRP-Regulated Posttranscriptional Network by High-Throughput Sequencing

(2012) K. A. Dittmar et al.   MOLECULAR AND CELLULAR BIOLOGY

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

(2010) Claude C Warzecha et al.   EMBO JOURNAL

Deciphering the splicing code

(2010) Yoseph Barash et al.   NATURE

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS