Deep neural networks for interpreting RNA-binding protein target preferences

Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA

(2019) Ei-Wen Yang et al.   Nature Communications

Discovery of Allele-Specific Protein-RNA Interactions in Human Transcriptomes

(2019) Emad Bahrami-Samani et al.   AMERICAN JOURNAL OF HUMAN GENETICS

SSMART: sequence-structure motif identification for RNA-binding proteins

(2018) Alina Munteanu et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Sequential regulatory activity prediction across chromosomes with convolutional neural networks

(2018) David R. Kelley et al.   GENOME RESEARCH

Sequence, Structure, and Context Preferences of Human RNA Binding Proteins

(2018) Daniel Dominguez et al.   MOLECULAR CELL

Deciphering human ribonucleoprotein regulatory networks

(2018) Neelanjan Mukherjee et al.   NUCLEIC ACIDS RESEARCH

ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data

(2017) David Heller et al.   NUCLEIC ACIDS RESEARCH

Highly accessible AU-rich regions in 3’ untranslated regions are hotspots for binding of regulatory factors

(2017) Mireya Plass et al.   PLoS Computational Biology

Advances and challenges in the detection of transcriptome-wide protein-RNA interactions

(2017) Emily C. Wheeler et al.   Wiley Interdisciplinary Reviews-RNA

Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins

(2016) Martin Stražar et al.   BIOINFORMATICS

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)

(2016) Eric L Van Nostrand et al.   NATURE METHODS

DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences

(2016) Daniel Quang et al.   NUCLEIC ACIDS RESEARCH

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

RNA Bind-n-Seq: Quantitative Assessment of the Sequence and Structural Binding Specificity of RNA Binding Proteins

(2014) Nicole Lambert et al.   MOLECULAR CELL

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

The RNA-Binding Protein QKI Suppresses Cancer-Associated Aberrant Splicing

(2014) Feng-Yang Zong et al.   PLoS Genetics

GraphProt: modeling binding preferences of RNA-binding proteins

(2014) Daniel Maticzka et al.   GENOME BIOLOGY

Enrichment of processed pseudogene transcripts in L1-ribonucleoprotein particles

(2013) Prabhat K. Mandal et al.   HUMAN MOLECULAR GENETICS

mRNA 3′ End Processing Factors: A Phylogenetic Comparison

(2012) Sarah K. Darmon et al.   COMPARATIVE AND FUNCTIONAL GENOMICS

Genome-wide Analysis of Pre-mRNA 3′ End Processing Reveals a Decisive Role of Human Cleavage Factor I in the Regulation of 3′ UTR Length

(2012) Georges Martin et al.   Cell Reports

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

The RNA-binding Protein HuR Opposes the Repression ofERBB-2Gene Expression by MicroRNA miR-331-3p in Prostate Cancer Cells

(2011) Michael R. Epis et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Integrative Regulatory Mapping Indicates that the RNA-Binding Protein HuR Couples Pre-mRNA Processing and mRNA Stability

(2011) Neelanjan Mukherjee et al.   MOLECULAR CELL

A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins

(2011) Shivendra Kishore et al.   NATURE METHODS

Crystal Structure of a Human Cleavage Factor CFIm25/CFIm68/RNA Complex Provides an Insight into Poly(A) Site Recognition and RNA Looping

(2011) Qin Yang et al.   STRUCTURE

mRNA export and cancer

(2011) Nadeem Siddiqui et al.   Wiley Interdisciplinary Reviews-RNA

Identification of RNA-protein interaction networks using PAR-CLIP

(2011) Manuel Ascano et al.   Wiley Interdisciplinary Reviews-RNA

PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data

(2011) David L Corcoran et al.   GENOME BIOLOGY

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

(2010) Julian König et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins

(2010) Hilal Kazan et al.   PLoS Computational Biology

Evidence-ranked motif identification

(2010) Stoyan Georgiev et al.   GENOME BIOLOGY

RNA and Disease

(2009) Thomas A. Cooper et al.   CELL