A deep learning framework for modeling structural features of RNA-binding protein targets

CLIPdb: a CLIP-seq database for protein-RNA interactions

(2015) Yu-Cheng T Yang et al.   BMC GENOMICS

Integrative Data Analysis of Multi-Platform Cancer Data with a Multimodal Deep Learning Approach

(2015) Muxuan Liang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Stabilization of the G-quadruplex at the VEGF IRES represses cap-independent translation

(2015) Anne Cammas et al.   RNA Biology

Deep learning of the tissue-regulated splicing code

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

Role of the N6-methyladenosine RNA mark in gene regulation and its implications on development and disease

(2014) U. Chandola et al.   Briefings in Functional Genomics

Identifying mRNA sequence elements for target recognition by human Argonaute proteins

(2014) J. Li et al.   GENOME RESEARCH

Structures of Human ALKBH5 Demethylase Reveal a Unique Binding Mode for Specific Single-strandedN6-Methyladenosine RNA Demethylation

(2014) Chao Xu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

MOV10 Is a 5′ to 3′ RNA Helicase Contributing to UPF1 mRNA Target Degradation by Translocation along 3′ UTRs

(2014) Lea H. Gregersen et al.   MOLECULAR CELL

GraphProt: modeling binding preferences of RNA-binding proteins

(2014) Daniel Maticzka et al.   GENOME BIOLOGY

CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data

(2014) Tsukasa Fukunaga et al.   GENOME BIOLOGY

New Insights into Functional Roles of the Polypyrimidine Tract-Binding Protein

(2013) Maria Romanelli et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Deep Architectures and Deep Learning in Chemoinformatics: The Prediction of Aqueous Solubility for Drug-Like Molecules

(2013) Alessandro Lusci et al.   Journal of Chemical Information and Modeling

N6-methyl-adenosine modification in messenger and long non-coding RNA

(2013) Tao Pan   TRENDS IN BIOCHEMICAL SCIENCES

Finding the target sites of RNA-binding proteins

(2013) Xiao Li et al.   Wiley Interdisciplinary Reviews-RNA

Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae

(2013) Mallory A Freeberg et al.   GENOME BIOLOGY

Deep Neural Networks for Acoustic Modeling in Speech Recognition: The Shared Views of Four Research Groups

(2012) Geoffrey Hinton et al.   IEEE SIGNAL PROCESSING MAGAZINE

TDP-43 and FUS RNA-binding Proteins Bind Distinct Sets of Cytoplasmic Messenger RNAs and Differently Regulate Their Post-transcriptional Fate in Motoneuron-like Cells

(2012) Claudia Colombrita et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

ALKBH5 Is a Mammalian RNA Demethylase that Impacts RNA Metabolism and Mouse Fertility

(2012) Guanqun Zheng et al.   MOLECULAR CELL

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

(2012) Dan Dominissini et al.   NATURE

Global or local? Predicting secondary structure and accessibility in mRNAs

(2012) Sita J. Lange et al.   NUCLEIC ACIDS RESEARCH

Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data

(2012) Cem Sievers et al.   NUCLEIC ACIDS RESEARCH

Effect of a natural mutation in the 5′ untranslated region on the translational control of p53 mRNA

(2012) D Khan et al.   ONCOGENE

Secondary RNA structure and nucleotide specificity contribute to internal initiation mediated by the human tau 5′ leader

(2012) Bethany L. Veo et al.   RNA Biology

Annexin A2 and PSF proteins interact with p53 IRES and regulate translation of p53 mRNA

(2012) Arandkar Sharathchandra et al.   RNA Biology

mRNAs containing the histone 3' stem-loop are degraded primarily by decapping mediated by oligouridylation of the 3' end

(2012) W. Su et al.   RNA

Reversible RNA adenosine methylation in biological regulation

(2012) Guifang Jia et al.   TRENDS IN GENETICS

Identification of Ewing’s sarcoma protein as a G-quadruplex DNA- and RNA-binding protein

(2011) Kentaro Takahama et al.   FEBS Journal

Characterization of a Family of RanBP2-Type Zinc Fingers that Can Recognize Single-Stranded RNA

(2011) Cuong D. Nguyen et al.   JOURNAL OF MOLECULAR BIOLOGY

U1 snRNA Directly Interacts with Polypyrimidine Tract-Binding Protein during Splicing Repression

(2011) Shalini Sharma et al.   MOLECULAR CELL

RNA targets of wild-type and mutant FET family proteins

(2011) Jessica I Hoell et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

doRiNA: a database of RNA interactions in post-transcriptional regulation

(2011) Gerd Anders et al.   NUCLEIC ACIDS RESEARCH

Effect of mutations on the p53 IRES RNA structure: Implications for de-regulation of the synthesis of p53 isoforms

(2011) Richa Grover et al.   RNA Biology

How to Grow a Mind: Statistics, Structure, and Abstraction

(2011) J. B. Tenenbaum et al.   SCIENCE

R3D Align: global pairwise alignment of RNA 3D structures using local superpositions

(2010) Ryan R. Rahrig et al.   BIOINFORMATICS

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

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

On the significance of an RNA tertiary structure prediction

(2010) C. E. Hajdin et al.   RNA

Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure

(2010) X. Li et al.   RNA

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

(2010) Hilal Kazan et al.   PLoS Computational Biology

Genome-wide Analysis of PTB-RNA Interactions Reveals a Strategy Used by the General Splicing Repressor to Modulate Exon Inclusion or Skipping

(2009) Yuanchao Xue et al.   MOLECULAR CELL

IRESite—a tool for the examination of viral and cellular internal ribosome entry sites

(2009) Martin Mokrejš et al.   NUCLEIC ACIDS RESEARCH

Next-generation SELEX identifies sequence and structural determinants of splicing factor binding in human pre-mRNA sequence

(2009) D. C. Reid et al.   RNA

Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts

(2008) J. R. Sanford et al.   GENOME RESEARCH

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

(2008) Donny D. Licatalosi et al.   NATURE

RNA-binding proteins in human genetic disease

(2008) Kiven E. Lukong et al.   TRENDS IN GENETICS