Identifying Cancer-Specific circRNA–RBP Binding Sites Based on Deep Learning

Construction of Complex Features for Computational Predicting ncRNA-Protein Interaction

(2019) Qiguo Dai et al.   Frontiers in Genetics

Deep learning of the back-splicing code for circular RNA formation

(2019) Jun Wang et al.   BIOINFORMATICS

Predicting RNA–protein binding sites and motifs through combining local and global deep convolutional neural networks

(2018) Xiaoyong Pan et al.   BIOINFORMATICS

Prediction of RNA-protein sequence and structure binding preferences using deep convolutional and recurrent neural networks

(2018) Xiaoyong Pan et al.   BMC GENOMICS

Feature-Based and String-Based Models for Predicting RNA-Protein Interaction

(2018) Donald Adjeroh et al.   MOLECULES

RPiRLS: Quantitative Predictions of RNA Interacting with Any Protein of Known Sequence

(2018) Wen-Jun Shen et al.   MOLECULES

CircR2Disease: a manually curated database for experimentally supported circular RNAs associated with various diseases

(2018) Chunyan Fan et al.   Database-The Journal of Biological Databases and Curation

CSCD: a database for cancer-specific circular RNAs

(2017) Siyu Xia et al.   NUCLEIC ACIDS RESEARCH

Identification of HuR target circular RNAs uncovers suppression of PABPN1 translation by CircPABPN1

(2017) Kotb Abdelmohsen et al.   RNA Biology

Circular RNAs: Identification, biogenesis and function

(2016) Karoline K. Ebbesen et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Convolutional neural network architectures for predicting DNA–protein binding

(2016) Haoyang Zeng et al.   BIOINFORMATICS

Comprehensive characterization of tissue-specific circular RNAs in the human and mouse genomes

(2016) Siyu Xia et al.   BRIEFINGS IN BIOINFORMATICS

Heterogeneous nuclear ribonucleoprotein K is associated with poor prognosis and regulates proliferation and apoptosis in bladder cancer

(2016) Xu Chen et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

Circular RNAs: a new frontier in the study of human diseases

(2016) Yonghua Chen et al.   JOURNAL OF MEDICAL GENETICS

Foxo3 circular RNA retards cell cycle progression via forming ternary complexes with p21 and CDK2

(2016) William W. Du et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Daniel Quang et al.   NUCLEIC ACIDS RESEARCH

DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants

(2016) Janet Piñero et al.   NUCLEIC ACIDS RESEARCH

The emerging role and clinical implication of human exonic circular RNA

(2016) Dongbin Lyu et al.   RNA Biology

HnRNP-L promotes prostate cancer progression by enhancing cell cycling and inhibiting apoptosis

(2016) Xumin Zhou et al.   Oncotarget

Mini Review: Circular RNAs as Potential Clinical Biomarkers for Disorders in the Central Nervous System

(2016) Dan Lu et al.   Frontiers in Genetics

circRNADb: A comprehensive database for human circular RNAs with protein-coding annotations

(2016) Xiaoping Chen et al.   Scientific Reports

Circular RNA: A new star of noncoding RNAs

(2015) Shibin Qu et al.   CANCER LETTERS

Mechanisms of RNA loading into exosomes

(2015) Teresa Janas et al.   FEBS LETTERS

SRSF1-Regulated Alternative Splicing in Breast Cancer

(2015) Olga Anczuków et al.   MOLECULAR CELL

Deep learning

(2015) Yann LeCun et al.   NATURE

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

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

Deep Convolutional Neural Networks for Large-scale Speech Tasks

(2015) Tara N. Sainath et al.   NEURAL NETWORKS

Alternative splicing of TIA-1 in human colon cancer regulates VEGF isoform expression, angiogenesis, tumour growth and bevacizumab resistance

(2014) Maryam A. Hamdollah Zadeh et al.   Molecular Oncology

Brain metastasis is predetermined in early stages of cutaneous melanoma by CD44v6 expression through epigenetic regulation of the spliceosome

(2014) Diego M. Marzese et al.   Pigment Cell & Melanoma Research

circBase: a database for circular RNAs

(2014) Petar Glažar et al.   RNA

GraphProt: modeling binding preferences of RNA-binding proteins

(2014) Daniel Maticzka et al.   GENOME BIOLOGY

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

Natural RNA circles function as efficient microRNA sponges

(2013) Thomas B. Hansen et al.   NATURE

Correction: Cell-Type Specific Features of Circular RNA Expression

(2013) Julia Salzman et al.   PLoS Genetics

Circular RNAs are abundant, conserved, and associated with ALU repeats

(2012) W. R. Jeck et al.   RNA

Predicting RNA-Protein Interactions Using Only Sequence Information

(2011) Usha K Muppirala 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

Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins

(2009) Debashish Ray et al.   NATURE BIOTECHNOLOGY

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

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

(2008) Donny D. Licatalosi et al.   NATURE