CRBSP:Prediction of CircRNA-RBP Binding Sites Based on Multimodal Intermediate Fusion

CRBPDL: Identification of circRNA-RBP interaction sites using an ensemble neural network approach

(2022) Mengting Niu et al.   PLoS Computational Biology

MAGCNSE: predicting lncRNA-disease associations using multi-view attention graph convolutional network and stacking ensemble model

(2022) Ying Liang et al.   BMC BIOINFORMATICS

Identification of miRNA–disease associations via deep forest ensemble learning based on autoencoder

(2022) Wei Liu et al.   BRIEFINGS IN BIOINFORMATICS

Hyb4mC: a hybrid DNA2vec-based model for DNA N4-methylcytosine sites prediction

(2022) Ying Liang et al.   BMC BIOINFORMATICS

Identifying the sequence specificities of circRNA-binding proteins based on a capsule network architecture

(2021) Zhengfeng Wang et al.   BMC BIOINFORMATICS

iLearnPlus: a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization

(2021) Zhen Chen et al.   NUCLEIC ACIDS RESEARCH

A brief review of circRNA biogenesis, detection and function

(2021) Ying Liang et al.   CURRENT GENOMICS

Prediction of RBP binding sites on circRNAs using an LSTM-based deep sequence learning architecture

(2021) Zhengfeng Wang et al.   BRIEFINGS IN BIOINFORMATICS

MathFeature: feature extraction package for DNA, RNA and protein sequences based on mathematical descriptors

(2021) Robson P Bonidia et al.   BRIEFINGS IN BIOINFORMATICS

Identification of DNA N6-methyladenine sites by integration of sequence features

(2020) Hao-Tian Wang et al.   Epigenetics & Chromatin

PASSION: an ensemble neural network approach for identifying the binding sites of RBPs on circRNAs

(2020) Cangzhi Jia et al.   BIOINFORMATICS

ProtFold-DFG: protein fold recognition by combining Directed Fusion Graph and PageRank algorithm

(2020) Jiangyi Shao et al.   BRIEFINGS IN BIOINFORMATICS

Identification of Drug–Target Interactions via Dual Laplacian Regularized Least Squares with Multiple Kernel Fusion

(2020) Yijie Ding et al.   KNOWLEDGE-BASED SYSTEMS

RBPsuite: RNA-protein binding sites prediction suite based on deep learning

(2020) Xiaoyong Pan et al.   BMC GENOMICS

DriverML: a machine learning algorithm for identifying driver genes in cancer sequencing studies

(2019) Yi Han et al.   NUCLEIC ACIDS RESEARCH

Identification of Key Genes and Circular RNAs in Human Gastric Cancer

(2019) Shuhong Hao et al.   MEDICAL SCIENCE MONITOR

CRIP: predicting circRNA-RBP interaction sites using a codon-based encoding and hybrid deep neural networks

(2019) Kaiming Zhang et al.   RNA

Comprehensive characterization of circular RNAs in ~ 1000 human cancer cell lines

(2019) Hang Ruan et al.   Genome Medicine

4mCpred-EL: An Ensemble Learning Framework for Identification of DNA N4-methylcytosine Sites in the Mouse Genome

(2019) Manavalan et al.   Cells

Identification of membrane protein types via multivariate information fusion with Hilbert–Schmidt Independence Criterion

(2019) Hao Wang et al.   NEUROCOMPUTING

ACPred-FL: a sequence-based predictor using effective feature representation to improve the prediction of anti-cancer peptides

(2018) Leyi Wei 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

Multimodal Machine Learning: A Survey and Taxonomy

(2018) Tadas Baltrusaitis et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

4mCPred: Machine Learning Methods for DNA N4-methylcytosine sites Prediction

(2018) Wenying He et al.   BIOINFORMATICS

Identification of protein subcellular localization via integrating evolutionary and physicochemical information into Chou’s general PseAAC

(2018) Yinan Shen et al.   JOURNAL OF THEORETICAL BIOLOGY

Identifying sigma70 promoters with novel pseudo nucleotide composition

(2017) Hao Lin et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

EnhancerPred2.0: predicting enhancers and their strength based on position-specific trinucleotide propensity and electron–ion interaction potential feature selection

(2017) Wenying He et al.   Molecular BioSystems

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

CircRNA: a novel type of biomarker for cancer

(2017) He-da Zhang et al.   Breast Cancer

The emerging role and clinical implication of human exonic circular RNA

(2016) Dongbin Lyu et al.   RNA Biology

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

(2016) Xiaoping Chen et al.   Scientific Reports

iORI-PseKNC: A predictor for identifying origin of replication with pseudo k-tuple nucleotide composition

(2015) Wen-Chao Li et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

Mechanisms of RNA loading into exosomes

(2015) Teresa Janas et al.   FEBS LETTERS

Identification of protein-interacting nucleotides in a RNA sequence using composition profile of tri-nucleotides

(2015) Bharat Panwar et al.   GENOMICS

Circular RNAs in the Mammalian Brain Are Highly Abundant, Conserved, and Dynamically Expressed

(2015) Agnieszka Rybak-Wolf et al.   MOLECULAR CELL

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

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Exon-intron circular RNAs regulate transcription in the nucleus

(2015) Zhaoyong Li et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Multimodal Data Fusion: An Overview of Methods, Challenges, and Prospects

(2015) Dana Lahat et al.   PROCEEDINGS OF THE IEEE

CircInteractome: A web tool for exploring circular RNAs and their interacting proteins and microRNAs

(2015) Dawood B. Dudekula et al.   RNA Biology

Exon-intron circular RNAs regulate transcription in the nucleus

(2015) Zhaoyong Li et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

PseKNC: A flexible web server for generating pseudo K-tuple nucleotide composition

(2014) Wei Chen et al.   ANALYTICAL BIOCHEMISTRY

iRSpot-TNCPseAAC: Identify Recombination Spots with Trinucleotide Composition and Pseudo Amino Acid Components

(2014) Wang-Ren Qiu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

circBase: a database for circular RNAs

(2014) Petar Glažar et al.   RNA

Improved and Promising Identification of Human MicroRNAs by Incorporating a High-Quality Negative Set

(2013) Leyi Wei et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Natural RNA circles function as efficient microRNA sponges

(2013) Thomas B. Hansen et al.   NATURE

starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data

(2013) Jun-Hao Li et al.   NUCLEIC ACIDS RESEARCH

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

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

(2012) W. R. Jeck et al.   RNA

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