Related references
Note: Only part of the references are listed.Adaptive multi-source multi-view latent feature learning for inferring potential disease-associated miRNAs
Qiu Xiao et al.
BRIEFINGS IN BIOINFORMATICS (2021)
Application of deep learning methods in biological networks
Shuting Jin et al.
BRIEFINGS IN BIOINFORMATICS (2021)
MNDR v3.0: mammal ncRNA-disease repository with increased coverage and annotation
Lin Ning et al.
NUCLEIC ACIDS RESEARCH (2021)
The roles of circRNAs in cancers: Perspectives from molecular functions
Yi-Zhi Cao et al.
GENE (2021)
EVLncRNAs 2.0: an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments
Bailing Zhou et al.
NUCLEIC ACIDS RESEARCH (2021)
Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long
Jinyang Zhang et al.
NATURE BIOTECHNOLOGY (2021)
Deep Matrix Factorization Improves Prediction of Human CircRNA-Disease Associations
Chengqian Lu et al.
IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS (2021)
A novel essential protein identification method based on PPI networks and gene expression data
Jiancheng Zhong et al.
BMC BIOINFORMATICS (2021)
Predicting circRNA-disease associations based on autoencoder and graph embedding
Jing Yang et al.
INFORMATION SCIENCES (2021)
A survey on deep learning in DNA/RNA motif mining
Ying He et al.
BRIEFINGS IN BIOINFORMATICS (2021)
Closing the circle: current state and perspectives of circular RNA databases
Marieke Vromman et al.
BRIEFINGS IN BIOINFORMATICS (2021)
The bioinformatics toolbox for circRNA discovery and analysis
Liang Chen et al.
BRIEFINGS IN BIOINFORMATICS (2021)
deepBase v3.0: expression atlas and interactive analysis of ncRNAs from thousands of deep-sequencing data
Fangzhou Xie et al.
NUCLEIC ACIDS RESEARCH (2021)
iCDA-CMG: identifying circRNA-disease associations by federating multi-similarity fusion and collective matrix completion
Qiu Xiao et al.
MOLECULAR GENETICS AND GENOMICS (2021)
Predicting human disease-associated circRNAs based on locality-constrained linear coding
Erxia Ge et al.
GENOMICS (2020)
Predicting disease-associated circular RNAs using deep forests combined with positive-unlabeled learning methods
Xiangxiang Zeng et al.
BRIEFINGS IN BIOINFORMATICS (2020)
An efficient approach based on multi-sources information to predict circRNA-disease associations using deep convolutional neural network
Lei Wang et al.
BIOINFORMATICS (2020)
Visualization of circular RNAs and their internal splicing events from transcriptomic data
Yi Zheng et al.
BIOINFORMATICS (2020)
Accurate quantification of circular RNAs identifies extensive circular isoform switching events
Jinyang Zhang et al.
NATURE COMMUNICATIONS (2020)
Integrating random walk with restart and k-Nearest Neighbor to identify novel circRNA-disease association
Xiujuan Lei et al.
SCIENTIFIC REPORTS (2020)
CircMiner: accurate and rapid detection of circular RNA through splice-aware pseudo-alignment scheme
Hossein Asghari et al.
BIOINFORMATICS (2020)
Prediction of circRNA-disease associations based on inductive matrix completion
Menglu Li et al.
BMC MEDICAL GENOMICS (2020)
iCDA-CGR: Identification of circRNA-disease associations based on Chaos Game Representation
Kai Zheng et al.
PLoS Computational Biology (2020)
CircParser: a novel streamlined pipeline for circular RNA structure and host gene prediction in non-model organisms
Artem Nedoluzhko et al.
PEERJ (2020)
The Circular RNA Landscape of Non-Small Cell Lung Cancer Cells
Nele Van Der Steen et al.
CANCERS (2020)
A SARS-CoV-2 protein interaction map reveals targets for drug repurposing
David E. Gordon et al.
NATURE (2020)
Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2
Yadi Zhou et al.
CELL DISCOVERY (2020)
Predicting novel CircRNA-disease associations based on random walk and logistic regression model
Yulian Ding et al.
COMPUTATIONAL BIOLOGY AND CHEMISTRY (2020)
An ensemble approach for CircRNA-disease association prediction based on autoencoder and deep neural network
K. Deepthi et al.
GENE (2020)
Breast Cancer Candidate Gene Detection Through Integration of Subcellular Localization Data With Protein-Protein Interaction Networks
Xiwei Tang et al.
IEEE TRANSACTIONS ON NANOBIOSCIENCE (2020)
Targeting Mitochondria-Located circRNA SCAR Alleviates NASH via Reducing mROS Output
Qiyi Zhao et al.
CELL (2020)
An in-silico method with graph-based multi-label learning for large-scale prediction of circRNA-disease associations
Qiu Xiao et al.
GENOMICS (2020)
Prioritizing CircRNA-Disease Associations With Convolutional Neural Network Based on Multiple Similarity Feature Fusion
Chunyan Fan et al.
FRONTIERS IN GENETICS (2020)
Potential circRNA-disease association prediction using DeepWalk and network consistency projection
Guanghui Li et al.
JOURNAL OF BIOMEDICAL INFORMATICS (2020)
A novel virtual screening procedure identifies Pralatrexate as inhibitor of SARS-CoV-2 RdRp and it reduces viral replication in vitro
Haiping Zhang et al.
PLOS COMPUTATIONAL BIOLOGY (2020)
CircR2Cancer: a manually curated database of associations between circRNAs and cancers
Wei Lan et al.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2020)
Capsule Network Based Modeling of Multi-omics Data for Discovery of Breast Cancer-Related Genes
Chen Peng et al.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2020)
RNA-Protein Binding Sites Prediction via Multi Scale Convolutional Gated Recurrent Unit Networks
Zhen Shen et al.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2020)
CircAtlas: an integrated resource of one million highly accurate circular RNAs from 1070 vertebrate transcriptomes
Wanying Wu et al.
GENOME BIOLOGY (2020)
Circad: a comprehensive manually curated resource of circular RNA associated with diseases
Mercy Rophina et al.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2020)
TRCirc: a resource for transcriptional regulation information of circRNAs
Zhidong Tang et al.
BRIEFINGS IN BIOINFORMATICS (2019)
LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases
Zhenyu Bao et al.
NUCLEIC ACIDS RESEARCH (2019)
CeModule: an integrative framework for discovering regulatory patterns from genomic data in cancer
Qiu Xiao et al.
BMC BIOINFORMATICS (2019)
The Landscape of Circular RNA in Cancer
Josh N. Vo et al.
CELL (2019)
Multi-view manifold regularized learning-based method for prioritizing candidate disease miRNAs
Qiu Xiao et al.
KNOWLEDGE-BASED SYSTEMS (2019)
Genome-wide identification of cancer-specific alternative splicing in circRNA
Jing Feng et al.
MOLECULAR CANCER (2019)
CircFunBase: a database for functional circular RNAs
Xianwen Meng et al.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2019)
Expanded Expression Landscape and Prioritization of Circular RNAs in Mammals
Peifeng Ji et al.
CELL REPORTS (2019)
deepDR: a network-based deep learning approach to in silico drug repositioning
Xiangxiang Zeng et al.
BIOINFORMATICS (2019)
CircRNAwrap - a flexible pipeline for circRNA identification, transcript prediction, and abundance estimation
Lin Li et al.
FEBS LETTERS (2019)
DCDE: An Efficient Deep Convolutional Divergence Encoding Method for Human Promoter Recognition
Wenxuan Xu et al.
IEEE TRANSACTIONS ON NANOBIOSCIENCE (2019)
Circular RNAs in Cancer: emerging functions in hallmarks, stemness, resistance and roles as potential biomarkers
Min Su et al.
MOLECULAR CANCER (2019)
Circular RNAs open a new chapter in cardiovascular biology
Simona Aufiero et al.
NATURE REVIEWS CARDIOLOGY (2019)
Circbank: a comprehensive database for circRNA with standard nomenclature
Ming Liu et al.
RNA BIOLOGY (2019)
SpliceV: analysis and publication quality printing of linear and circular RNA splicing, expression and regulation
Nathan Ungerleider et al.
BMC BIOINFORMATICS (2019)
Past, present, and future of circRNAs
Ines Lucia Patop et al.
EMBO JOURNAL (2019)
Fusion of multiple heterogeneous networks for predicting circRNA-disease associations
Lei Deng et al.
SCIENTIFIC REPORTS (2019)
Circ-Foxo3 is positively associated with the Foxo3 gene and leads to better prognosis of acute myeloid leukemia patients
Jiao Zhou et al.
BMC CANCER (2019)
CircNR3C1 inhibits proliferation of bladder cancer cells by sponging miR-27a-3p and downregulating cyclin D1 expression
Fuxin Zheng et al.
CANCER LETTERS (2019)
The biogenesis, biology and characterization of circular RNAs
Lasse S. Kristensen et al.
NATURE REVIEWS GENETICS (2019)
Comprehensive characterization of circular RNAs in ∼ 1000 human cancer cell lines
Hang Ruan et al.
GENOME MEDICINE (2019)
Predicting circRNA-Disease Associations Based on circRNA Expression Similarity and Functional Similarity
Yongtian Wang et al.
FRONTIERS IN GENETICS (2019)
Predicting circRNA-Disease Associations Based on Improved Collaboration Filtering Recommendation System With Multiple Data
Xiujuan Lei et al.
FRONTIERS IN GENETICS (2019)
BRWSP: Predicting circRNA-Disease Associations Based on Biased Random Walk to Search Paths on a Multiple Heterogeneous Network
Xiujuan Lei et al.
COMPLEXITY (2019)
Integrating Bipartite Network Projection and KATZ Measure to Identify Novel CircRNA-Disease Associations
Qi Zhao et al.
IEEE TRANSACTIONS ON NANOBIOSCIENCE (2019)
Circular RNA CircFndc3b modulates cardiac repair after myocardial infarction via FUS/VEGF-A axis
Venkata Naga Srikanth Garikipati et al.
NATURE COMMUNICATIONS (2019)
Computational Prediction of Human Disease- Associated circRNAs Based on Manifold Regularization Learning Framework
Qiu Xiao et al.
IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS (2019)
MCLPMDA: A novel method for miRNA-disease association prediction based on matrix completion and label propagation
Sheng-Peng Yu et al.
JOURNAL OF CELLULAR AND MOLECULAR MEDICINE (2019)
LncACTdb 2.0: an updated database of experimentally supported ceRNA interactions curated from low- and high-throughput experiments
Peng Wang et al.
NUCLEIC ACIDS RESEARCH (2019)
Reconstruction of full-length circular RNAs enables isoform-level quantification
Yi Zheng et al.
GENOME MEDICINE (2019)
AtCircDB: a tissue-specific database for Arabidopsis circular RNAs
Jiazhen Ye et al.
BRIEFINGS IN BIOINFORMATICS (2019)
NCPCDA: network consistency projection for circRNA-disease association prediction
Guanghui Li et al.
RSC ADVANCES (2019)
CircAST: Full-length Assembly and Quantification of Alternatively Spliced Isoforms in Circular RNAs
Jing Wu et al.
GENOMICS PROTEOMICS & BIOINFORMATICS (2019)
GBDTCDA: Predicting circRNA-disease Associations Based on Gradient Boosting Decision Tree with Multiple Biological Data Fusion
Xiujuan Lei et al.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES (2019)
Predicting CircRNA-Disease Associations Through Linear Neighborhood Label Propagation Method
Wen Zhang et al.
IEEE ACCESS (2019)
exoRBase: a database of circRNA, lncRNA and mRNA in human blood exosomes
Shengli Li et al.
NUCLEIC ACIDS RESEARCH (2018)
CSCD: a database for cancer-specific circular RNAs
Siyu Xia et al.
NUCLEIC ACIDS RESEARCH (2018)
Circular RNA: An emerging non-coding RNA as a regulator and biomarker in cancer
Bing Chen et al.
CANCER LETTERS (2018)
Discovering Synergistic Drug Combination from a Computational Perspective
Pingjian Ding et al.
CURRENT TOPICS IN MEDICINAL CHEMISTRY (2018)
LMMO: A Large Margin Approach for Refining Regulatory Motifs
Lin Zhu et al.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2018)
Predicting microRNA-disease associations using label propagation based on linear neighborhood similarity
Guanghui Li et al.
JOURNAL OF BIOMEDICAL INFORMATICS (2018)
circRNA disease: a manually curated database of experimentally supported circRNA-disease associations
Zheng Zhao et al.
CELL DEATH & DISEASE (2018)
HDncRNA: a comprehensive database of non-coding RNAs associated with heart diseases
Wen-Jing Wang et al.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2018)
CircR2Disease: a manually curated database for experimentally supported circular RNAs associated with various diseases
Chunyan Fan et al.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2018)
The Biogenesis, Functions, and Challenges of Circular RNAs
Xiang Li et al.
MOLECULAR CELL (2018)
Circ2Disease: a manually curated database of experimentally validated circRNAs in human disease
Dongxia Yao et al.
SCIENTIFIC REPORTS (2018)
CIRCpedia v2: An Updated Database for Comprehensive Circular RNA Annotation and Expression Comparison
Rui Dong et al.
GENOMICS PROTEOMICS & BIOINFORMATICS (2018)
Circular RNAs: Promising Biomarkers for Human Diseases
Zhongrong Zhang et al.
EBIOMEDICINE (2018)
DWNN-RLS: regularized least squares method for predicting circRNA-disease associations
Cheng Yan et al.
BMC BIOINFORMATICS (2018)
PWCDA: Path Weighted Method for Predicting circRNA-Disease Associations
Xiujuan Lei et al.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2018)
A review of network-based approaches to drug repositioning
Maryam Lotfi Shahreza et al.
BRIEFINGS IN BIOINFORMATICS (2018)
A graph regularized non-negative matrix factorization method for identifying microRNA-disease associations
Qiu Xiao et al.
BIOINFORMATICS (2018)
Prediction of CircRNA-Disease Associations Using KATZ Model Based on Heterogeneous Networks
Chunyan Fan et al.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES (2018)
Induction of tumor apoptosis through a circular RNA enhancing Foxo3 activity
William W. Du et al.
CELL DEATH AND DIFFERENTIATION (2017)
The circular RNA ciRS-7 promotes APP and BACE1 degradation in an NF-κB-dependent manner
Zhemin Shi et al.
FEBS JOURNAL (2017)
Circular RNA circMTO1 Acts as the Sponge of MicroRNA-9 to Suppress Hepatocellular Carcinoma Progression
Dan Han et al.
HEPATOLOGY (2017)
A novel approach for predicting microRNA-disease associations by unbalanced bi-random walk on heterogeneous network
Jiawei Luo et al.
JOURNAL OF BIOMEDICAL INFORMATICS (2017)
Identification of circular RNAs with host gene-independent expression in human model systems for cardiac differentiation and disease
D. Siede et al.
JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY (2017)
Circ-ZNF609 Is a Circular RNA that Can Be Translated and Functions in Myogenesis
Ivano Legnini et al.
MOLECULAR CELL (2017)
Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function
Monika Piwecka et al.
SCIENCE (2017)
PlantCircNet: a database for plant circRNA-miRNA-mRNA regulatory networks
Peijing Zhang et al.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2017)
Silencing Of Circular RNA-ZNF609 Ameliorates Vascular Endothelial Dysfunction
Chang Liu et al.
THERANOSTICS (2017)
FUCHS-towards full circular RNA characterization using RNAseq
Franziska Metge et al.
PEERJ (2017)
Predicting MicroRNA-Disease Associations Using Network Topological Similarity Based on DeepWalk
Guanghui Li et al.
IEEE ACCESS (2017)
Novel human microbe-disease association prediction using network consistency projection
Wenzheng Bao et al.
BMC BIOINFORMATICS (2017)
Circular RNA WDR77 target FGF-2 to regulate vascular smooth muscle cells proliferation and migration by sponging miR-124
Junjiang Chen et al.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2017)
Genome-wide profiling of Sus scrofa circular RNAs across nine organs and three developmental stages
Guoming Liang et al.
DNA RESEARCH (2017)
The role of circRNAs in cancers
Ling-Ping Zhu et al.
BIOSCIENCE REPORTS (2017)
CircPro: an integrated tool for the identification of circRNAs with protein-coding potential
Xianwen Meng et al.
BIOINFORMATICS (2017)
Circular RNA MYLK as a competing endogenous RNA promotes bladder cancer progression through modulating VEGFA/VEGFR2 signaling pathway
Zhenyu Zhong et al.
CANCER LETTERS (2017)
CircHIPK3 sponges miR-558 to suppress heparanase expression in bladder cancer cells
Yawei Li et al.
EMBO REPORTS (2017)
Quantifying circular RNA expression from RNA-seq data using model-based framework
Musheng Li et al.
BIOINFORMATICS (2017)
Circular RNA ciRS-7-A Promising Prognostic Biomarker and a Potential Therapeutic Target in Colorectal Cancer
Wenhao Weng et al.
CLINICAL CANCER RESEARCH (2017)
Circular BANP, an upregulated circular RNA that modulates cell proliferation in colorectal cancer
Mingchen Zhu et al.
BIOMEDICINE & PHARMACOTHERAPY (2017)
Circular RNA profile identifies circPVT1 as a proliferative factor and prognostic marker in gastric cancer
Jie Chen et al.
CANCER LETTERS (2017)
Circular RNAs: Biogenesis, Function and Role in Human Diseases
John Greene et al.
FRONTIERS IN MOLECULAR BIOSCIENCES (2017)
SomamiR 2.0: a database of cancer somatic mutations altering microRNA-ceRNA interactions
Anindya Bhattacharya et al.
NUCLEIC ACIDS RESEARCH (2016)
CircNet: a database of circular RNAs derived from transcriptome sequencing data
Yu-Chen Liu et al.
NUCLEIC ACIDS RESEARCH (2016)
CircInteractome: A web tool for exploring circular RNAs and their interacting proteins and microRNAs
Dawood B. Dudekulay et al.
RNA BIOLOGY (2016)
Diverse alternative back-splicing and alternative splicing landscape of circular RNAs
Xiao-Ou Zhang et al.
GENOME RESEARCH (2016)
Predicting Hub Genes Associated with Cervical Cancer through Gene Co-Expression Networks
Su-Ping Deng et al.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2016)
Circular RNAs: a new frontier in the study of human diseases
Yonghua Chen et al.
JOURNAL OF MEDICAL GENETICS (2016)
Circular RNA profiling reveals an abundant circHIPK3 that regulates cell growth by sponging multiple miRNAs
Qiupeng Zheng et al.
NATURE COMMUNICATIONS (2016)
Circular non-coding RNA ANRIL modulates ribosomal RNA maturation and atherosclerosis in humans
Lesca M. Holdt et al.
NATURE COMMUNICATIONS (2016)
Comprehensive identification of internal structure and alternative splicing events in circular RNAs
Yuan Gao et al.
NATURE COMMUNICATIONS (2016)
The Circular RNA Cdr1as Act as an Oncogene in Hepatocellular Carcinoma through Targeting miR-7 Expression
Lei Yu et al.
PLOS ONE (2016)
circRNADb: A comprehensive database for human circular RNAs with protein-coding annotations
Xiaoping Chen et al.
SCIENTIFIC REPORTS (2016)
The RNA Binding Protein Quaking Regulates Formation of circRNAs
Simon J. Conn et al.
CELL (2015)
Prioritization of potential candidate disease genes by topological similarity of protein-protein interaction network and phenotype data
Jiawei Luo et al.
JOURNAL OF BIOMEDICAL INFORMATICS (2015)
Widespread noncoding circular RNAs in plants
Chu-Yu Ye et al.
NEW PHYTOLOGIST (2015)
CIRI: an efficient and unbiased algorithm for de novo circular RNA identification
Yuan Gao et al.
GENOME BIOLOGY (2015)
The multilayered complexity of ceRNA crosstalk and competition
Yvonne Tay et al.
NATURE (2014)
starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data
Jun-Hao Li et al.
NUCLEIC ACIDS RESEARCH (2014)
Circular RNA Is Expressed across the Eukaryotic Tree of Life
Peter L. Wang et al.
PLOS ONE (2014)
circBase: a database for circular RNAs
Petar Glazar et al.
RNA (2014)
Genome-wide Analysis of Drosophila Circular RNAs Reveals Their Structural and Sequence Properties and Age-Dependent Neural Accumulation
Jakub O. Westholm et al.
CELL REPORTS (2014)
Expanded identification and characterization of mammalian circular RNAs
Junjie U. Guo et al.
GENOME BIOLOGY (2014)
Natural RNA circles function as efficient microRNA sponges
Thomas B. Hansen et al.
NATURE (2013)
Circular RNAs are a large class of animal RNAs with regulatory potency
Sebastian Memczak et al.
NATURE (2013)
Cell-Type Specific Features of Circular RNA Expression
Julia Salzman et al.
PLOS GENETICS (2013)
Circ2Traits: a comprehensive database for circular RNA potentially associated with disease and traits
Suman Ghosal et al.
Frontiers in Genetics (2013)
Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types
Julia Salzman et al.
PLOS ONE (2012)
ViennaRNA Package 2.0
Ronny Lorenz et al.
ALGORITHMS FOR MOLECULAR BIOLOGY (2011)
A text-mining analysis of the human phenome
MA van Driel et al.
EUROPEAN JOURNAL OF HUMAN GENETICS (2006)
Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing
Hitoshi Suzuki et al.
NUCLEIC ACIDS RESEARCH (2006)