RNMFLP: Predicting circRNA–disease associations based on robust nonnegative matrix factorization and label propagation

Circular RNAs in body fluids as cancer biomarkers: the new frontier of liquid biopsies

(2021) Sumeng Wang et al.   Molecular Cancer

Robust automated graph regularized discriminative non-negative matrix factorization

(2021) Xianzhong Long et al.   MULTIMEDIA TOOLS AND APPLICATIONS

NSL2CD: identifying potential circRNA–disease associations based on network embedding and subspace learning

(2021) Qiu Xiao et al.   BRIEFINGS IN BIOINFORMATICS

Identification of miRNA–disease associations via multiple information integration with Bayesian ranking

(2021) Chi-Chi Zhu et al.   BRIEFINGS IN BIOINFORMATICS

Predicting potential small molecule–miRNA associations based on bounded nuclear norm regularization

(2021) Xing Chen et al.   BRIEFINGS IN BIOINFORMATICS

SCMFMDA: Predicting microRNA-disease associations based on similarity constrained matrix factorization

(2021) Lei Li et al.   PLoS Computational Biology

CRPGCN: predicting circRNA-disease associations using graph convolutional network based on heterogeneous network

(2021) Zhihao Ma et al.   BMC BIOINFORMATICS

Ensemble of kernel ridge regression-based small molecule–miRNA association prediction in human disease

(2021) Chun-Chun Wang et al.   BRIEFINGS IN BIOINFORMATICS

The diverse roles of circular RNAs in pancreatic cancer

(2021) Sian Chen et al.   PHARMACOLOGY & THERAPEUTICS

Graph regularized L2,1-nonnegative matrix factorization for miRNA-disease association prediction

(2020) Zhen Gao et al.   BMC BIOINFORMATICS

LDGRNMF: LncRNA-disease associations prediction based on graph regularized non-negative matrix factorization

(2020) Mei-Neng Wang et al.   NEUROCOMPUTING

PrGeFNE: Predicting disease-related genes by fast network embedding

(2020) Ju Xiang et al.   METHODS

Deep-belief network for predicting potential miRNA-disease associations

(2020) Xing Chen et al.   BRIEFINGS IN BIOINFORMATICS

GAERF: predicting lncRNA-disease associations by graph auto-encoder and random forest

(2020) Qing-Wen Wu et al.   BRIEFINGS IN BIOINFORMATICS

The roles of circRNAs in cancers: Perspectives from molecular functions

(2020) Yi-Zhi Cao et al.   GENE

Simultaneous Interrogation of Cancer Omics to Identify Subtypes With Significant Clinical Differences

(2019) Aodan Xu et al.   Frontiers in Genetics

Circular RNA biogenesis is decreased in postmortem cortical gray matter in schizophrenia and may alter the bioavailability of associated miRNA

(2019) Ebrahim Mahmoudi et al.   NEUROPSYCHOPHARMACOLOGY

Adaptive boosting-based computational model for predicting potential miRNA-disease associations

(2019) Yan Zhao et al.   BIOINFORMATICS

Circular RNA circHIPK3 modulates autophagy via MIR124-3p-STAT3-PRKAA/AMPKα signaling in STK11 mutant lung cancer

(2019) Xiuyuan Chen et al.   Autophagy

Ensemble of decision tree reveals potential miRNA-disease associations

(2019) Xing Chen et al.   PLoS Computational Biology

Predicting human disease-associated circRNAs based on locality-constrained linear coding

(2019) Erxia Ge et al.   GENOMICS

Prediction of potential miRNA-disease associations using matrix decomposition and label propagation

(2019) Jia Qu et al.   KNOWLEDGE-BASED SYSTEMS

The Role of Circular RNA CDR1as/ciRS-7 in Regulating Tumor Microenvironment: A Pan-Cancer Analysis

(2019) Zou et al.   Biomolecules

NCMCMDA: miRNA–disease association prediction through neighborhood constraint matrix completion

(2019) Xing Chen et al.   BRIEFINGS IN BIOINFORMATICS

BNPMDA: Bipartite Network Projection for MiRNA–Disease Association prediction

(2018) Xing Chen et al.   BIOINFORMATICS

The Advances and Challenges of Deep Learning Application in Biological Big Data Processing

(2018) Li Peng et al.   Current Bioinformatics

The differentially expressed circular ribonucleic acids of primary hepatic carcinoma following liver transplantation as new diagnostic biomarkers for primary hepatic carcinoma

(2018) Weiguo Sui et al.   TUMOR BIOLOGY

circRNA disease: a manually curated database of experimentally supported circRNA-disease associations

(2018) Zheng Zhao et al.   Cell Death & Disease

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

A novel plasma circular RNA circFARSA is a potential biomarker for non-small cell lung cancer

(2018) Dong Hang et al.   Cancer Medicine

HOGMMNC: a higher order graph matching with multiple network constraints model for gene–drug regulatory modules identification

(2018) Jiazhou Chen et al.   BIOINFORMATICS

Circ2Disease: a manually curated database of experimentally validated circRNAs in human disease

(2018) Dongxia Yao et al.   Scientific Reports

MDHGI: Matrix Decomposition and Heterogeneous Graph Inference for miRNA-disease association prediction

(2018) Xing Chen et al.   PLoS Computational Biology

PWCDA: Path Weighted Method for Predicting circRNA-Disease Associations

(2018) Xiujuan Lei et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Recovering hidden diagonal structures via non-negative matrix factorization with multiple constraints

(2017) Xi Yang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

PDL1 And LDHA act as ceRNAs in triple negative breast cancer by regulating miR-34a

(2017) Xiaojia Huang et al.   JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH

CircRNA: functions and properties of a novel potential biomarker for cancer

(2017) Shujuan Meng et al.   Molecular Cancer

ZKSCAN1gene and its related circular RNA (circZKSCAN1) both inhibit hepatocellular carcinoma cell growth, migration, and invasion but through different signaling pathways

(2017) Zhicheng Yao et al.   Molecular Oncology

Over-expression of CircRNA_100876 in non-small cell lung cancer and its prognostic value

(2017) Jun-Tao Yao et al.   PATHOLOGY RESEARCH AND PRACTICE

RKNNMDA: Ranking-based KNN for MiRNA-Disease Association prediction

(2017) Xing Chen et al.   RNA Biology

NRDTD: a database for clinically or experimentally supported non-coding RNAs and drug targets associations

(2017) Xing Chen et al.   Database-The Journal of Biological Databases and Curation

Polymorphisms and expression pattern of circular RNA circ-ITCH contributes to the carcinogenesis of hepatocellular carcinoma

(2017) Wenzhi Guo et al.   Oncotarget

A novel information fusion strategy based on a regularized framework for identifying disease-related microRNAs

(2017) Li Peng et al.   RSC Advances

LRSSLMDA: Laplacian Regularized Sparse Subspace Learning for MiRNA-Disease Association prediction

(2017) Xing Chen et al.   PLoS Computational Biology

PBMDA: A novel and effective path-based computational model for miRNA-disease association prediction

(2017) Zhu-Hong You et al.   PLoS Computational Biology

Ensemble Teaching for Hybrid Label Propagation

(2017) Chen Gong et al.   IEEE Transactions on Cybernetics

Drug–target interaction prediction: databases, web servers and computational models

(2015) Xing Chen et al.   BRIEFINGS IN BIOINFORMATICS

An Efficient Non-Negative Matrix-Factorization-Based Approach to Collaborative Filtering for Recommender Systems

(2014) Xin Luo et al.   IEEE Transactions on Industrial Informatics

Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data

(2014) Warren A. Kibbe et al.   NUCLEIC ACIDS RESEARCH

Low-Rank Matrix Approximation with Manifold Regularization

(2013) Zhenyue Zhang et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Solving quasi-variational inequalities via their KKT conditions

(2013) Francisco Facchinei et al.   MATHEMATICAL PROGRAMMING

Circular Intronic Long Noncoding RNAs

(2013) Yang Zhang et al.   MOLECULAR CELL

Natural RNA circles function as efficient microRNA sponges

(2013) Thomas B. Hansen et al.   NATURE

Gaussian interaction profile kernels for predicting drug–target interaction

(2011) Twan van Laarhoven et al.   BIOINFORMATICS

DOSim: An R package for similarity between diseases based on Disease Ontology

(2011) Jiang Li et al.   BMC BIOINFORMATICS

Inferring the human microRNA functional similarity and functional network based on microRNA-associated diseases

(2010) Dong Wang et al.   BIOINFORMATICS