Data resources and computational methods for lncRNA-disease association prediction

Prediction of lncRNA-disease association based on a Laplace normalized random walk with restart algorithm on heterogeneous networks

(2022) Liugen Wang et al.   BMC BIOINFORMATICS

Multi-channel graph attention autoencoders for disease-related lncRNAs prediction

(2022) Nan Sheng et al.   BRIEFINGS IN BIOINFORMATICS

Dynamical Analysis of a Boolean Network Model of the Oncogene Role of lncRNA ANRIL and lncRNA UFC1 in Non-Small Cell Lung Cancer

(2022) Shantanu Gupta et al.   Biomolecules

The role of a ceRNA regulatory network based on lncRNA MALAT1 site in cancer progression

(2021) Kai Su et al.   BIOMEDICINE & PHARMACOTHERAPY

A representation learning model based on variational inference and graph autoencoder for predicting lncRNA-disease associations

(2021) Zhuangwei Shi et al.   BMC BIOINFORMATICS

IPCARF: improving lncRNA-disease association prediction using incremental principal component analysis feature selection and a random forest classifier

(2021) Rong Zhu et al.   BMC BIOINFORMATICS

Locoregional therapy in de novo metastatic breast cancer. The unanswered question

(2021) Maria-Joao Cardoso et al.   BREAST

BiGAN: LncRNA-disease association prediction based on bidirectional generative adversarial network

(2021) Qiang Yang et al.   BMC BIOINFORMATICS

GCRFLDA: scoring lncRNA-disease associations using graph convolution matrix completion with conditional random field

(2021) Yongxian Fan et al.   BRIEFINGS IN BIOINFORMATICS

GANLDA: Graph attention network for lncRNA-disease associations prediction

(2021) Wei Lan et al.   NEUROCOMPUTING

LncRNAs as putative biomarkers and therapeutic targets for Parkinson’s disease

(2021) Eskandar Taghizadeh et al.   NEUROLOGICAL SCIENCES

SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec

(2021) Jianwei Li et al.   BMC BIOINFORMATICS

Prediction of drug–disease associations by integrating common topologies of heterogeneous networks and specific topologies of subnets

(2021) Ling Gao et al.   BRIEFINGS IN BIOINFORMATICS

Heterogeneous graph attention network based on meta-paths for lncRNA–disease association prediction

(2021) Xiaosa Zhao et al.   BRIEFINGS IN BIOINFORMATICS

LncRNAWiki 2.0: a knowledgebase of human long non-coding RNAs with enhanced curation model and database system

(2021) Lin Liu et al.   NUCLEIC ACIDS RESEARCH

LncACTdb 3.0: an updated database of experimentally supported ceRNA interactions and personalized networks contributing to precision medicine

(2021) Peng Wang et al.   NUCLEIC ACIDS RESEARCH

LGFC-CNN: Prediction of lncRNA-Protein Interactions by Using Multiple Types of Features through Deep Learning

(2021) Lan Huang et al.   Genes

Multi-level transcriptome sequencing identifies COL1A1 as a candidate marker in human heart failure progression

(2020) Xiumeng Hua et al.   BMC Medicine

LDAI-ISPS: LncRNA–Disease Associations Inference Based on Integrated Space Projection Scores

(2020) Yi Zhang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Human Long Noncoding RNA Interactome: Detection, Characterization and Function

(2020) Kazimierczyk et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

(2020) Mei-Neng Wang et al.   NEUROCOMPUTING

LncRNA PTENP1 inhibits cervical cancer progression by suppressing miR-106b

(2020) Yingrui Fan et al.   Artificial Cells Nanomedicine and Biotechnology

A random forest based computational model for predicting novel lncRNA-disease associations

(2020) Dengju Yao et al.   BMC BIOINFORMATICS

Attentional multi-level representation encoding based on convolutional and variance autoencoders for lncRNA–disease association prediction

(2020) Nan Sheng et al.   BRIEFINGS IN BIOINFORMATICS

HOTAIR LncRNA: A novel oncogenic propellant in human cancer

(2020) Taruna Rajagopal et al.   CLINICA CHIMICA ACTA

Inferring LncRNA-disease Associations Based On Graph Autoencoder Matrix Completion

(2020) Ximin Wu et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

SDLDA: lncRNA-disease association prediction based on singular value decomposition and deep learning

(2020) Min Zeng et al.   METHODS

Exosome-transmitted lncRNA UFC1 promotes non-small-cell lung cancer progression by EZH2-mediated epigenetic silencing of PTEN expression

(2020) Xueyan Zang et al.   Cell Death & Disease

Predicting Human lncRNA-Disease Associations Based on Geometric Matrix Completion

(2020) Chengqian Lu et al.   IEEE Journal of Biomedical and Health Informatics

Long Non-Coding RNA MNX1-AS1 Promotes Progression of Triple Negative Breast Cancer by Enhancing Phosphorylation of Stat3

(2020) Junhua Li et al.   Frontiers in Oncology

LDNFSGB: prediction of long non-coding rna and disease association using network feature similarity and gradient boosting

(2020) Yuan Zhang et al.   BMC BIOINFORMATICS

Recent advances on the roles of LncRNAs in cardiovascular disease

(2020) Yexian Fang et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

LncMirNet: Predicting LncRNA–miRNA Interaction Based on Deep Learning of Ribonucleic Acid Sequences

(2020) Sen Yang et al.   MOLECULES

LncExpDB: an expression database of human long non-coding RNAs

(2020) Zhao Li et al.   NUCLEIC ACIDS RESEARCH

MNDR v3.0: mammal ncRNA–disease repository with increased coverage and annotation

(2020) Lin Ning et al.   NUCLEIC ACIDS RESEARCH

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

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

Neuro-protective roles of long non-coding RNA MALAT1 in Alzheimer's disease with the involvement of the microRNA-30b/CNR1 network and the following PI3K/AKT activation

(2020) Li Li et al.   EXPERIMENTAL AND MOLECULAR PATHOLOGY

Comprehensive Review on Alzheimer’s Disease: Causes and Treatment

(2020) Zeinab Breijyeh et al.   MOLECULES

Gene regulation by long non-coding RNAs and its biological functions

(2020) Luisa Statello et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

EVLncRNAs 2.0: an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments

(2020) Bailing Zhou et al.   NUCLEIC ACIDS RESEARCH

Lnc2Cancer 3.0: an updated resource for experimentally supported lncRNA/circRNA cancer associations and web tools based on RNA-seq and scRNA-seq data

(2020) Yue Gao et al.   NUCLEIC ACIDS RESEARCH

WGRCMF: A Weighted Graph Regularized Collaborative Matrix Factorization Method for Predicting Novel LncRNA-Disease Associations

(2020) Jin-Xing Liu et al.   IEEE Journal of Biomedical and Health Informatics

Association of the Plasma Long Non-coding RNA MEG3 With Parkinson's Disease

(2020) Yi Quan et al.   Frontiers in Neurology

Graph Convolutional Autoencoder and Fully-Connected Autoencoder with Attention Mechanism Based Method for Predicting Drug-Disease Associations

(2020) Ping Xuan et al.   IEEE Journal of Biomedical and Health Informatics

MHRWR: Prediction of lncRNA-Disease Associations Based on Multiple Heterogeneous Networks

(2020) Xiaowei Zhao et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

DMFLDA: A Deep Learning Framework for Predicting lncRNA–Disease Associations

(2020) Min Zeng et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

A Probabilistic Matrix Factorization Method for Identifying lncRNA-disease Associations

(2019) Zhanwei Xuan et al.   Genes

Prediction of lncRNA-disease associations by integrating diverse heterogeneous information sources with RWR algorithm and positive pointwise mutual information

(2019) Xiao-Nan Fan et al.   BMC BIOINFORMATICS

A learning-based framework for miRNA-disease association identification using neural networks

(2019) Jiajie Peng et al.   BIOINFORMATICS

Dual Convolutional Neural Networks With Attention Mechanisms Based Method for Predicting Disease-Related lncRNA Genes

(2019) Ping Xuan et al.   Frontiers in Genetics

A novel collaborative filtering model for LncRNA-disease association prediction based on the Naïve Bayesian classifier

(2019) Jingwen Yu et al.   BMC BIOINFORMATICS

Long Non-coding RNA BACE1-AS May Serve as an Alzheimer’s Disease Blood-Based Biomarker

(2019) Seyedeh Nahid Fotuhi et al.   JOURNAL OF MOLECULAR NEUROSCIENCE

Weighted matrix factorization on multi-relational data for LncRNA-disease association prediction

(2019) Yuehui Wang et al.   METHODS

LLCLPLDA: a novel model for predicting lncRNA–disease associations

(2019) Guobo Xie et al.   MOLECULAR GENETICS AND GENOMICS

CNNDLP: A Method Based on Convolutional Autoencoder and Convolutional Neural Network with Adjacent Edge Attention for Predicting lncRNA–Disease Associations

(2019) Ping Xuan et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

LDAPred: A Method Based on Information Flow Propagation and a Convolutional Neural Network for the Prediction of Disease-Associated lncRNAs

(2019) Ping Xuan et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Network Diffusion Approach to Predict LncRNA Disease Associations Using Multi-Type Biological Networks: LION

(2019) Marissa Sumathipala et al.   Frontiers in Physiology

DNILMF-LDA: Prediction of lncRNA-Disease Associations by Dual-Network Integrated Logistic Matrix Factorization and Bayesian Optimization

(2019) Yan Li et al.   Genes

Graph Convolutional Network and Convolutional Neural Network Based Method for Predicting lncRNA-Disease Associations

(2019) Xuan et al.   Cells

The role of long noncoding RNA in major human disease

(2019) Xiaoli Zhang et al.   BIOORGANIC CHEMISTRY

A novel algorithm based on bi-random walks to identify disease-related lncRNAs

(2019) Jialu Hu et al.   BMC BIOINFORMATICS

Downregulation of lncRNA UCA1 ameliorates the damage of dopaminergic neurons, reduces oxidative stress and inflammation in Parkinson's disease through the inhibition of the PI3K/Akt signaling pathway

(2019) Lijun Cai et al.   INTERNATIONAL IMMUNOPHARMACOLOGY

LncRNA UCA1 functions as a ceRNA to promote prostate cancer progression via Sponging miR143

(2019) Yanlan Yu et al.   Molecular Therapy-Nucleic Acids

Deep Learning Enables Accurate Prediction of Interplay Between lncRNA and Disease

(2019) Jialu Hu et al.   Frontiers in Genetics

H19 lncRNA: Roles in tumorigenesis

(2019) Soudeh Ghafouri-Fard et al.   BIOMEDICINE & PHARMACOTHERAPY

The role of lncRNA MALAT1 in cardiovascular disease

(2019) Youyou Yan et al.   IUBMB LIFE

IDLDA: An Improved Diffusion Model for Predicting LncRNA–Disease Associations

(2019) Qi Wang et al.   Frontiers in Genetics

LDAH2V: Exploring Meta-Paths Across Multiple Networks for lncRNA-Disease Association Prediction

(2019) Lei Deng et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Long non-coding RNA UCA1 promotes lung cancer cell proliferation and migration via microRNA-193a/HMGB1 axis

(2018) Hongyu Wu et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Prediction of lncRNA–disease associations based on inductive matrix completion

(2018) Chengqian Lu et al.   BIOINFORMATICS

deepNF: deep network fusion for protein function prediction

(2018) Vladimir Gligorijević et al.   BIOINFORMATICS

TINCR suppresses proliferation and invasion through regulating miR-544a/FBXW7 axis in lung cancer

(2018) Xiaochun Liu et al.   BIOMEDICINE & PHARMACOTHERAPY

Long non-coding RNA CHRF facilitates cardiac hypertrophy through regulating Akt3 via miR-93

(2018) Yang Wo et al.   CARDIOVASCULAR PATHOLOGY

LncRNA H19-elevated LIN28B promotes lung cancer progression through sequestering miR-196b

(2018) Jin Ren et al.   CELL CYCLE

A Novel Method for LncRNA-Disease Association Prediction Based on an lncRNA-disease Association Network

(2018) pengyao ping et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Long noncoding RNA MALAT1 enhances the docetaxel resistance of prostate cancer cells via miR-145-5p-mediated regulation of AKAP12

(2018) Dong Xue et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

TPGLDA: Novel prediction of associations between lncRNAs and diseases via lncRNA-disease-gene tripartite graph

(2018) Liang Ding et al.   Scientific Reports

A Novel Probability Model for LncRNA–Disease Association Prediction Based on the Naïve Bayesian Classifier

(2018) Jingwen Yu et al.   Genes

Computational models for lncRNA function prediction and functional similarity calculation

(2018) Xing Chen et al.   Briefings in Functional Genomics

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

HMDD v3.0: a database for experimentally supported human microRNA–disease associations

(2018) Zhou Huang et al.   NUCLEIC ACIDS RESEARCH

LNCipedia 5: towards a reference set of human long non-coding RNAs

(2018) Pieter-Jan Volders et al.   NUCLEIC ACIDS RESEARCH

Human Disease Ontology 2018 update: classification, content and workflow expansion

(2018) Lynn M Schriml et al.   NUCLEIC ACIDS RESEARCH

LncRNA2Target v2.0: a comprehensive database for target genes of lncRNAs in human and mouse

(2018) Liang Cheng et al.   NUCLEIC ACIDS RESEARCH

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources

(2018) Sebastian Köhler et al.   NUCLEIC ACIDS RESEARCH

Altered Levels of Long NcRNAs Meg3 and Neat1 in Cell And Animal Models Of Huntington’s Disease

(2018) Kaushik Chanda et al.   RNA Biology

HOTAIR genetic variants are associated with prostate cancer and benign prostate hyperplasia in an Iranian population

(2017) Mohammad Taheri et al.   GENE

Drug-Target Interaction Prediction with Graph Regularized Matrix Factorization

(2017) Ali Ezzat et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Integrating Multiple Heterogeneous Networks for Novel LncRNA-disease Association Inference

(2017) Jingpu Zhang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

LncRNA XIST regulates myocardial infarction by targeting miR-130a-3p

(2017) Tao Zhou et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Global, regional, and national incidence, prevalence, and years lived with disability for 328 diseases and injuries for 195 countries, 1990–2016: a systematic analysis for the Global Burden of Disease Study 2016

(2017) Theo Vos et al.   LANCET

LncRNAs: macromolecules with big roles in neurobiology and neurological diseases

(2017) Ye Chen et al.   METABOLIC BRAIN DISEASE

An atlas of human long non-coding RNAs with accurate 5′ ends

(2017) Chung-Chau Hon et al.   NATURE

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

BRWLDA: bi-random walks for predicting lncRNA-disease associations

(2017) Guoxian Yu et al.   Oncotarget

Global network random walk for predicting potential human lncRNA-disease associations

(2017) Changlong Gu et al.   Scientific Reports

Circulating lncRNA H19 in plasma as a novel biomarker for breast cancer

(2016) Kaijiong Zhang et al.   Cancer Biomarkers

Altered Long Noncoding RNA Expression Precedes the Course of Parkinson’s Disease—a Preliminary Report

(2016) Theo F. J. Kraus et al.   MOLECULAR NEUROBIOLOGY

Altered Expression of the Long Noncoding RNA NEAT1 in Huntington’s Disease

(2016) Jun-Sang Sunwoo et al.   MOLECULAR NEUROBIOLOGY

RAID v2.0: an updated resource of RNA-associated interactions across organisms

(2016) Ying Yi et al.   NUCLEIC ACIDS RESEARCH

Non-coding RNAs in Development and Disease: Background, Mechanisms, and Therapeutic Approaches

(2016) Julia Beermann et al.   PHYSIOLOGICAL REVIEWS

IRWRLDA: improved random walk with restart for lncRNA-disease association prediction

(2016) Xing Chen et al.   Oncotarget

Prioritizing candidate disease-related long non-coding RNAs by walking on the heterogeneous lncRNA and disease network

(2015) Meng Zhou et al.   Molecular BioSystems

The emerging role of lncRNAs in cancer

(2015) Maite Huarte   NATURE MEDICINE

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers

(2015) Shangwei Ning et al.   NUCLEIC ACIDS RESEARCH

NONCODE 2016: an informative and valuable data source of long non-coding RNAs

(2015) Yi Zhao et al.   NUCLEIC ACIDS RESEARCH

Circulating Long Noncoding RNA, LIPCAR, Predicts Survival in Patients With Heart Failure

(2014) Regalla Kumarswamy et al.   CIRCULATION RESEARCH

Inferring novel lncRNA–disease associations based on a random walk model of a lncRNA functional similarity network

(2014) Jie Sun et al.   Molecular BioSystems

Long Noncoding RNA ANRIL Promotes Non-Small Cell Lung Cancer Cell Proliferation and Inhibits Apoptosis by Silencing KLF2 and P21 Expression

(2014) F.-q. Nie et al.   MOLECULAR CANCER THERAPEUTICS

OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders

(2014) Joanna S. Amberger et al.   NUCLEIC ACIDS RESEARCH

A Network Based Method for Analysis of lncRNA-Disease Associations and Prediction of lncRNAs Implicated in Diseases

(2014) Xiaofei Yang et al.   PLoS One

Novel human lncRNA–disease association inference based on lncRNA expression profiles

(2013) Xing Chen et al.   BIOINFORMATICS

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

NONCODEv4: exploring the world of long non-coding RNA genes

(2013) Chaoyong Xie et al.   NUCLEIC ACIDS RESEARCH

lncRNome: a comprehensive knowledgebase of human long noncoding RNAs

(2013) Deeksha Bhartiya et al.   Database-The Journal of Biological Databases and Curation

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

LNCipedia: a database for annotated human lncRNA transcript sequences and structures

(2012) Pieter-Jan Volders et al.   NUCLEIC ACIDS RESEARCH

LncRNADisease: a database for long-non-coding RNA-associated diseases

(2012) Geng Chen et al.   NUCLEIC ACIDS RESEARCH

Analysis of Transcriptome Complexity Through RNA Sequencing in Normal and Failing Murine Hearts

(2011) Jae-Hyung Lee et al.   CIRCULATION RESEARCH

Molecular Mechanisms of Long Noncoding RNAs

(2011) Kevin C. Wang et al.   MOLECULAR CELL

Long noncoding RNAs and human disease

(2011) Orly Wapinski et al.   TRENDS IN CELL BIOLOGY

Selective cell death in neurodegeneration: Why are some neurons spared in vulnerable regions?

(2010) K.L. Double et al.   PROGRESS IN NEUROBIOLOGY

Epigenetic mutations of the imprinted IGF2-H19 domain in Silver-Russell syndrome (SRS): results from a large cohort of patients with SRS and SRS-like phenotypes

(2008) D Bartholdi et al.   JOURNAL OF MEDICAL GENETICS