Association predictions of genomics, proteinomics, transcriptomics, microbiome, metabolomics, pathomics, radiomics, drug, symptoms, environment factor, and disease networks: A comprehensive approach

Role of artificial intelligence in integrated analysis of multi-omics and imaging data in cancer research

(2020) Nam Nhut Phan et al.   Translational Cancer Research

Predicting lncRNA–Protein Interactions With miRNAs as Mediators in a Heterogeneous Network Model

(2020) Yuan-Ke Zhou et al.   Frontiers in Genetics

Predicting Microbe-Disease Association by Learning Graph Representations and Rule-Based Inference on the Heterogeneous Network

(2020) Xiujuan Lei et al.   Frontiers in Microbiology

Graph-based prediction of Protein-protein interactions with attributed signed graph embedding

(2020) Fang Yang et al.   BMC BIOINFORMATICS

Harnessing endophenotypes and network medicine for Alzheimer's drug repurposing

(2020) Jiansong Fang et al.   MEDICINAL RESEARCH REVIEWS

Variational graph auto-encoders for miRNA-disease association prediction

(2020) Yulian Ding et al.   METHODS

Deep learning-based survival prediction for multiple cancer types using histopathology images

(2020) Ellery Wulczyn et al.   PLoS One

Leveraging the Comparative Toxicogenomics Database to fill in knowledge gaps for environmental health: a test case for air pollution-induced cardiovascular disease

(2020) Allan Peter Davis et al.   TOXICOLOGICAL SCIENCES

Predicting Human lncRNA-Disease Associations Based on Geometric Matrix Completion

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

Integrative Network Fusion: A Multi-Omics Approach in Molecular Profiling

(2020) Marco Chierici et al.   Frontiers in Oncology

MIPDH: A Novel Computational Model for Predicting microRNA–mRNA Interactions by DeepWalk on a Heterogeneous Network

(2020) Leon Wong et al.   ACS Omega

Learning Representations to Predict Intermolecular Interactions on Large-Scale Heterogeneous Molecular Association Network

(2020) Hai-Cheng Yi et al.   iScience

Relational completion based non-negative matrix factorization for predicting metabolite-disease associations

(2020) Xiujuan Lei et al.   KNOWLEDGE-BASED SYSTEMS

Artificial intelligence and machine learning‐aided drug discovery in central nervous system diseases: State‐of‐the‐arts and future directions

(2020) Sezen Vatansever et al.   MEDICINAL RESEARCH REVIEWS

Predicting Metabolite-Disease Associations Based on Spy Strategy and ABC Algorithm

(2020) Xiujuan Lei et al.   Frontiers in Molecular Biosciences

Prediction of disease-associated circRNAs via circRNA–disease pair graph and weighted nuclear norm minimization

(2020) Yuchen Zhang et al.   KNOWLEDGE-BASED SYSTEMS

Expanded Expression Landscape and Prioritization of Circular RNAs in Mammals

(2019) Peifeng Ji et al.   Cell Reports

Gene-Environment Interaction in the Era of Precision Medicine

(2019) Jingjing Li et al.   CELL

A novel mRNA-miRNA-lncRNA competing endogenous RNA triple sub-network associated with prognosis of pancreatic cancer

(2019) Wenlong Wang et al.   Aging-US

The Pathosome: A Dynamic Three‐Dimensional View of Disease–Environment Interaction

(2019) Peter Lenart et al.   BIOESSAYS

Identifying the reactive metabolites of tyrosine kinase inhibitors in a comprehensive approach: Implications for drug‐drug interactions and hepatotoxicity

(2019) Marie‐Noëlle Paludetto et al.   MEDICINAL RESEARCH REVIEWS

GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis

(2019) Zefang Tang et al.   NUCLEIC ACIDS RESEARCH

Comparative Analysis of CT and MRI Diagnosis of Large Vestibular Aqueduct Syndrome (LVAS) in Children

(2019) Ling Yang et al.   JCPSP-Journal of the College of Physicians and Surgeons Pakistan

Radiogenomics of breast cancer using dynamic contrast enhanced MRI and gene expression profiling

(2019) Albert C. Yeh et al.   CANCER IMAGING

Inferring Interaction Networks From Multi-Omics Data

(2019) Johann S. Hawe et al.   Frontiers in Genetics

Structured gene‐environment interaction analysis

(2019) Mengyun Wu et al.   BIOMETRICS

Integration of Bioinformatic Predictions and Experimental Data to Identify circRNA-miRNA Associations

(2019) Martina Dori et al.   Genes

Bringing radiomics into a multi-omics framework for a comprehensive genotype–phenotype characterization of oncological diseases

(2019) Mario Zanfardino et al.   Journal of Translational Medicine

A network-based approach to identify deregulated pathways and drug effects in metabolic syndrome

(2019) Karla Misselbeck et al.   Nature Communications

Disease phenotype synonymous prediction through network representation learning from PubMed database

(2019) Shiwen Ma et al.   ARTIFICIAL INTELLIGENCE IN MEDICINE

Neural inductive matrix completion with graph convolutional networks for miRNA-disease association prediction

(2019) Jin Li et al.   BIOINFORMATICS

Integrate multi-omics data with biological interaction networks using Multi-view Factorization AutoEncoder (MAE)

(2019) Tianle Ma et al.   BMC GENOMICS

SemaTyP: a knowledge graph based literature mining method for drug discovery

(2018) Shengtian Sang et al.   BMC BIOINFORMATICS

HNMDA: heterogeneous network-based miRNA–disease association prediction

(2018) Li-Hong Peng et al.   MOLECULAR GENETICS AND GENOMICS

Predict MiRNA-Disease Association with Collaborative Filtering

(2018) Yatong Jiang et al.   NEUROINFORMATICS

Predicting cancer outcomes from histology and genomics using convolutional networks

(2018) Pooya Mobadersany et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Review of Drug Repositioning Approaches and Resources

(2018) Hanqing Xue et al.   International Journal of Biological Sciences

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

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

(2018) Dongxia Yao et al.   Scientific Reports

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

Predicting disease-genes based on network information loss and protein complexes in heterogeneous network

(2018) Xiujuan Lei et al.   INFORMATION SCIENCES

Human pathway-based disease network

(2017) Liang Yu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

An oral cavity squamous cell carcinoma quantitative histomorphometric-based image classifier of nuclear morphology can risk stratify patients for disease-specific survival

(2017) Cheng Lu et al.   MODERN PATHOLOGY

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

(2017) Shujuan Meng et al.   Molecular Cancer

exoRBase: a database of circRNA, lncRNA and mRNA in human blood exosomes

(2017) Shengli Li et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2017) et al.   NUCLEIC ACIDS RESEARCH

NONCODEV5: a comprehensive annotation database for long non-coding RNAs

(2017) ShuangSang Fang et al.   NUCLEIC ACIDS RESEARCH

miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions

(2017) Chih-Hung Chou et al.   NUCLEIC ACIDS RESEARCH

DrugBank 5.0: a major update to the DrugBank database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

HMDB 4.0: the human metabolome database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

Identifying important nodes by adaptive LeaderRank

(2017) Shuang Xu et al.   PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS

ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data

(2016) Ke-Ren Zhou 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

Analysis of multi-source metabolomic data using joint and individual variation explained (JIVE)

(2015) Julia Kuligowski et al.   ANALYST

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

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

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

HeteSim: A General Framework for Relevance Measure in Heterogeneous Networks

(2014) Chuan Shi et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

An overview of MetaMap: historical perspective and recent advances

(2014) Alan R Aronson et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Similarity network fusion for aggregating data types on a genomic scale

(2014) Bo Wang et al.   NATURE METHODS

LncRBase: An Enriched Resource for lncRNA Information

(2014) Sohini Chakraborty et al.   PLoS One

circBase: a database for circular RNAs

(2014) Petar Glažar et al.   RNA

Human symptoms–disease network

(2014) XueZhong Zhou et al.   Nature Communications

The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository

(2013) Kenneth Clark et al.   JOURNAL OF DIGITAL IMAGING

A framework for human microbiome research

(2012)   NATURE

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

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

(2010) Dong Wang et al.   BIOINFORMATICS

Imaging genomics

(2010) Paul M Thompson et al.   CURRENT OPINION IN NEUROLOGY

Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis

(2009) Ronglai Shen et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targets

(2008) Liang-Hui Chu et al.   BMC Systems Biology

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH