BioERP: biomedical heterogeneous network-based self-supervised representation learning approach for entity relationship predictions

Network-based prediction of drug–target interactions using an arbitrary-order proximity embedded deep forest

(2020) Xiangxiang Zeng et al.   BIOINFORMATICS

COVID-19: consider cytokine storm syndromes and immunosuppression

(2020) Puja Mehta et al.   LANCET

Predicting Candidate Genes From Phenotypes, Functions, And Anatomical Site Of Expression

(2020) Jun Chen et al.   BIOINFORMATICS

Semantic similarity and machine learning with ontologies

(2020) Maxat Kulmanov et al.   BRIEFINGS IN BIOINFORMATICS

PharmKG: a dedicated knowledge graph benchmark for bomedical data mining

(2020) Shuangjia Zheng et al.   BRIEFINGS IN BIOINFORMATICS

deepDR: A network-based deep learning approach to in silico drug repositioning

(2019) Xiangxiang Zeng et al.   BIOINFORMATICS

Predicting Drug–Target Interaction Using a Novel Graph Neural Network with 3D Structure-Embedded Graph Representation

(2019) Jaechang Lim et al.   Journal of Chemical Information and Modeling

NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions

(2018) Fangping Wan et al.   BIOINFORMATICS

Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations

(2018) Fatima Zohra Smaili et al.   BIOINFORMATICS

Modeling polypharmacy side effects with graph convolutional networks

(2018) Marinka Zitnik et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

A Comprehensive Survey of Graph Embedding: Problems, Techniques and Applications

(2018) HongYun Cai et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

Heterogeneous Information Network Embedding for Recommendation

(2018) Chuan Shi et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

HerGePred: Heterogeneous Network Embedding Representation for Disease Gene Prediction

(2018) Kuo Yang et al.   IEEE Journal of Biomedical and Health Informatics

A novel approach for drug response prediction in cancer cell lines via network representation learning

(2018) Jianghong Yang et al.   BIOINFORMATICS

OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction

(2018) Fatima Zohra Smaili et al.   BIOINFORMATICS

Feature assisted stacked attentive shortest dependency path based Bi-LSTM model for protein–protein interaction

(2018) Shweta Yadav et al.   KNOWLEDGE-BASED SYSTEMS

Network embedding-based representation learning for single cell RNA-seq data

(2017) Xiangyu Li et al.   NUCLEIC ACIDS RESEARCH

A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information

(2017) Yunan Luo et al.   Nature Communications

Predicting drug target interactions using meta-path-based semantic network analysis

(2016) Gang Fu et al.   BMC BIOINFORMATICS

HPIDB 2.0: a curated database for host–pathogen interactions

(2016) Mais G. Ammari et al.   Database-The Journal of Biological Databases and Curation

Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study

(2015) J. M. Villaveces et al.   Database-The Journal of Biological Databases and Curation

New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence

(2014) Mengfei Cao et al.   BIOINFORMATICS

Inductive matrix completion for predicting gene-disease associations

(2014) N. Natarajan et al.   BIOINFORMATICS

Kernelized Bayesian Matrix Factorization

(2014) Mehmet Gonen et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Drug–target interaction prediction through domain-tuned network-based inference

(2013) Salvatore Alaimo et al.   BIOINFORMATICS

Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses

(2013) U. Martin Singh-Blom et al.   PLoS One

Drug–target interaction prediction by learning from local information and neighbors

(2012) Jian-Ping Mei et al.   BIOINFORMATICS