DeepSG2PPI: A Protein-Protein Interaction Prediction Method Based on Deep Learning

TransformerGO: Predicting protein-protein interactions by modelling the attention between sets of gene ontology terms

(2022) Ioan Ieremie et al.   BIOINFORMATICS

InfersentPPI: Prediction of Protein-Protein Interaction Using Protein Sentence Embedding With Gene Ontology Information

(2022) Meijing Li et al.   Frontiers in Genetics

Mass spectrometry‐based protein–protein interaction networks for the study of human diseases

(2021) Alicia L Richards et al.   Molecular Systems Biology

Protein–Protein Interaction Prediction Based on Spectral Radius and General Regression Neural Network

(2021) Hanxiao Xu et al.   JOURNAL OF PROTEOME RESEARCH

Comparison of path-based centrality measures in protein-protein interaction networks revealed proteins with phenotypic relevance during adaptation to changing nitrogen environments

(2021) Max Gilbert et al.   Journal of Proteomics

PecanPy: a fast, efficient, and parallelized Python implementation of node2vec

(2021) Renming Liu et al.   BIOINFORMATICS

Performance improvement for a 2D convolutional neural network by using SSC encoding on protein–protein interaction tasks

(2021) Yang Wang et al.   BMC BIOINFORMATICS

FAD-BERT: Improved prediction of FAD binding sites using pre-training of deep bidirectional transformers

(2021) Quang-Thai Ho et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Learning spatial structures of proteins improves protein–protein interaction prediction

(2021) Bosheng Song et al.   BRIEFINGS IN BIOINFORMATICS

A deep learning model for plant lncRNA-protein interaction prediction with graph attention

(2020) Jael Sanyanda Wekesa et al.   MOLECULAR GENETICS AND GENOMICS

DELPHI: accurate deep ensemble model for protein interaction sites prediction

(2020) Yiwei Li et al.   BIOINFORMATICS

The Gene Ontology resource: enriching a GOld mine

(2020) et al.   NUCLEIC ACIDS RESEARCH

Conjoint Feature Representation of GO and Protein Sequence for PPI Prediction Based on an Inception RNN Attention Network

(2020) Lingling Zhao et al.   Molecular Therapy-Nucleic Acids

MultiPredGO: Deep Multi-Modal Protein Function Prediction by Amalgamating Protein Structure, Sequence, and Interaction Information

(2020) Swagarika Jaharlal Giri et al.   IEEE Journal of Biomedical and Health Informatics

DeepFunc: A Deep Learning Framework for Accurate Prediction of Protein Functions from Protein Sequences and Interactions

(2019) Fuhao Zhang et al.   PROTEOMICS

Multifaceted protein–protein interaction prediction based on Siamese residual RCNN

(2019) Muhao Chen et al.   BIOINFORMATICS

Protein-protein interaction prediction using a hybrid feature representation and a stacked generalization scheme

(2019) Kuan-Hsi Chen et al.   BMC BIOINFORMATICS

Multi-modal deep learning model for auxiliary diagnosis of Alzheimer’s disease

(2019) Fan Zhang et al.   NEUROCOMPUTING

Predicting Protein-Protein Interactions from Matrix-Based Protein Sequence Using Convolution Neural Network and Feature-Selective Rotation Forest

(2019) Lei Wang et al.   Scientific Reports

An integration of deep learning with feature embedding for protein–protein interaction prediction

(2019) Yu Yao et al.   PeerJ

Inferring novel genes related to oral cancer with a network embedding method and one-class learning algorithms

(2019) Lei Chen et al.   GENE THERAPY

Next-generation interactomics: considerations for the use of co-elution to measure protein interaction networks

(2019) Daniela Salas et al.   MOLECULAR & CELLULAR PROTEOMICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Next-Generation Machine Learning for Biological Networks

(2018) Diogo M. Camacho et al.   CELL

Predicting protein-protein interactions using high-quality non-interacting pairs

(2018) Long Zhang et al.   BMC BIOINFORMATICS

Prediction of RNA-protein interactions by combining deep convolutional neural network with feature selection ensemble method

(2018) Lei Wang et al.   JOURNAL OF THEORETICAL BIOLOGY

Extracting Coevolutionary Features from Protein Sequences for Predicting Protein-Protein Interactions

(2017) Lun Hu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Protein-Protein Interactions Prediction Using a Novel Local Conjoint Triad Descriptor of Amino Acid Sequences

(2017) Jun Wang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

DeepPPI: Boosting Prediction of Protein–Protein Interactions with Deep Neural Networks

(2017) Xiuquan Du et al.   Journal of Chemical Information and Modeling

Accelerating Very Deep Convolutional Networks for Classification and Detection

(2016) Xiangyu Zhang et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Phospho-tyrosine dependent protein-protein interaction network

(2015) A. Grossmann et al.   Molecular Systems Biology

A simple feature construction method for predicting upstream/downstream signal flow in human protein-protein interaction networks

(2015) Suyu Mei et al.   Scientific Reports

Using Weighted Sparse Representation Model Combined with Discrete Cosine Transformation to Predict Protein-Protein Interactions from Protein Sequence

(2015) Yu-An Huang et al.   Biomed Research International

Detecting Protein-Protein Interactions with a Novel Matrix-Based Protein Sequence Representation and Support Vector Machines

(2015) Zhu-Hong You et al.   Biomed Research International

Identification of novel kinase inhibitors by targeting a kinase-related apoptotic protein-protein interaction network in HeLa cells

(2014) Z. Shi et al.   CELL PROLIFERATION

Analysis and identification of toxin targets by topological properties in protein–protein interaction network

(2014) Lei Yang et al.   JOURNAL OF THEORETICAL BIOLOGY

Ensemble learning prediction of protein–protein interactions using proteins functional annotations

(2014) Indrajit Saha et al.   Molecular BioSystems

Protein–protein interaction networks: the puzzling riches

(2013) Shoshana J Wodak et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Defining the Protein–Protein Interaction Network of the Human Hippo Pathway

(2013) Wenqi Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

Identification of hepatocellular carcinoma related genes with k-th shortest paths in a protein–protein interaction network

(2013) Min Jiang et al.   Molecular BioSystems

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

Detecting disease genes based on semi-supervised learning and protein–protein interaction networks

(2011) Thanh-Phuong Nguyen et al.   ARTIFICIAL INTELLIGENCE IN MEDICINE

Gene Ontology-driven inference of protein–protein interactions using inducers

(2011) Stefan R. Maetschke et al.   BIOINFORMATICS

Prioritizing cancer-related genes with aberrant methylation based on a weighted protein-protein interaction network

(2011) Hui Liu et al.   BMC Systems Biology

Simple sequence-based kernels do not predict protein-protein interactions

(2010) J. Yu et al.   BIOINFORMATICS

Semantic and layered protein function prediction from PPI networks

(2010) Wei Zhu et al.   JOURNAL OF THEORETICAL BIOLOGY

DOMINE: a comprehensive collection of known and predicted domain-domain interactions

(2010) Sailu Yellaboina et al.   NUCLEIC ACIDS RESEARCH

Integration of Gene Ontology-based similarities for supporting analysis of protein–protein interaction networks

(2010) Haiying Wang et al.   PATTERN RECOGNITION LETTERS

Prediction of Protein-Protein Interactions from Protein Sequence Using Local Descriptors

(2010) Lei Yang et al.   PROTEIN AND PEPTIDE LETTERS

The analysis of the drug–targets based on the topological properties in the human protein–protein interaction network

(2009) Mingzhu Zhu et al.   JOURNAL OF DRUG TARGETING