Graph Convolutional Network based Virus-Human Protein-Protein Interaction Prediction for Novel Viruses

DeepViral: prediction of novel virus–host interactions from protein sequences and infectious disease phenotypes

(2021) Wang Liu-Wei et al.   BIOINFORMATICS

Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV

(2021) Alexey Stukalov et al.   NATURE

Transfer learning via multi-scale convolutional neural layers for human–virus protein–protein interaction prediction

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D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions

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A survey of current trends in computational predictions of protein-protein interactions

(2020) Yanbin Wang et al.   Frontiers of Computer Science

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

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Transfer learning with convolutional neural networks for cancer survival prediction using gene-expression data

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

(2020) Jun Chen et al.   BIOINFORMATICS

Graph embedding-based novel protein interaction prediction via higher-order graph convolutional network

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The BioGRID database: A comprehensive biomedical resource of curated protein, genetic and chemical interactions

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Machine learning techniques for sequence-based prediction of viral–host interactions between SARS-CoV-2 and human proteins

(2020) Lopamudra Dey et al.   Biomedical Journal

UniProt: the universal protein knowledgebase in 2021

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g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

(2019) Uku Raudvere et al.   NUCLEIC ACIDS RESEARCH

PathoPhenoDB, linking human pathogens to their phenotypes in support of infectious disease research

(2019) Şenay Kafkas et al.   Scientific Data

Predicting Interactions between Virus and Host Proteins Using Repeat Patterns and Composition of Amino Acids

(2018) Saud Alguwaizani et al.   Journal of Healthcare Engineering

A generalized approach to predicting protein-protein interactions between virus and host

(2018) Xiang Zhou et al.   BMC GENOMICS

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Sebastian Köhler et al.   NUCLEIC ACIDS RESEARCH

HPIDB 2.0: a curated database for host–pathogen interactions

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

DeNovo: virus-host sequence-based protein–protein interaction prediction

(2015) Fatma-Elzahraa Eid et al.   BIOINFORMATICS

VirusMentha: a new resource for virus-host protein interactions

(2014) Alberto Calderone et al.   NUCLEIC ACIDS RESEARCH

VirHostNet 2.0: surfing on the web of virus/host molecular interactions data

(2014) Thibaut Guirimand et al.   NUCLEIC ACIDS RESEARCH

Prediction of Interactions between Viral and Host Proteins Using Supervised Machine Learning Methods

(2014) Ranjan Kumar Barman et al.   PLoS One

PHISTO: pathogen–host interaction search tool

(2013) Saliha Durmuş Tekir et al.   BIOINFORMATICS

Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis

(2013) Philipp Blohm et al.   NUCLEIC ACIDS RESEARCH

What Evidence Is There for the Homology of Protein-Protein Interactions?

(2012) Anna C. F. Lewis et al.   PLoS Computational Biology