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

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

(2021) Wang Liu-Wei et al.   BIOINFORMATICS

Current status and future perspectives of computational studies on human–virus protein–protein interactions

(2021) Xianyi Lian et al.   BRIEFINGS IN BIOINFORMATICS

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

(2020) David E. Gordon et al.   NATURE

HVIDB: a comprehensive database for human–virus protein–protein interactions

(2020) Xiaodi Yang et al.   BRIEFINGS IN BIOINFORMATICS

MultiPLIER: A Transfer Learning Framework for Transcriptomics Reveals Systemic Features of Rare Disease

(2019) Jaclyn N. Taroni et al.   Cell Systems

Multifaceted protein–protein interaction prediction based on Siamese residual RCNN

(2019) Muhao Chen et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Unsupervised Transfer Learning via Multi-Scale Convolutional Sparse Coding for Biomedical Applications

(2018) Hang Chang et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

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

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

Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis

(2018) Priya S. Shah et al.   CELL

CORUM: the comprehensive resource of mammalian protein complexes—2019

(2018) Madalina Giurgiu et al.   NUCLEIC ACIDS RESEARCH

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

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

Role of Herpes Simplex Virus 1 γ34.5 in the Regulation of IRF3 Signaling

(2017) Richard Manivanh et al.   JOURNAL OF VIROLOGY

HIPPIE v2.0: enhancing meaningfulness and reliability of protein–protein interaction networks

(2016) Gregorio Alanis-Lobato et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase

(2016)   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

Evolutionary profiles improve protein–protein interaction prediction from sequence

(2015) Tobias Hamp et al.   BIOINFORMATICS

A deep learning framework for modeling structural features of RNA-binding protein targets

(2015) Sai Zhang et al.   NUCLEIC ACIDS RESEARCH

Transfer Learning for Visual Categorization: A Survey

(2015) Ling Shao et al.   IEEE Transactions on Neural Networks and Learning Systems

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

Predicting protein–protein interactions between human and hepatitis C virus via an ensemble learning method

(2014) Abbasali Emamjomeh et al.   Molecular BioSystems

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

PHISTO: pathogen–host interaction search tool

(2013) Saliha Durmuş Tekir et al.   BIOINFORMATICS

Prediction of protein-protein interactions from amino acid sequences with ensemble extreme learning machines and principal component analysis

(2013) Zhu-Hong You et al.   BMC BIOINFORMATICS

Prediction of protein-protein interactions between viruses and human by an SVM model

(2012) Guangyu Cui et al.   BMC BIOINFORMATICS

Supervised learning and prediction of physical interactions between human and HIV proteins

(2011) Matthew D. Dyer et al.   INFECTION GENETICS AND EVOLUTION

Viral Organization of Human Proteins

(2010) Stefan Wuchty et al.   PLoS One

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

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

Ebola Virus Protein VP35 Impairs the Function of Interferon Regulatory Factor-Activating Kinases IKK  and TBK-1

(2009) K. C. Prins et al.   JOURNAL OF VIROLOGY

Optimizing amino acid groupings for GPCR classification

(2008) M. N. Davies et al.   BIOINFORMATICS

Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature

(2008) Jiansheng Wu et al.   BIOINFORMATICS

Control of TANK-binding Kinase 1-mediated Signaling by the γ134.5 Protein of Herpes Simplex Virus 1

(2008) Dustin Verpooten et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Using support vector machine combined with auto covariance to predict protein–protein interactions from protein sequences

(2008) Yanzhi Guo et al.   NUCLEIC ACIDS RESEARCH

The Landscape of Human Proteins Interacting with Viruses and Other Pathogens

(2008) Matthew D. Dyer et al.   PLoS Pathogens