DeepTrio: a ternary prediction system for protein–protein interaction using mask multiple parallel convolutional neural networks

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

(2021) Wang Liu-Wei et al.   BIOINFORMATICS

Multifaceted protein–protein interaction prediction based on Siamese residual RCNN

(2019) Muhao Chen et al.   BIOINFORMATICS

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

(2019) Yu Yao et al.   PeerJ

Protein Docking Model Evaluation by 3D Deep Convolutional Neural Networks

(2019) Xiao Wang et al.   BIOINFORMATICS

Molecular basis for the interaction between human choline kinase alpha and the SH3 domain of the c-Src tyrosine kinase

(2019) Stefanie L. Kall et al.   Scientific Reports

DeepSol: a deep learning framework for sequence-based protein solubility prediction

(2018) Sameer Khurana et al.   BIOINFORMATICS

DeepFam: deep learning based alignment-free method for protein family modeling and prediction

(2018) Seokjun Seo et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Deep Neural Network Based Predictions of Protein Interactions Using Primary Sequences

(2018) Hang Li et al.   MOLECULES

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

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

The BioGRID interaction database: 2019 update

(2018) Rose Oughtred et al.   NUCLEIC ACIDS RESEARCH

Explaining nonlinear classification decisions with deep Taylor decomposition

(2017) Grégoire Montavon et al.   PATTERN RECOGNITION

DeepChrome: deep-learning for predicting gene expression from histone modifications

(2016) Ritambhara Singh et al.   BIOINFORMATICS

Mutant Calreticulin Requires Both Its Mutant C-terminus and the Thrombopoietin Receptor for Oncogenic Transformation

(2016) S. Elf et al.   Cancer Discovery

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Predicting Protein-Protein Interactions from Primary Protein Sequences Using a Novel Multi-Scale Local Feature Representation Scheme and the Random Forest

(2015) Zhu-Hong You et al.   PLoS One

Protein–protein interactions and genetic diseases: The interactome

(2014) Kasper Lage   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Prediction of protein-protein interactions from amino acid sequences using a novel multi-scale continuous and discontinuous feature set

(2014) Zhu-Hong You et al.   BMC BIOINFORMATICS

Somatic CALR Mutations in Myeloproliferative Neoplasms with Nonmutated JAK2

(2013) J. Nangalia et al.   NEW ENGLAND JOURNAL OF MEDICINE

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Intrinsically Disordered Proteins in Human Diseases: Introducing the D2 Concept

(2008) Vladimir N. Uversky et al.   Annual Review of Biophysics

The Graph Neural Network Model

(2008) F. Scarselli et al.   IEEE TRANSACTIONS ON NEURAL NETWORKS

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

(2008) Yanzhi Guo et al.   NUCLEIC ACIDS RESEARCH