PhosIDN: an integrated deep neural network for improving protein phosphorylation site prediction by combining sequence and protein–protein interaction information

DeepKinZero: Zero-Shot Learning for Predicting Kinase-Phosphosite Associations Involving Understudied Kinases

(2020) Iman Deznabi et al.   BIOINFORMATICS

SAINT: Self-Attention Augmented Inception-Inside-Inception Network Improves Protein Secondary Structure Prediction

(2020) Mostofa Rafid Uddin et al.   BIOINFORMATICS

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

(2020) Rose Oughtred et al.   PROTEIN SCIENCE

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

(2018) Sameer Khurana et al.   BIOINFORMATICS

Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome

(2018) Fuyi Li et al.   BIOINFORMATICS

PTM-ssMP: A Web Server for Predicting Different Types of Post-translational Modification Sites Using Novel Site-specific Modification Profile

(2018) Yu Liu et al.   International Journal of Biological Sciences

Using deep learning to model the hierarchical structure and function of a cell

(2018) Jianzhu Ma et al.   NATURE METHODS

OUP accepted manuscript

(2018)   BRIEFINGS IN BIOINFORMATICS

DeepPhos: prediction of protein phosphorylation sites with deep learning

(2018) Fenglin Luo et al.   BIOINFORMATICS

Capsule network for protein post-translational modification site prediction

(2018) Duolin Wang et al.   BIOINFORMATICS

PhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection

(2017) Jiangning Song et al.   Scientific Reports

Accuratein silicoprediction of species-specific methylation sites based on information gain feature optimization

(2016) Ping-Ping Wen et al.   BIOINFORMATICS

The Roles of Post-translational Modifications in the Context of Protein Interaction Networks

(2015) Guangyou Duan et al.   PLoS Computational Biology

PhosphoSVM: prediction of phosphorylation sites by integrating various protein sequence attributes with a support vector machine

(2014) Yongchao Dou et al.   AMINO ACIDS

Prediction of protein kinase-specific phosphorylation sites in hierarchical structure using functional information and random forest

(2014) Wenwen Fan et al.   AMINO ACIDS

Nuclear Localization of p38 MAPK in Response to DNA Damage

(2012) C. David Wood et al.   International Journal of Biological Sciences

Systematic Analysis of Protein Phosphorylation Networks From Phosphoproteomic Data

(2012) Chunxia Song et al.   MOLECULAR & CELLULAR PROTEOMICS

Computational prediction of eukaryotic phosphorylation sites

(2011) B. Trost et al.   BIOINFORMATICS

pROC: an open-source package for R and S+ to analyze and compare ROC curves

(2011) Xavier Robin et al.   BMC BIOINFORMATICS

PostMod: sequence based prediction of kinase-specific phosphorylation sites with indirect relationship

(2010) Inkyung Jung et al.   BMC BIOINFORMATICS

Musite, a Tool for Global Prediction of General and Kinase-specific Phosphorylation Sites

(2010) Jianjiong Gao et al.   MOLECULAR & CELLULAR PROTEOMICS

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Identifying Human Kinase-Specific Protein Phosphorylation Sites by Integrating Heterogeneous Information from Various Sources

(2010) Tingting Li et al.   PLoS One

GPS 2.0, a Tool to Predict Kinase-specific Phosphorylation Sites in Hierarchy

(2008) Yu Xue et al.   MOLECULAR & CELLULAR PROTEOMICS