A Novel Phosphorylation Site-Kinase Network-Based Method for the Accurate Prediction of Kinase-Substrate Relationships

From phosphoproteins to phosphoproteomes: a historical account

(2017) Andrea Venerando et al.   FEBS Journal

Inferring Disease Associated Phosphorylation Sites via Random Walk on Multi-Layer Heterogeneous Network

(2016) Xiaoyi Xu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

A novel method for predicting post-translational modifications on serine and threonine sites by using site-modification network profiles

(2015) Minghui Wang et al.   Molecular BioSystems

Kinase Identification with Supervised Laplacian Regularized Least Squares

(2015) Ao Li et al.   PLoS One

Deciphering kinase–substrate relationships by analysis of domain-specific phosphorylation network

(2014) Nikhil Prakash Damle et al.   BIOINFORMATICS

Improving the performance of protein kinase identification via high dimensional protein–protein interactions and substrate structure data

(2014) Xiaoyi Xu et al.   Molecular BioSystems

Ultradeep Human Phosphoproteome Reveals a Distinct Regulatory Nature of Tyr and Ser/Thr-Based Signaling

(2014) Kirti Sharma et al.   Cell Reports

Learning a peptide-protein binding affinity predictor with kernel ridge regression

(2013) Sébastien Giguère et al.   BMC BIOINFORMATICS

PKIS: computational identification of protein kinases for experimentally discovered protein phosphorylation sites

(2013) Liang Zou et al.   BMC BIOINFORMATICS

Using networks to measure similarity between genes: association index selection

(2013) Juan I Fuxman Bass et al.   NATURE METHODS

A comprehensive evaluation of multicategory classification methods for microbiomic data

(2013) Alexander Statnikov et al.   Microbiome

Structural biomarkers predict onset of knee pain: data from the osteoarthritis initiative

(2012) J.G. Tamez-Pena et al.   OSTEOARTHRITIS AND CARTILAGE

Gaussian interaction profile kernels for predicting drug–target interaction

(2011) Twan van Laarhoven et al.   BIOINFORMATICS

MINT, the molecular interaction database: 2012 update

(2011) Luana Licata et al.   NUCLEIC ACIDS RESEARCH

PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse

(2011) P. V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

Phosphoproteome analysis of human liver tissue by long-gradient nanoflow LC coupled with multiple stage MS analysis

(2010) Guanghui Han et al.   ELECTROPHORESIS

Phospho.ELM: a database of phosphorylation sites--update 2011

(2010) H. Dinkel et al.   NUCLEIC ACIDS RESEARCH

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

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

Reversed-Phase-Reversed-Phase Liquid Chromatography Approach with High Orthogonality for Multidimensional Separation of Phosphopeptides

(2009) Chunxia Song et al.   ANALYTICAL CHEMISTRY

Identification of substrates for Ser/Thr kinases using residue-based statistical pair potentials

(2009) Narendra Kumar et al.   BIOINFORMATICS

Predicting sulfotyrosine sites using the random forest algorithm with significantly improved prediction accuracy

(2009) Zheng Yang   BMC BIOINFORMATICS

The Predikin webserver: improved prediction of protein kinase peptide specificity using structural information

(2008) N. F. W. Saunders et al.   NUCLEIC ACIDS RESEARCH

Prediction of PK-specific phosphorylation site based on information entropy

(2008) MingHui Wang et al.   Science in China. Series C, Life sciences / Chinese Academy of Sciences