Bioinformatics toolbox for exploring protein phosphorylation network

Kinase-targeted cancer therapies: progress, challenges and future directions

(2018) Khushwant S. Bhullar et al.   Molecular Cancer

eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks

(2018) Daniel J B Clarke et al.   NUCLEIC ACIDS RESEARCH

The crucial role of protein phosphorylation in cell signaling and its use as targeted therapy (Review)

(2017) Fatima Ardito et al.   INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE

iPTMnet: an integrated resource for protein post-translational modification network discovery

(2017) Hongzhan Huang et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Minghui Wang et al.   Biomed Research International

ksrMKL: a novel method for identification of kinase–substrate relationships using multiple kernel learning

(2017) Minghui Wang et al.   PeerJ

CAMK2γ antagonizes mTORC1 activation during hepatocarcinogenesis

(2016) Z Meng et al.   ONCOGENE

Unraveling Kinase Activation Dynamics Using Kinase-Substrate Relationships from Temporal Large-Scale Phosphoproteomics Studies

(2016) Westa Domanova et al.   PLoS One

Prediction of kinase–substrate relations based on heterogeneous networks

(2015) Haichun Li et al.   Journal of Bioinformatics and Computational Biology

PhosphoPICK: modelling cellular context to map kinase-substrate phosphorylation events

(2014) Ralph Patrick et al.   BIOINFORMATICS

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

(2014) Nikhil Prakash Damle et al.   BIOINFORMATICS

KinomeXplorer: an integrated platform for kinome biology studies

(2014) Heiko Horn et al.   NATURE METHODS

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

(2014) Peter V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

PhosphoNetworks: a database for human phosphorylation networks

(2013) J. Hu et al.   BIOINFORMATICS

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

(2013) Liang Zou et al.   BMC BIOINFORMATICS

Construction of human activity-based phosphorylation networks

(2013) R. H. Newman et al.   Molecular Systems Biology

Systematic Analysis of Protein Phosphorylation Networks From Phosphoproteomic Data

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

A systems approach identifies HIPK2 as a key regulator of kidney fibrosis

(2012) Yuanmeng Jin et al.   NATURE MEDICINE

A Rho kinase (ROCK) inhibitor, fasudil, prevents matrix metalloproteinase-9-related hemorrhagic transformation in mice treated with tissue plasminogen activator

(2012) M. Ishiguro et al.   NEUROSCIENCE

PhosPhAt goes kinases—searchable protein kinase target information in the plant phosphorylation site database PhosPhAt

(2012) Monika Zulawski et al.   NUCLEIC ACIDS RESEARCH

Sensitive kinase assay linked with phosphoproteomics for identifying direct kinase substrates

(2012) L. Xue et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers

(2011) Edward Y. Chen et al.   BIOINFORMATICS

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

A quantitative literature-curated gold standard for kinase-substrate pairs

(2011) Sara Sharifpoor et al.   GENOME BIOLOGY

A Summary of Computational Resources for Protein Phosphorylation

(2010) Yu Xue et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

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

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

RegPhos: a system to explore the protein kinase–substrate phosphorylation network in humans

(2010) Tzong-Yi Lee et al.   NUCLEIC ACIDS RESEARCH

Deciphering Protein Kinase Specificity Through Large-Scale Analysis of Yeast Phosphorylation Site Motifs

(2010) J. Mok et al.   Science Signaling

Experimental and computational tools useful for (re)construction of dynamic kinase–substrate networks

(2009) Chris Soon Heng Tan et al.   PROTEOMICS

PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database

(2008) Chia-Ying Yang et al.   BIOINFORMATICS

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

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