SELPHI: correlation-based identification of kinase-associated networks from global phospho-proteomics data sets

Identifying novel targets of oncogenic EGF receptor signaling in lung cancer through global phosphoproteomics

(2015) Xu Zhang et al.   PROTEOMICS

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

SMART: recent updates, new developments and status in 2015

(2014) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Temporal regulation of EGF signalling networks by the scaffold protein Shc1

(2013) Yong Zheng et al.   NATURE

GeneMANIA Prediction Server 2013 Update

(2013) Khalid Zuberi et al.   NUCLEIC ACIDS RESEARCH

The eukaryotic linear motif resource ELM: 10 years and counting

(2013) Holger Dinkel et al.   NUCLEIC ACIDS RESEARCH

The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation inSaccharomyces cerevisiae

(2013) Miguel Cacho Teixeira et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Towards Systematic Discovery of Signaling Networks in Budding Yeast Filamentous Growth Stress Response Using Interventional Phosphorylation Data

(2013) Yan Zhang et al.   PLoS Computational Biology

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

(2012) Limin Fu et al.   BIOINFORMATICS

Global Snapshot of the Influence of Endocytosis upon EGF Receptor Signaling Output

(2012) Jasminka Omerovic et al.   JOURNAL OF PROTEOME RESEARCH

YAP modifies cancer cell sensitivity to EGFR and survivin inhibitors and is negatively regulated by the non-receptor type protein tyrosine phosphatase 14

(2012) J-M Huang et al.   ONCOGENE

HGF induces novel EGFR functions involved in resistance formation to tyrosine kinase inhibitors

(2012) S Gusenbauer et al.   ONCOGENE

AnimalTFDB: a comprehensive animal transcription factor database

(2011) H.-M. Zhang 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

ProteoConnections: A bioinformatics platform to facilitate proteome and phosphoproteome analyses

(2011) Mathieu Courcelles et al.   PROTEOMICS

Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data

(2010) Haruna Imamura et al.   BMC BIOINFORMATICS

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

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

Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis

(2010) J. V. Olsen et al.   Science Signaling

Next generation software for functional trend analysis

(2009) G. F. Berriz et al.   BIOINFORMATICS

Global Effects of Kinase Inhibitors on Signaling Networks Revealed by Quantitative Phosphoproteomics

(2009) Cuiping Pan et al.   MOLECULAR & CELLULAR PROTEOMICS

Improved visualization of protein consensus sequences by iceLogo

(2009) Niklaas Colaert et al.   NATURE METHODS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Global and Site-Specific Quantitative Phosphoproteomics: Principles and Applications

(2008) Boris Macek et al.   Annual Review of Pharmacology and Toxicology

Comparative analysis of function and interaction of transcription factors in nematodes: Extensive conservation of orthology coupled to rapid sequence evolution

(2008) Wilfried Haerty et al.   BMC GENOMICS

Linear Motif Atlas for Phosphorylation-Dependent Signaling

(2008) M. L. Miller et al.   Science Signaling