EPSD: a well-annotated data resource of protein phosphorylation sites in eukaryotes

Mechanisms of PTEN loss in cancer: It’s all about diversity

(2019) Virginia Álvarez-Garcia et al.   SEMINARS IN CANCER BIOLOGY

The International Cancer Genome Consortium Data Portal

(2019) Junjun Zhang et al.   NATURE BIOTECHNOLOGY

The Cancer Genome Atlas: Creating Lasting Value beyond Its Data

(2018) Carolyn Hutter et al.   CELL

Targeting the PI3K pathway in cancer: are we making headway?

(2018) Filip Janku et al.   Nature Reviews Clinical Oncology

IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding

(2018) Bálint Mészáros et al.   NUCLEIC ACIDS RESEARCH

In vivo brain GPCR signaling elucidated by phosphoproteomics

(2018) Jeffrey J. Liu et al.   SCIENCE

PTMD: A Database of Human Disease-associated Post-translational Modifications

(2018) Haodong Xu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

IID 2018 update: context-specific physical protein–protein interactions in human, model organisms and domesticated species

(2018) Max Kotlyar et al.   NUCLEIC ACIDS RESEARCH

dbPTM in 2019: exploring disease association and cross-talk of post-translational modifications

(2018) Kai-Yao Huang et al.   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

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy

(2018) Stephen K Burley et al.   NUCLEIC ACIDS RESEARCH

COSMIC: the Catalogue Of Somatic Mutations In Cancer

(2018) John G Tate et al.   NUCLEIC ACIDS RESEARCH

FPD: A comprehensive phosphorylation database in fungi

(2017) Youhuang Bai et al.   Fungal Biology

TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions

(2017) Heonjong Han et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Hongzhan Huang et al.   NUCLEIC ACIDS RESEARCH

BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery

(2017) Hayley M Dingerdissen et al.   NUCLEIC ACIDS RESEARCH

Network Analysis Reveals A Signaling Regulatory Loop in the PIK3CA -mutated Breast Cancer Predicting Survival Outcome

(2017) Shauna R. McGee et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer

(2016) Justin M. Drake et al.   CELL

Spotlight on Volasertib: Preclinical and Clinical Evaluation of a Promising Plk1 Inhibitor

(2016) J. Van den Bossche et al.   MEDICINAL RESEARCH REVIEWS

A scored human protein–protein interaction network to catalyze genomic interpretation

(2016) Taibo Li et al.   NATURE METHODS

Evolution of protein phosphorylation across 18 fungal species

(2016) R. A. Studer et al.   SCIENCE

dbPAF: an integrative database of protein phosphorylation in animals and fungi

(2016) Shahid Ullah et al.   Scientific Reports

High-throughput phosphoproteomics reveals in vivo insulin signaling dynamics

(2015) Sean J Humphrey et al.   NATURE BIOTECHNOLOGY

MIMP: predicting the impact of mutations on kinase-substrate phosphorylation

(2015) Omar Wagih et al.   NATURE METHODS

Protein Phosphorylation: A Major Switch Mechanism for Metabolic Regulation

(2015) Sean J. Humphrey et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Reconfiguring phosphorylation signaling by genetic polymorphisms affects cancer susceptibility

(2015) Yongbo Wang et al.   Journal of Molecular Cell Biology

LymPHOS 2.0: an update of a phosphosite database of primary human T cells

(2015) Tien Dung Nguyen et al.   Database-The Journal of Biological Databases and Curation

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

(2014) Ralph Patrick et al.   BIOINFORMATICS

3Dmol.js: molecular visualization with WebGL

(2014) N. Rego et al.   BIOINFORMATICS

The human DEPhOsphorylation database DEPOD: a 2015 update

(2014) Guangyou Duan et al.   NUCLEIC ACIDS RESEARCH

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

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

SysPTM 2.0: an updated systematic resource for post-translational modification

(2014) J. Li et al.   Database-The Journal of Biological Databases and Curation

dbPPT: a comprehensive database of protein phosphorylation in plants

(2014) Han Cheng et al.   Database-The Journal of Biological Databases and Curation

PSEA: Kinase-specific prediction and analysis of human phosphorylation substrates

(2014) Sheng-Bao Suo et al.   Scientific Reports

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

Dynamic Adipocyte Phosphoproteome Reveals that Akt Directly Regulates mTORC2

(2013) Sean J. Humphrey et al.   Cell Metabolism

mentha: a resource for browsing integrated protein-interaction networks

(2013) Alberto Calderone et al.   NATURE METHODS

P3DB 3.0: From plant phosphorylation sites to protein networks

(2013) Qiuming Yao et al.   NUCLEIC ACIDS RESEARCH

Cancer systems biology in the genome sequencing era: Part 1, dissecting and modeling of tumor clones and their networks

(2013) Edwin Wang et al.   SEMINARS IN CANCER BIOLOGY

Cancer systems biology in the genome sequencing era: Part 2, evolutionary dynamics of tumor clonal networks and drug resistance

(2013) Edwin Wang et al.   SEMINARS IN CANCER BIOLOGY

Signaling Network Assessment of Mutations and Copy Number Variations Predict Breast Cancer Subtype-Specific Drug Targets

(2013) Naif Zaman et al.   Cell Reports

HINT: High-quality protein interactomes and their applications in understanding human disease

(2012) Jishnu Das et al.   BMC Systems Biology

Systematic analysis of the Plk-mediated phosphoregulation in eukaryotes

(2012) Z. Liu et al.   BRIEFINGS IN BIOINFORMATICS

Systematic Functional Prioritization of Protein Posttranslational Modifications

(2012) Pedro Beltrao et al.   CELL

HuPho: the human phosphatase portal

(2012) Susanna Liberti et al.   FEBS Journal

Systematic Analysis of Protein Phosphorylation Networks From Phosphoproteomic Data

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

The Chromosomal Passenger Complex Activates Polo Kinase at Centromeres

(2012) Mar Carmena et al.   PLOS BIOLOGY

Medicago PhosphoProtein Database: a repository for Medicago truncatula phosphoprotein data

(2012) Christopher M. Rose et al.   Frontiers in Plant Science

The human phosphotyrosine signaling network: Evolution and hotspots of hijacking in cancer

(2011) L. Li et al.   GENOME RESEARCH

PINA v2.0: mining interactome modules

(2011) Mark J. Cowley et al.   NUCLEIC ACIDS RESEARCH

Prediction of 492 human protein kinase substrate specificities

(2011) Javad Safaei et al.   Proteome Science

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

(2010) Inkyung Jung et al.   BMC BIOINFORMATICS

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

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

PHOSIDA 2011: the posttranslational modification database

(2010) F. Gnad 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

Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites

(2010) A. Zanzoni et al.   NUCLEIC ACIDS RESEARCH

GPS 2.1: enhanced prediction of kinase-specific phosphorylation sites with an algorithm of motif length selection

(2010) Y. Xue et al.   PROTEIN ENGINEERING DESIGN & SELECTION

PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae

(2010) C. Stark et al.   Database-The Journal of Biological Databases and Curation

SysPTM: A Systematic Resource for Proteomic Research on Post-translational Modifications

(2009) Hong Li et al.   MOLECULAR & CELLULAR PROTEOMICS

PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update

(2009) Pawel Durek et al.   NUCLEIC ACIDS RESEARCH

Large-Scale Phosphoprotein Analysis in Medicago truncatula Roots Provides Insight into in Vivo Kinase Activity in Legumes

(2009) P. A. Grimsrud et al.   PLANT PHYSIOLOGY

LymPHOS: Design of a phosphosite database of primary human T cells

(2009) David Ovelleiro et al.   PROTEOMICS

Weak functional constraints on phosphoproteomes

(2009) Christian R. Landry et al.   TRENDS IN GENETICS

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

(2008) Chia-Ying Yang et al.   BIOINFORMATICS

iRefIndex: A consolidated protein interaction database with provenance

(2008) Sabry Razick et al.   BMC BIOINFORMATICS

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

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

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

P3DB: a plant protein phosphorylation database

(2008) J. Gao et al.   NUCLEIC ACIDS RESEARCH