Machine Learning of Global Phosphoproteomic Profiles Enables Discrimination of Direct versus Indirect Kinase Substrates

CDC28 phosphorylates Cac1p and regulates the association of chromatin assembly factor i with chromatin

(2015) Daniel CB Jeffery et al.   CELL CYCLE

Sample Collection Method Bias Effects in Quantitative Phosphoproteomics

(2015) Evgeny Kanshin et al.   JOURNAL OF PROTEOME RESEARCH

Phosphoproteome dynamics of Saccharomyces cerevisiae under heat shock and cold stress

(2015) E. Kanshin et al.   Molecular Systems Biology

High-throughput phosphoproteomics reveals in vivo insulin signaling dynamics

(2015) Sean J Humphrey et al.   NATURE BIOTECHNOLOGY

The I-TASSER Suite: protein structure and function prediction

(2015) Jianyi Yang et al.   NATURE METHODS

A Cell-Signaling Network Temporally Resolves Specific versus Promiscuous Phosphorylation

(2015) Evgeny Kanshin et al.   Cell Reports

Machine Learning Assisted Design of Highly Active Peptides for Drug Discovery

(2015) Sébastien Giguère et al.   PLoS Computational Biology

MS-Viewer: A Web-based Spectral Viewer for Proteomics Results

(2014) Peter R. Baker et al.   MOLECULAR & CELLULAR PROTEOMICS

KinomeXplorer: an integrated platform for kinome biology studies

(2014) Heiko Horn et al.   NATURE METHODS

Phosphorylation Site Dynamics of Early T-cell Receptor Signaling

(2014) Lily A. Chylek et al.   PLoS One

Method for identifying phosphorylated substrates of specific cyclin/cyclin-dependent kinase complexes

(2014) Y. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phosphoproteomic analysis identifies the tumor suppressor PDCD4 as a RSK substrate negatively regulated by 14-3-3

(2014) J. A. Galan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cyclin-dependent kinases

(2014) Marcos Malumbres   GENOME BIOLOGY

Snf1/AMPK promotes SBF and MBF-dependent transcription in budding yeast

(2013) Sara Busnelli et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

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

(2013) Sébastien Giguère et al.   BMC BIOINFORMATICS

Displacement of N/Q-rich Peptides on TiO2 Beads Enhances the Depth and Coverage of Yeast Phosphoproteome Analyses

(2013) Evgeny Kanshin et al.   JOURNAL OF PROTEOME RESEARCH

The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update

(2013) I. Sadowski et al.   Database-The Journal of Biological Databases and Curation

The Filamentous Growth MAPK Pathway Responds to Glucose Starvation Through the Mig1/2 Transcriptional Repressors in Saccharomyces cerevisiae

(2012) S. Karunanithi et al.   GENETICS

Phosphorylation of Yeast Hexokinase 2 Regulates Its Nucleocytoplasmic Shuttling

(2012) Paula Fernández-García et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Protein abundance is key to distinguish promiscuous from functional phosphorylation based on evolutionary information

(2012) E. D. Levy et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

Software Lock Mass by Two-Dimensional Minimization of Peptide Mass Errors

(2011) Jürgen Cox et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

System-Wide Temporal Characterization of the Proteome and Phosphoproteome of Human Embryonic Stem Cell Differentiation

(2011) K. T. G. Rigbolt et al.   Science Signaling

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

(2011) Sara Sharifpoor et al.   GENOME BIOLOGY

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

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

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

Signaling Through Cooperation

(2010) E. D. Levy et al.   SCIENCE

A Global Protein Kinase and Phosphatase Interaction Network in Yeast

(2010) A. Breitkreutz et al.   SCIENCE

Phosphoproteomic Analysis Reveals Interconnected System-Wide Responses to Perturbations of Kinases and Phosphatases in Yeast

(2010) B. Bodenmiller et al.   Science Signaling

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

Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator

(2009) Renata Usaite et al.   Molecular Systems Biology

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

(2009) Da Wei Huang et al.   Nature Protocols

Global Analysis of Cdk1 Substrate Phosphorylation Sites Provides Insights into Evolution

(2009) L. J. Holt et al.   SCIENCE

Weak functional constraints on phosphoproteomes

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

Global and Site-Specific Quantitative Phosphoproteomics: Principles and Applications

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

I-TASSER server for protein 3D structure prediction

(2008) Yang Zhang   BMC BIOINFORMATICS

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

SNF1/AMPK pathways in yeast

(2007) Kristina Hedbacker   Frontiers in Bioscience-Landmark

Physiological characterization of glucose repression in the strains with SNF1 and SNF4 genes deleted

(2007) R USAITE et al.   JOURNAL OF BIOTECHNOLOGY