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

Computational Analysis of Phosphoproteomics: Progresses and Perspectives

(2012) Jian Ren et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

PaxDb, a Database of Protein Abundance Averages Across All Three Domains of Life

(2012) M. Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

Genome-Wide Evolutionary Conservation of N-Glycosylation Sites

(2011) C. Park et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rampant Purifying Selection Conserves Positions with Posttranslational Modifications in Human Proteins

(2011) V. E. Gray et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phosphorylation network rewiring by gene duplication

(2011) L. Freschi et al.   Molecular Systems Biology

A large-scale method to measure absolute protein phosphorylation stoichiometries

(2011) Ronghu Wu et al.   NATURE METHODS

Evaluating Experimental Bias and Completeness in Comparative Phosphoproteomics Analysis

(2011) Jos Boekhorst et al.   PLoS One

Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions

(2011) M. Heo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phosphoproteomic Analysis Identifies Grb10 as an mTORC1 Substrate That Negatively Regulates Insulin Signaling

(2011) Y. Yu et al.   SCIENCE

A Cell Cycle Phosphoproteome of the Yeast Centrosome

(2011) J. M. Keck et al.   SCIENCE

Sequence, Structure, and Network Evolution of Protein Phosphorylation

(2011) C. S. H. Tan   Science Signaling

Phosphorylated and Nonphosphorylated Serine and Threonine Residues Evolve at Different Rates in Mammals

(2010) S. C.-C. Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of Protein Phosphorylation for Distinct Functional Modules in Vertebrate Genomes

(2010) Z. Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of Characterized Phosphorylation Sites in Budding Yeast

(2010) A. N. Nguyen Ba et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular characterization of the evolution of phagosomes

(2010) Jonathan Boulais et al.   Molecular Systems Biology

The phosphoproteome of toll-like receptor-activated macrophages

(2010) Gabriele Weintz et al.   Molecular Systems Biology

Generating and navigating proteome maps using mass spectrometry

(2010) Christian H. Ahrens et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Decoding signalling networks by mass spectrometry-based proteomics

(2010) Chunaram Choudhary et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

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

Nonspecific binding limits the number of proteins in a cell and shapes their interaction networks

(2010) M. E. Johnson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

ATM-Dependent and -Independent Dynamics of the Nuclear Phosphoproteome After DNA Damage

(2010) A. Bensimon et al.   Science Signaling

Moving from transcriptional to phospho-evolution: generalizing regulatory evolution?

(2010) Alan M. Moses et al.   TRENDS IN GENETICS

Global Analysis of Cdk1 Substrate Phosphorylation Sites Provides Insights into Evolution

(2009) L. J. Holt et al.   SCIENCE

Cell Signaling in Space and Time: Where Proteins Come Together and When They're Apart

(2009) J. D. Scott et al.   SCIENCE

Comparative Analysis Reveals Conserved Protein Phosphorylation Networks Implicated in Multiple Diseases

(2009) C. S. H. Tan et al.   Science Signaling

How Perfect Can Protein Interactomes Be?

(2009) E. D. Levy et al.   Science Signaling

Weak functional constraints on phosphoproteomes

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

Comparative conservation analysis of the human mitotic phosphoproteome

(2008) Rainer Malik et al.   BIOINFORMATICS

A Multidimensional Chromatography Technology for In-depth Phosphoproteome Analysis

(2008) Claudio P. Albuquerque et al.   MOLECULAR & CELLULAR PROTEOMICS

Constraints imposed by non-functional protein–protein interactions on gene expression and proteome size

(2008) Jingshan Zhang et al.   Molecular Systems Biology

Human Protein Reference Database--2009 update

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

Different phosphorylation states of the anaphase promoting complex in response to antimitotic drugs: A quantitative proteomic analysis

(2008) J. A. J. Steen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A quantitative atlas of mitotic phosphorylation

(2008) N. Dephoure et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tight Regulation of Unstructured Proteins: From Transcript Synthesis to Protein Degradation

(2008) J. Gsponer et al.   SCIENCE

Non-functional phosphorylations?

(2008) Gustav E. Lienhard   TRENDS IN BIOCHEMICAL SCIENCES

Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes

(2008) Jos Boekhorst et al.   GENOME BIOLOGY