Phosphorylation Variation during the Cell Cycle Scales with Structural Propensities of Proteins

1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data

(2012) Juergen Cox et al.   BMC BIOINFORMATICS

Structures of inactive retinoblastoma protein reveal multiple mechanisms for cell cycle control

(2012) J. R. Burke et al.   GENES & DEVELOPMENT

Dynamic optimization of signal transductionvia intrinsic disorder

(2011) L. Michel Espinoza-Fonseca   Molecular BioSystems

Cascades of multisite phosphorylation control Sic1 destruction at the onset of S phase

(2011) Mardo Kõivomägi et al.   NATURE

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

(2011) S. Powell et al.   NUCLEIC ACIDS RESEARCH

Cooperativity within proximal phosphorylation sites is revealed from large-scale proteomics data

(2010) Regev Schweiger et al.   Biology Direct

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

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

Local control of a disorder–order transition in 4E-BP1 underpins regulation of translation via eIF4E

(2010) Shirley Tait et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis

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

Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins

(2009) Pawel Durek et al.   BMC BIOINFORMATICS

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Controlling Peptide Folding with Repulsive Interactions between Phosphorylated Amino Acids and Tryptophan

(2009) Alexander J. Riemen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

ELM: the status of the 2010 eukaryotic linear motif resource

(2009) Cathryn M. Gould et al.   NUCLEIC ACIDS RESEARCH

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

Intrinsic Disorder in Protein Interactions: Insights From a Comprehensive Structural Analysis

(2009) Jessica H. Fong et al.   PLoS Computational Biology

Regulation of Cell Division by Intrinsically Unstructured Proteins: Intrinsic Flexibility, Modularity, and Signaling Conduits†

(2008) Charles A. Galea et al.   BIOCHEMISTRY

Thermodynamic and Structural Basis of Phosphorylation-Induced Disorder-to-Order Transition in the Regulatory Light Chain of Smooth Muscle Myosin

(2008) L. Michel Espinoza-Fonseca et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Charge environments around phosphorylation sites in proteins

(2008) James Kitchen et al.   BMC STRUCTURAL BIOLOGY