Published in Sci Signal on January 12, 2010
A tissue-specific atlas of mouse protein phosphorylation and expression. Cell (2010) 8.65
Systematic and quantitative assessment of the ubiquitin-modified proteome. Mol Cell (2011) 7.30
A proteome-scale map of the human interactome network. Cell (2014) 3.91
Decoding signalling networks by mass spectrometry-based proteomics. Nat Rev Mol Cell Biol (2010) 3.78
Proteomic analysis of lysine acetylation sites in rat tissues reveals organ specificity and subcellular patterns. Cell Rep (2012) 2.66
PHOSIDA 2011: the posttranslational modification database. Nucleic Acids Res (2010) 2.61
The extended PP1 toolkit: designed to create specificity. Trends Biochem Sci (2010) 2.51
The phosphoproteomes of Plasmodium falciparum and Toxoplasma gondii reveal unusual adaptations within and beyond the parasites' boundaries. Cell Host Microbe (2011) 2.25
Global mitotic phosphorylation of C2H2 zinc finger protein linker peptides. Cell Cycle (2011) 2.25
Integrated proteomic analysis of post-translational modifications by serial enrichment. Nat Methods (2013) 2.22
SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways. Mol Cell (2013) 2.17
Cancer biology and NuRD: a multifaceted chromatin remodelling complex. Nat Rev Cancer (2011) 2.10
Akt-mediated phosphorylation of Bmi1 modulates its oncogenic potential, E3 ligase activity, and DNA damage repair activity in mouse prostate cancer. J Clin Invest (2012) 2.03
Global identification and characterization of both O-GlcNAcylation and phosphorylation at the murine synapse. Mol Cell Proteomics (2012) 2.03
Mre11-Rad50-Nbs1 conformations and the control of sensing, signaling, and effector responses at DNA double-strand breaks. DNA Repair (Amst) (2010) 1.96
Phosphorylation in protein-protein binding: effect on stability and function. Structure (2011) 1.96
A large synthetic peptide and phosphopeptide reference library for mass spectrometry-based proteomics. Nat Biotechnol (2013) 1.93
The Plk1-dependent phosphoproteome of the early mitotic spindle. Mol Cell Proteomics (2010) 1.91
Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging. Nat Methods (2011) 1.87
A large-scale method to measure absolute protein phosphorylation stoichiometries. Nat Methods (2011) 1.87
PR-Set7 and H4K20me1: at the crossroads of genome integrity, cell cycle, chromosome condensation, and transcription. Genes Dev (2012) 1.81
Temporal changes in Hec1 phosphorylation control kinetochore-microtubule attachment stability during mitosis. J Cell Sci (2011) 1.79
Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers. Mol Syst Biol (2013) 1.78
Dissociation by Pelota, Hbs1 and ABCE1 of mammalian vacant 80S ribosomes and stalled elongation complexes. EMBO J (2011) 1.76
Status of large-scale analysis of post-translational modifications by mass spectrometry. Mol Cell Proteomics (2013) 1.72
Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues. Nat Commun (2012) 1.72
A structural model for regulation of NHEJ by DNA-PKcs autophosphorylation. DNA Repair (Amst) (2010) 1.71
Cdc14 phosphatases preferentially dephosphorylate a subset of cyclin-dependent kinase (Cdk) sites containing phosphoserine. J Biol Chem (2011) 1.68
Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis. Mol Biosyst (2011) 1.62
DNA double strand break repair via non-homologous end-joining. Transl Cancer Res (2013) 1.61
Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation. Nat Methods (2013) 1.60
Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. Mol Cell Proteomics (2012) 1.58
IFITMs restrict the replication of multiple pathogenic viruses. J Mol Biol (2013) 1.52
Estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometry. Mol Cell Proteomics (2011) 1.51
Post-translational modifications regulate class IIa histone deacetylase (HDAC) function in health and disease. Mol Cell Proteomics (2015) 1.49
Correct interpretation of comprehensive phosphorylation dynamics requires normalization by protein expression changes. Mol Cell Proteomics (2011) 1.47
T cell receptor (TCR)-induced tyrosine phosphorylation dynamics identifies THEMIS as a new TCR signalosome component. J Biol Chem (2010) 1.44
Repo-Man coordinates chromosomal reorganization with nuclear envelope reassembly during mitotic exit. Dev Cell (2011) 1.43
Rapid and reproducible single-stage phosphopeptide enrichment of complex peptide mixtures: application to general and phosphotyrosine-specific phosphoproteomics experiments. Anal Chem (2011) 1.40
The mutational landscape of phosphorylation signaling in cancer. Sci Rep (2013) 1.39
Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes, and mitochondria. Mol Cell Proteomics (2010) 1.38
Unraveling Kinase Activation Dynamics Using Kinase-Substrate Relationships from Temporal Large-Scale Phosphoproteomics Studies. PLoS One (2016) 1.38
When ubiquitination meets phosphorylation: a systems biology perspective of EGFR/MAPK signalling. Cell Commun Signal (2013) 1.36
Acetylation dynamics and stoichiometry in Saccharomyces cerevisiae. Mol Syst Biol (2014) 1.35
Absolute quantification of protein and post-translational modification abundance with stable isotope-labeled synthetic peptides. Nat Protoc (2011) 1.34
Cell division: control of the chromosomal passenger complex in time and space. Chromosoma (2013) 1.34
O-GlcNAc transferase regulates mitotic chromatin dynamics. J Biol Chem (2010) 1.33
Mapping and analysis of phosphorylation sites: a quick guide for cell biologists. Mol Biol Cell (2013) 1.33
Quantitative proteomic analysis of histone modifications. Chem Rev (2015) 1.32
M phase phosphorylation of the epigenetic regulator UHRF1 regulates its physical association with the deubiquitylase USP7 and stability. Proc Natl Acad Sci U S A (2012) 1.32
Combination of chemical genetics and phosphoproteomics for kinase signaling analysis enables confident identification of cellular downstream targets. Mol Cell Proteomics (2011) 1.32
Systematic phosphorylation analysis of human mitotic protein complexes. Sci Signal (2011) 1.31
DNA-PK: a dynamic enzyme in a versatile DSB repair pathway. DNA Repair (Amst) (2014) 1.31
Evolution and functional cross-talk of protein post-translational modifications. Mol Syst Biol (2013) 1.30
Mass-spectrometric exploration of proteome structure and function. Nature (2016) 1.28
Quantitative proteomics reveals the basis for the biochemical specificity of the cell-cycle machinery. Mol Cell (2011) 1.27
Regulation of mitochondrial respiration and apoptosis through cell signaling: cytochrome c oxidase and cytochrome c in ischemia/reperfusion injury and inflammation. Biochim Biophys Acta (2011) 1.27
Multidimensional proteomics for cell biology. Nat Rev Mol Cell Biol (2015) 1.26
Structural basis for protein phosphatase 1 regulation and specificity. FEBS J (2012) 1.26
Transient ATM kinase inhibition disrupts DNA damage-induced sister chromatid exchange. Sci Signal (2010) 1.25
Characterization of the mechanisms controlling Greatwall activity. Mol Cell Biol (2011) 1.25
Determinants for activation of the atypical AGC kinase Greatwall during M phase entry. Mol Cell Biol (2012) 1.25
Loss of ATM kinase activity leads to embryonic lethality in mice. J Cell Biol (2012) 1.23
Stoichiometry of site-specific lysine acetylation in an entire proteome. J Biol Chem (2014) 1.19
Tumor suppressor activity of the ERK/MAPK pathway by promoting selective protein degradation. Genes Dev (2013) 1.18
Identification of lysine succinylation substrates and the succinylation regulatory enzyme CobB in Escherichia coli. Mol Cell Proteomics (2013) 1.17
Regulation of yeast central metabolism by enzyme phosphorylation. Mol Syst Biol (2012) 1.15
The multiple-specificity landscape of modular peptide recognition domains. Mol Syst Biol (2011) 1.14
Thyroid hormone receptor interacting protein 13 (TRIP13) AAA-ATPase is a novel mitotic checkpoint-silencing protein. J Biol Chem (2014) 1.14
Identification of CRM1-dependent Nuclear Export Cargos Using Quantitative Mass Spectrometry. Mol Cell Proteomics (2012) 1.14
KIBRA protein phosphorylation is regulated by mitotic kinase aurora and protein phosphatase 1. J Biol Chem (2011) 1.14
Cyclin-dependent kinase 16/PCTAIRE kinase 1 is activated by cyclin Y and is essential for spermatogenesis. Mol Cell Biol (2011) 1.12
GTSE1 is a microtubule plus-end tracking protein that regulates EB1-dependent cell migration. PLoS One (2012) 1.12
Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes. Mol Syst Biol (2015) 1.12
Microphthalmia-associated transcription factor in melanoma development and MAP-kinase pathway targeted therapy. Pigment Cell Melanoma Res (2015) 1.12
Cdk1-dependent destruction of Eco1 prevents cohesion establishment after S phase. Mol Cell (2011) 1.11
A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells. Elife (2014) 1.10
Evaluating multiplexed quantitative phosphopeptide analysis on a hybrid quadrupole mass filter/linear ion trap/orbitrap mass spectrometer. Anal Chem (2015) 1.10
Aurora at the pole and equator: overlapping functions of Aurora kinases in the mitotic spindle. Open Biol (2013) 1.09
Aurora B controls kinetochore-microtubule attachments by inhibiting Ska complex-KMN network interaction. J Cell Biol (2012) 1.09
Controlling DNA-end resection: a new task for CDKs. Front Genet (2013) 1.09
On the molecular mechanisms of mitotic kinase activation. Open Biol (2012) 1.08
Superoxide dismutase 1 acts as a nuclear transcription factor to regulate oxidative stress resistance. Nat Commun (2014) 1.08
Cytoplasmic Metadherin (MTDH) provides survival advantage under conditions of stress by acting as RNA-binding protein. J Biol Chem (2011) 1.07
Single-cell analyses of transcriptional heterogeneity during drug tolerance transition in cancer cells by RNA sequencing. Proc Natl Acad Sci U S A (2014) 1.07
Matrix elasticity regulates lamin-A,C phosphorylation and turnover with feedback to actomyosin. Curr Biol (2014) 1.07
Uncovering ubiquitin and ubiquitin-like signaling networks. Chem Rev (2011) 1.06
Absolute proteome and phosphoproteome dynamics during the cell cycle of Schizosaccharomyces pombe (Fission Yeast). Mol Cell Proteomics (2014) 1.06
Greatwall-phosphorylated Endosulfine is both an inhibitor and a substrate of PP2A-B55 heterotrimers. Elife (2014) 1.06
Phosphorylation of mammalian cytochrome c and cytochrome c oxidase in the regulation of cell destiny: respiration, apoptosis, and human disease. Adv Exp Med Biol (2012) 1.05
Structural polymorphism in the N-terminal oligomerization domain of NPM1. Proc Natl Acad Sci U S A (2014) 1.05
PP2A/B55 and Fcp1 regulate Greatwall and Ensa dephosphorylation during mitotic exit. PLoS Genet (2014) 1.04
Structural insights into NHEJ: building up an integrated picture of the dynamic DSB repair super complex, one component and interaction at a time. DNA Repair (Amst) (2014) 1.03
The coming of age of phosphoproteomics--from large data sets to inference of protein functions. Mol Cell Proteomics (2013) 1.03
In vitro RNase and nucleic acid binding activities implicate coilin in U snRNA processing. PLoS One (2012) 1.03
Interaction of Sororin protein with polo-like kinase 1 mediates resolution of chromosomal arm cohesion. J Biol Chem (2011) 1.03
Regulation of cardiac proteasomes by ubiquitination, SUMOylation, and beyond. J Mol Cell Cardiol (2013) 1.03
CDK1 phosphorylation of YAP promotes mitotic defects and cell motility and is essential for neoplastic transformation. Cancer Res (2013) 1.03
Online nanoflow multidimensional fractionation for high efficiency phosphopeptide analysis. Mol Cell Proteomics (2011) 1.02
A solid phase extraction-based platform for rapid phosphoproteomic analysis. Methods (2011) 1.02
Improved prediction of signal peptides: SignalP 3.0. J Mol Biol (2004) 48.40
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol (2008) 38.00
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature (2002) 37.66
SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods (2011) 33.90
Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics (2002) 30.58
Mass spectrometry-based proteomics. Nature (2003) 28.94
Enterotypes of the human gut microbiome. Nature (2011) 24.36
Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell (2006) 20.92
Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science (2009) 20.49
Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc (2007) 19.50
miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev (2002) 19.24
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res (2010) 18.73
STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res (2012) 18.26
Universal sample preparation method for proteome analysis. Nat Methods (2009) 16.88
In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protoc (2006) 16.56
Andromeda: a peptide search engine integrated into the MaxQuant environment. J Proteome Res (2011) 14.82
Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal Chem (2003) 13.58
STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic Acids Res (2006) 12.16
Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat Protoc (2007) 10.71
Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics (2005) 10.67
Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap. Mol Cell Proteomics (2005) 10.60
STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res (2005) 10.44
Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature (2008) 10.28
The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol (2007) 10.24
A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol (2007) 9.90
Proteomic characterization of the human centrosome by protein correlation profiling. Nature (2003) 8.74
Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics (2004) 7.76
Mass spectrometry-based proteomics turns quantitative. Nat Chem Biol (2005) 7.52
Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature (2010) 7.51
Nucleolar proteome dynamics. Nature (2005) 7.32
Polo-like kinases and the orchestration of cell division. Nat Rev Mol Cell Biol (2004) 7.22
A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biol (2002) 7.12
Directed proteomic analysis of the human nucleolus. Curr Biol (2002) 7.04
Richness of human gut microbiome correlates with metabolic markers. Nature (2013) 6.93
Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics. Proc Natl Acad Sci U S A (2003) 6.87
Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci (2003) 6.85
Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Cell (2003) 6.77
Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell (2007) 6.62
Emerging landscape of oncogenic signatures across human cancers. Nat Genet (2013) 6.48
Mechanism of regulation of WAVE1-induced actin nucleation by Rac1 and Nck. Nature (2002) 6.26
Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites. Glycobiology (2004) 6.13
Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci (2003) 5.94
The Polo kinase Plk4 functions in centriole duplication. Nat Cell Biol (2005) 5.84
Large-scale proteomic analysis of the human spliceosome. Genome Res (2002) 5.75
Specificity in Toll-like receptor signalling through distinct effector functions of TRAF3 and TRAF6. Nature (2005) 5.72
Plk4-induced centriole biogenesis in human cells. Dev Cell (2007) 5.68
Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature (2002) 5.48
Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol (2011) 5.48
Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle. Mol Cell (2008) 5.38
The centrosomal protein nephrocystin-6 is mutated in Joubert syndrome and activates transcription factor ATF4. Nat Genet (2006) 5.36
Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat Biotechnol (2004) 5.22
A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC). Nat Protoc (2006) 5.21
Analysis and prediction of leucine-rich nuclear export signals. Protein Eng Des Sel (2004) 5.15
Dynamic complex formation during the yeast cell cycle. Science (2005) 5.11
Recurrent R-spondin fusions in colon cancer. Nature (2012) 5.10
Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol Cell Proteomics (2005) 5.07
Higher-energy C-trap dissociation for peptide modification analysis. Nat Methods (2007) 5.04
SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell (2008) 5.02
Role of Hec1 in spindle checkpoint signaling and kinetochore recruitment of Mad1/Mad2. Science (2002) 4.94
Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factors. Proc Natl Acad Sci U S A (2003) 4.87
A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics. Nat Protoc (2009) 4.84
An Aboriginal Australian genome reveals separate human dispersals into Asia. Science (2011) 4.84
Trypsin cleaves exclusively C-terminal to arginine and lysine residues. Mol Cell Proteomics (2004) 4.79
Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli. Cell (2005) 4.78
A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed. Mol Cell Proteomics (2009) 4.75
Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer. Nat Genet (2012) 4.70
PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. Genome Biol (2007) 4.66
A mammalian organelle map by protein correlation profiling. Cell (2006) 4.54
Feature-based prediction of non-classical and leaderless protein secretion. Protein Eng Des Sel (2004) 4.54
Aurora-A overexpression reveals tetraploidization as a major route to centrosome amplification in p53-/- cells. EMBO J (2002) 4.54
Mining electronic health records: towards better research applications and clinical care. Nat Rev Genet (2012) 4.42
A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Mol Cell Proteomics (2011) 4.40
Active cyclin B1-Cdk1 first appears on centrosomes in prophase. Nat Cell Biol (2003) 4.31
Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell (2010) 4.31
Exploring the functional interactions between Aurora B, INCENP, and survivin in mitosis. Mol Biol Cell (2003) 4.28
The ABC's (and XYZ's) of peptide sequencing. Nat Rev Mol Cell Biol (2004) 4.24
Human Proteinpedia enables sharing of human protein data. Nat Biotechnol (2008) 4.21
Paraspeckles: a novel nuclear domain. Curr Biol (2002) 4.19
Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell (2013) 4.16
Quantitative proteomics reveals subset-specific viral recognition in dendritic cells. Immunity (2010) 4.03
Structure of a Survivin-Borealin-INCENP core complex reveals how chromosomal passengers travel together. Cell (2007) 3.98
Nuclear pore components are involved in the transcriptional regulation of dosage compensation in Drosophila. Mol Cell (2006) 3.98
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res (2011) 3.94
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
Cep164, a novel centriole appendage protein required for primary cilium formation. J Cell Biol (2007) 3.88
PICH, a centromere-associated SNF2 family ATPase, is regulated by Plk1 and required for the spindle checkpoint. Cell (2007) 3.80
Axin-mediated CKI phosphorylation of beta-catenin at Ser 45: a molecular switch for the Wnt pathway. Genes Dev (2002) 3.80
The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins. Genome Biol (2006) 3.79