Published in Cell Stem Cell on August 07, 2009
Decoding signalling networks by mass spectrometry-based proteomics. Nat Rev Mol Cell Biol (2010) 3.78
An expanded Oct4 interaction network: implications for stem cell biology, development, and disease. Cell Stem Cell (2010) 3.60
Next-generation proteomics: towards an integrative view of proteome dynamics. Nat Rev Genet (2012) 2.39
CDK1-dependent phosphorylation of EZH2 suppresses methylation of H3K27 and promotes osteogenic differentiation of human mesenchymal stem cells. Nat Cell Biol (2010) 2.36
SOX2 is an oncogene activated by recurrent 3q26.3 amplifications in human lung squamous cell carcinomas. PLoS One (2010) 2.21
Protein analysis by shotgun/bottom-up proteomics. Chem Rev (2013) 2.13
Phosphoproteomics for the masses. ACS Chem Biol (2010) 1.83
Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers. Mol Syst Biol (2013) 1.78
The PRKCI and SOX2 oncogenes are coamplified and cooperate to activate Hedgehog signaling in lung squamous cell carcinoma. Cancer Cell (2014) 1.65
Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis. Mol Biosyst (2011) 1.62
Preserved DNA Damage Checkpoint Pathway Protects against Complications in Long-Standing Type 1 Diabetes. Cell Metab (2015) 1.54
JNK-induced apoptosis, compensatory growth, and cancer stem cells. Cancer Res (2012) 1.52
Cell cycle-dependent chromatin shuttling of HBO1-JADE1 histone acetyl transferase (HAT) complex. Cell Cycle (2014) 1.45
The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells. Mol Syst Biol (2011) 1.44
Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium. Mol Syst Biol (2012) 1.44
Cyclin-dependent kinase 1 (CDK1)-mediated phosphorylation of enhancer of zeste 2 (Ezh2) regulates its stability. J Biol Chem (2011) 1.37
Lists2Networks: integrated analysis of gene/protein lists. BMC Bioinformatics (2010) 1.33
The CK1 Family: Contribution to Cellular Stress Response and Its Role in Carcinogenesis. Front Oncol (2014) 1.33
ERK1 and ERK2 regulate embryonic stem cell self-renewal through phosphorylation of Klf4. Nat Struct Mol Biol (2012) 1.30
Phosphorylation regulates human OCT4. Proc Natl Acad Sci U S A (2012) 1.19
Concise review: The Sox2-Oct4 connection: critical players in a much larger interdependent network integrated at multiple levels. Stem Cells (2013) 1.17
A chemical biology approach to myocardial regeneration. J Cardiovasc Transl Res (2011) 1.17
The transcriptional regulation of pluripotency. Cell Res (2012) 1.15
Phosphoproteomics in cancer. Mol Oncol (2010) 1.12
Protein post-translational modifications and regulation of pluripotency in human stem cells. Cell Res (2013) 1.12
Determination of protein interactome of transcription factor Sox2 in embryonic stem cells engineered for inducible expression of four reprogramming factors. J Biol Chem (2012) 1.10
Regulation of sororin by Cdk1-mediated phosphorylation. J Cell Sci (2011) 1.08
Toward a complete in silico, multi-layered embryonic stem cell regulatory network. Wiley Interdiscip Rev Syst Biol Med (2010) 1.06
Uncovering ubiquitin and ubiquitin-like signaling networks. Chem Rev (2011) 1.06
Enhancing the identification of phosphopeptides from putative basophilic kinase substrates using Ti (IV) based IMAC enrichment. Mol Cell Proteomics (2011) 1.05
Interaction of Sororin protein with polo-like kinase 1 mediates resolution of chromosomal arm cohesion. J Biol Chem (2011) 1.03
The cell cycle and pluripotency. Biochem J (2013) 1.03
Regulation of cardiac proteasomes by ubiquitination, SUMOylation, and beyond. J Mol Cell Cardiol (2013) 1.03
Online nanoflow multidimensional fractionation for high efficiency phosphopeptide analysis. Mol Cell Proteomics (2011) 1.02
Tyrosine phosphorylation profiling in FGF-2 stimulated human embryonic stem cells. PLoS One (2011) 0.99
The RB family is required for the self-renewal and survival of human embryonic stem cells. Nat Commun (2012) 0.99
Sororin is a master regulator of sister chromatid cohesion and separation. Cell Cycle (2012) 0.98
Rare cell proteomic reactor applied to stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics study of human embryonic stem cell differentiation. Mol Cell Proteomics (2010) 0.98
Phosphoproteomics identifies oncogenic Ras signaling targets and their involvement in lung adenocarcinomas. PLoS One (2011) 0.97
Partners and post-translational modifications of nuclear lamins. Chromosoma (2013) 0.97
Proteomic cornerstones of hematopoietic stem cell differentiation: distinct signatures of multipotent progenitors and myeloid committed cells. Mol Cell Proteomics (2012) 0.96
Sox2, a key factor in the regulation of pluripotency and neural differentiation. World J Stem Cells (2014) 0.95
Poly(ADP-ribose) polymerase 1 regulates nuclear reprogramming and promotes iPSC generation without c-Myc. J Exp Med (2012) 0.95
Sox2 uses multiple domains to associate with proteins present in Sox2-protein complexes. PLoS One (2010) 0.94
Large scale phosphoproteome profiles comprehensive features of mouse embryonic stem cells. Mol Cell Proteomics (2010) 0.94
Systems biology provides new insights into the molecular mechanisms that control the fate of embryonic stem cells. J Cell Physiol (2012) 0.93
Unraveling the global microRNAome responses to ionizing radiation in human embryonic stem cells. PLoS One (2012) 0.93
Chromatin insulator elements block transgene silencing in engineered human embryonic stem cell lines at a defined chromosome 13 locus. Stem Cells Dev (2011) 0.92
Identification of a phosphorylation-dependent nuclear localization motif in interferon regulatory factor 2 binding protein 2. PLoS One (2011) 0.91
Phosphoproteome of human glioblastoma initiating cells reveals novel signaling regulators encoded by the transcriptome. PLoS One (2012) 0.91
Oct transcription factors in development and stem cells: insights and mechanisms. Development (2013) 0.91
SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells. BMC Syst Biol (2010) 0.90
Regulation dynamics of Leishmania differentiation: deconvoluting signals and identifying phosphorylation trends. Mol Cell Proteomics (2014) 0.90
Inhibition of the protein kinase MK-2 protects podocytes from nephrotic syndrome-related injury. Am J Physiol Renal Physiol (2011) 0.89
14-3-3ζ interacts with stat3 and regulates its constitutive activation in multiple myeloma cells. PLoS One (2012) 0.88
Cyclin K-containing kinase complexes maintain self-renewal in murine embryonic stem cells. J Biol Chem (2012) 0.87
Sumoylation of Krüppel-like factor 4 inhibits pluripotency induction but promotes adipocyte differentiation. J Biol Chem (2013) 0.87
Proteomic analysis of stem cell differentiation and early development. Cold Spring Harb Perspect Biol (2012) 0.86
Yeast proteomics and protein microarrays. J Proteomics (2010) 0.86
LIN28 phosphorylation by MAPK/ERK couples signalling to the post-transcriptional control of pluripotency. Nat Cell Biol (2016) 0.86
AtMMS21, an SMC5/6 complex subunit, is involved in stem cell niche maintenance and DNA damage responses in Arabidopsis roots. Plant Physiol (2013) 0.85
Novel AKT phosphorylation sites identified in the pluripotency factors OCT4, SOX2 and KLF4. Cell Cycle (2015) 0.85
NANOG is multiply phosphorylated and directly modified by ERK2 and CDK1 in vitro. Stem Cell Reports (2014) 0.85
Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data. BMC Bioinformatics (2010) 0.85
Akt increases sox2 expression in adult hippocampal neural progenitor cells, but increased sox2 does not promote proliferation. Stem Cells Dev (2010) 0.84
Cleavage of E-cadherin and β-catenin by calpain affects Wnt signaling and spheroid formation in suspension cultures of human pluripotent stem cells. Mol Cell Proteomics (2014) 0.84
Important relationships between Rab and MICAL proteins in endocytic trafficking. World J Biol Chem (2010) 0.84
Controlled sumoylation of the mevalonate pathway enzyme HMGS-1 regulates metabolism during aging. Proc Natl Acad Sci U S A (2014) 0.83
Unraveling the human embryonic stem cell phosphoproteome. Cell Stem Cell (2009) 0.83
Comprehensive quantitative comparison of the membrane proteome, phosphoproteome, and sialiome of human embryonic and neural stem cells. Mol Cell Proteomics (2013) 0.83
Current strategies and findings in clinically relevant post-translational modification-specific proteomics. Expert Rev Proteomics (2015) 0.83
CDK1 plays an important role in the maintenance of pluripotency and genomic stability in human pluripotent stem cells. Cell Death Dis (2014) 0.83
Cyclin-dependent kinase-mediated Sox2 phosphorylation enhances the ability of Sox2 to establish the pluripotent state. J Biol Chem (2015) 0.82
The Importance of Ubiquitination and Deubiquitination in Cellular Reprogramming. Stem Cells Int (2016) 0.82
Evolution of the highly networked deubiquitinating enzymes USP4, USP15, and USP11. BMC Evol Biol (2015) 0.82
Aberrant expression and biological significance of Sox2, an embryonic stem cell transcriptional factor, in ALK-positive anaplastic large cell lymphoma. Blood Cancer J (2012) 0.82
Cancer Stem Cells in Glioblastoma Multiforme. Front Surg (2016) 0.82
Fine-tuning of iPSC derivation by an inducible reprogramming system at the protein level. Stem Cell Reports (2014) 0.81
Glycosyltransferase ST6GAL1 contributes to the regulation of pluripotency in human pluripotent stem cells. Sci Rep (2015) 0.81
Phosphoproteomic analysis: an emerging role in deciphering cellular signaling in human embryonic stem cells and their differentiated derivatives. Stem Cell Rev (2012) 0.81
Major remodelling of the murine stem cell kinome following differentiation in the hematopoietic compartment. J Proteome Res (2011) 0.81
Dynamic protein pathway activation mapping of adipose-derived stem cell differentiation implicates novel regulators of adipocyte differentiation. Mol Cell Proteomics (2013) 0.81
SOX2 Is Regulated Differently from NANOG and OCT4 in Human Embryonic Stem Cells during Early Differentiation Initiated with Sodium Butyrate. Stem Cells Int (2014) 0.81
Cooperation of Sox4 with β-catenin/p300 complex in transcriptional regulation of the Slug gene during divergent sarcomatous differentiation in uterine carcinosarcoma. BMC Cancer (2016) 0.80
Posttranslational regulation of self-renewal capacity: insights from proteome and phosphoproteome analyses of stem cell leukemia. Blood (2012) 0.80
Spatial phosphoprotein profiling reveals a compartmentalized extracellular signal-regulated kinase switch governing neurite growth and retraction. J Biol Chem (2011) 0.80
SOX2 O-GlcNAcylation alters its protein-protein interactions and genomic occupancy to modulate gene expression in pluripotent cells. Elife (2016) 0.80
Reversion to an embryonic alternative splicing program enhances leukemia stem cell self-renewal. Proc Natl Acad Sci U S A (2015) 0.79
Structure and function of steroid receptor RNA activator protein, the proposed partner of SRA noncoding RNA. J Mol Biol (2014) 0.79
Assessment of the Potential of CDK2 Inhibitor NU6140 to Influence the Expression of Pluripotency Markers NANOG, OCT4, and SOX2 in 2102Ep and H9 Cells. Int J Cell Biol (2014) 0.79
DDX6 Orchestrates Mammalian Progenitor Function through the mRNA Degradation and Translation Pathways. Mol Cell (2015) 0.79
Systems Proteomics View of the Endogenous Human Claudin Protein Family. J Proteome Res (2016) 0.79
Regulation of centriolar satellite integrity and its physiology. Cell Mol Life Sci (2016) 0.78
Mass spectrometry-based proteomics: qualitative identification to activity-based protein profiling. Wiley Interdiscip Rev Syst Biol Med (2012) 0.78
The L1TD1 protein interactome reveals the importance of post-transcriptional regulation in human pluripotency. Stem Cell Reports (2015) 0.78
Epigenetic Mechanisms Regulating Mesenchymal Stem Cell Differentiation. Curr Genomics (2015) 0.78
Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes. PLoS Comput Biol (2015) 0.78
The Oct1 transcription factor and epithelial malignancies: Old protein learns new tricks. Biochim Biophys Acta (2016) 0.77
Proteomics and pluripotency. Crit Rev Biochem Mol Biol (2011) 0.77
Structural basis for recognition and remodeling of the TBP:DNA:NC2 complex by Mot1. Elife (2015) 0.77
The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol (2007) 10.24
Characterization of human embryonic stem cell lines by the International Stem Cell Initiative. Nat Biotechnol (2007) 9.36
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res (2003) 6.86
The ecoresponsive genome of Daphnia pulex. Science (2011) 6.55
MicroRNAs in the human heart: a clue to fetal gene reprogramming in heart failure. Circulation (2007) 6.41
A promoter-level mammalian expression atlas. Nature (2014) 6.25
Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell (2012) 6.22
Lgr5 homologues associate with Wnt receptors and mediate R-spondin signalling. Nature (2011) 6.09
Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat Struct Mol Biol (2011) 6.02
Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat Biotechnol (2009) 5.41
Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics. Nat Protoc (2009) 4.61
RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions. Proc Natl Acad Sci U S A (2011) 4.58
Stem-cell-based therapy and lessons from the heart. Nature (2008) 4.54
Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins. BMC Bioinformatics (2004) 4.44
The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods (2013) 4.34
Efficient biotinylation and single-step purification of tagged transcription factors in mammalian cells and transgenic mice. Proc Natl Acad Sci U S A (2003) 4.28
Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide precolumns. Anal Chem (2004) 4.06
Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles. J Proteome Res (2009) 3.77
Linear motif atlas for phosphorylation-dependent signaling. Sci Signal (2008) 3.77
The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent '+4' cell markers. EMBO J (2012) 3.70
A high-quality catalog of the Drosophila melanogaster proteome. Nat Biotechnol (2007) 3.34
Quantitative phosphoproteomics of early elicitor signaling in Arabidopsis. Mol Cell Proteomics (2007) 3.33
Recombinant vitronectin is a functionally defined substrate that supports human embryonic stem cell self-renewal via alphavbeta5 integrin. Stem Cells (2008) 3.33
Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS Biol (2005) 3.28
Autotaxin, a secreted lysophospholipase D, is essential for blood vessel formation during development. Mol Cell Biol (2006) 3.24
Human embryonic stem cell-derived cardiomyocytes survive and mature in the mouse heart and transiently improve function after myocardial infarction. Stem Cell Res (2007) 3.04
Wnt signaling through inhibition of β-catenin degradation in an intact Axin1 complex. Cell (2012) 3.03
Thalidomide stimulates vessel maturation and reduces epistaxis in individuals with hereditary hemorrhagic telangiectasia. Nat Med (2010) 2.88
Cooperative binding of two acetylation marks on a histone tail by a single bromodomain. Nature (2009) 2.83
Tumour suppressor RNF43 is a stem-cell E3 ligase that induces endocytosis of Wnt receptors. Nature (2012) 2.76
The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search. Mol Cell Proteomics (2010) 2.64
Ethics. The ISSCR guidelines for human embryonic stem cell research. Science (2007) 2.62
ELM: the status of the 2010 eukaryotic linear motif resource. Nucleic Acids Res (2009) 2.59
Regulation of retromer recruitment to endosomes by sequential action of Rab5 and Rab7. J Cell Biol (2008) 2.56
GATA-1 forms distinct activating and repressive complexes in erythroid cells. EMBO J (2005) 2.56
Induced pluripotent stem cells: the new patient? Nat Rev Mol Cell Biol (2012) 2.50
MSQuant, an open source platform for mass spectrometry-based quantitative proteomics. J Proteome Res (2010) 2.40
Sequential waves of functionally related proteins are expressed when B cells prepare for antibody secretion. Immunity (2003) 2.40
Next-generation proteomics: towards an integrative view of proteome dynamics. Nat Rev Genet (2012) 2.39
Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics. Nat Biotechnol (2003) 2.37
The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels. Proc Natl Acad Sci U S A (2007) 2.36
Human embryonic stem cell-derived cardiomyocytes and cardiac repair in rodents. Circ Res (2008) 2.31
NKX2-5(eGFP/w) hESCs for isolation of human cardiac progenitors and cardiomyocytes. Nat Methods (2011) 2.29
Positive selection of tyrosine loss in metazoan evolution. Science (2009) 2.28
Nonprocessive methylation by Dot1 leads to functional redundancy of histone H3K79 methylation states. Nat Struct Mol Biol (2008) 2.27
Lipid II is an intrinsic component of the pore induced by nisin in bacterial membranes. J Biol Chem (2003) 2.26
GMP synthetase stimulates histone H2B deubiquitylation by the epigenetic silencer USP7. Mol Cell (2005) 2.21
Differential targeting of two distinct SWI/SNF-related Drosophila chromatin-remodeling complexes. Mol Cell Biol (2004) 2.18
Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases. Sci Signal (2009) 2.16
Prediction of drug-induced cardiotoxicity using human embryonic stem cell-derived cardiomyocytes. Stem Cell Res (2009) 2.13
The RNA-binding protein repertoire of embryonic stem cells. Nat Struct Mol Biol (2013) 2.12
Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach. Anal Chem (2009) 2.10
The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium. Mol Cell Proteomics (2012) 2.10
Improving the performance of a quadrupole time-of-flight instrument for macromolecular mass spectrometry. Anal Chem (2006) 2.06
Eukaryotic protein domains as functional units of cellular evolution. Sci Signal (2009) 2.06
Phosphopeptide fragmentation and analysis by mass spectrometry. J Mass Spectrom (2009) 2.04
Isl1Cre reveals a common Bmp pathway in heart and limb development. Development (2006) 2.04
A quest for human and mouse embryonic stem cell-specific proteins. Mol Cell Proteomics (2006) 2.04
Mass spectrometry-based proteomics and network biology. Annu Rev Biochem (2012) 2.02
Quantitative cancer proteomics: stable isotope labeling with amino acids in cell culture (SILAC) as a tool for prostate cancer research. Mol Cell Proteomics (2004) 2.00
TGF-beta1 induces efficient differentiation of human cardiomyocyte progenitor cells into functional cardiomyocytes in vitro. Stem Cell Res (2008) 1.98
WW domains provide a platform for the assembly of multiprotein networks. Mol Cell Biol (2005) 1.97
A large synthetic peptide and phosphopeptide reference library for mass spectrometry-based proteomics. Nat Biotechnol (2013) 1.93
Improved peptide identification by targeted fragmentation using CID, HCD and ETD on an LTQ-Orbitrap Velos. J Proteome Res (2011) 1.93
Cell-specific information processing in segregating populations of Eph receptor ephrin-expressing cells. Science (2009) 1.91
A mitotic phosphorylation feedback network connects Cdk1, Plk1, 53BP1, and Chk2 to inactivate the G(2)/M DNA damage checkpoint. PLoS Biol (2010) 1.90
Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeat-derived peptides. Proc Natl Acad Sci U S A (2004) 1.89
Phosphorylation networks regulating JNK activity in diverse genetic backgrounds. Science (2008) 1.86
Munc13-4 is an effector of rab27a and controls secretion of lysosomes in hematopoietic cells. Mol Biol Cell (2004) 1.85
Network medicine. FEBS Lett (2008) 1.84
Highly coordinated proteome dynamics during reprogramming of somatic cells to pluripotency. Cell Rep (2012) 1.84
Origin of monocytes and macrophages in a committed progenitor. Nat Immunol (2013) 1.84
A central role for TFIID in the pluripotent transcription circuitry. Nature (2013) 1.82
The leukemia-associated Mllt10/Af10-Dot1l are Tcf4/β-catenin coactivators essential for intestinal homeostasis. PLoS Biol (2010) 1.81
Highly robust, automated, and sensitive online TiO2-based phosphoproteomics applied to study endogenous phosphorylation in Drosophila melanogaster. J Proteome Res (2007) 1.80
Monitoring macromolecular complexes involved in the chaperonin-assisted protein folding cycle by mass spectrometry. Nat Methods (2005) 1.79
DNA damage activates a spatially distinct late cytoplasmic cell-cycle checkpoint network controlled by MK2-mediated RNA stabilization. Mol Cell (2010) 1.78
Ion mobility mass spectrometry of proteins and protein assemblies. Chem Soc Rev (2009) 1.77
Restriction landmark genome scanning identifies culture-induced DNA methylation instability in the human embryonic stem cell epigenome. Hum Mol Genet (2007) 1.68
Activation of FoxM1 during G2 requires cyclin A/Cdk-dependent relief of autorepression by the FoxM1 N-terminal domain. Mol Cell Biol (2008) 1.67
High-sensitivity Orbitrap mass analysis of intact macromolecular assemblies. Nat Methods (2012) 1.67
Enhanced cardiomyogenesis of human embryonic stem cells by a small molecular inhibitor of p38 MAPK. Differentiation (2007) 1.66
Archaeal (per)chlorate reduction at high temperature: an interplay of biotic and abiotic reactions. Science (2013) 1.64
High-resolution mass spectrometry of viral assemblies: molecular composition and stability of dimorphic hepatitis B virus capsids. Proc Natl Acad Sci U S A (2008) 1.64
Computational approaches to identify functional genetic variants in cancer genomes. Nat Methods (2013) 1.64
Novel binding partners of Ldb1 are required for haematopoietic development. Development (2006) 1.63
Native protein mass spectrometry: from intact oligomers to functional machineries. Curr Opin Chem Biol (2004) 1.61
Human Ccr4-Not complexes contain variable deadenylase subunits. Biochem J (2009) 1.61
An experimental correction for arginine-to-proline conversion artifacts in SILAC-based quantitative proteomics. Nat Methods (2007) 1.59