Published in PLoS One on November 10, 2010
Mathematical modelling of the MAP kinase pathway using proteomic datasets. PLoS One (2012) 0.86
Systematic parameter estimation in data-rich environments for cell signalling dynamics. Bioinformatics (2013) 0.85
Phosphoproteomics-based systems analysis of signal transduction networks. Front Physiol (2012) 0.84
PKIS: computational identification of protein kinases for experimentally discovered protein phosphorylation sites. BMC Bioinformatics (2013) 0.80
Research resource: identification of novel growth hormone-regulated phosphorylation sites by quantitative phosphoproteomics. Mol Endocrinol (2012) 0.77
Analytical reduction of combinatorial complexity arising from multiple protein modification sites. J R Soc Interface (2015) 0.75
Functional aspects of the EGF-induced MAP kinase cascade: a complex self-organizing system approach. PLoS One (2014) 0.75
Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell (2006) 20.92
Epidermal growth factor receptor mutations in lung cancer. Nat Rev Cancer (2007) 14.84
Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature (2008) 10.28
Biological robustness. Nat Rev Genet (2004) 9.98
Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors. Nat Biotechnol (2002) 6.68
A quantitative protein interaction network for the ErbB receptors using protein microarrays. Nature (2005) 5.75
Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat Biotechnol (2004) 5.22
Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules. Mol Cell Proteomics (2005) 4.33
Quantification of short term signaling by the epidermal growth factor receptor. J Biol Chem (1999) 4.19
Prediction and validation of the distinct dynamics of transient and sustained ERK activation. Nat Cell Biol (2005) 4.13
Cbl: many adaptations to regulate protein tyrosine kinases. Nat Rev Mol Cell Biol (2001) 4.11
Input-output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data. Mol Syst Biol (2009) 3.50
Phosphotyrosine interactome of the ErbB-receptor kinase family. Mol Syst Biol (2005) 3.48
Effects of HER2 overexpression on cell signaling networks governing proliferation and migration. Mol Syst Biol (2006) 3.01
SH2 domains prevent tyrosine dephosphorylation of the EGF receptor: identification of Tyr992 as the high-affinity binding site for SH2 domains of phospholipase C gamma. EMBO J (1992) 2.82
Inhibition of the EGF receptor by binding of MIG6 to an activating kinase domain interface. Nature (2007) 2.78
The EGF receptor family: spearheading a merger of signaling and therapeutics. Curr Opin Cell Biol (2007) 2.74
Dynamics of the Ras/ERK MAPK cascade as monitored by fluorescent probes. J Biol Chem (2006) 2.73
Ligand-dependent responses of the ErbB signaling network: experimental and modeling analyses. Mol Syst Biol (2007) 2.56
A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity. Biosystems (2005) 2.36
Phosphoproteomic analysis of Her2/neu signaling and inhibition. Proc Natl Acad Sci U S A (2006) 2.30
A novel proteomic screen for peptide-protein interactions. J Biol Chem (2003) 2.02
A computational model on the modulation of mitogen-activated protein kinase (MAPK) and Akt pathways in heregulin-induced ErbB signalling. Biochem J (2003) 2.00
Quantitative analysis of HER2-mediated effects on HER2 and epidermal growth factor receptor endocytosis: distribution of homo- and heterodimers depends on relative HER2 levels. J Biol Chem (2003) 1.93
Molecular mechanism for a role of SHP2 in epidermal growth factor receptor signaling. Mol Cell Biol (2003) 1.87
An integrated model of epidermal growth factor receptor trafficking and signal transduction. Biophys J (2003) 1.80
Differential feedback regulation of the MAPK cascade underlies the quantitative differences in EGF and NGF signalling in PC12 cells. FEBS Lett (2000) 1.65
Analysis of small human proteins reveals the translation of upstream open reading frames of mRNAs. Genome Res (2004) 1.63
Epidermal growth factor-receptor mutant lacking the autophosphorylation sites induces phosphorylation of Shc protein and Shc-Grb2/ASH association and retains mitogenic activity. Proc Natl Acad Sci U S A (1994) 1.51
Comparisons of tyrosine phosphorylated proteins in cells expressing lung cancer-specific alleles of EGFR and KRAS. Proc Natl Acad Sci U S A (2008) 1.51
A decompositional approach to parameter estimation in pathway modeling: a case study of the Akt and MAPK pathways and their crosstalk. Bioinformatics (2006) 1.44
Diversity of translation start sites may define increased complexity of the human short ORFeome. Mol Cell Proteomics (2007) 1.39
Mechanism of epidermal growth factor regulation of Vav2, a guanine nucleotide exchange factor for Rac. J Biol Chem (2002) 1.39
Sequence specificity in recognition of the epidermal growth factor receptor by protein tyrosine phosphatase 1B. J Biol Chem (1993) 1.36
Modeling the effects of HER/ErbB1-3 coexpression on receptor dimerization and biological response. Biophys J (2006) 1.36
The evolutionarily conserved EBR module of RALT/MIG6 mediates suppression of the EGFR catalytic activity. Oncogene (2007) 1.33
Signaling in small subcellular volumes. II. Stochastic and diffusion effects on synaptic network properties. Biophys J (2004) 1.29
Hybrid Petri net representation of gene regulatory network. Pac Symp Biocomput (2000) 1.26
A quantitative study of the recruitment potential of all intracellular tyrosine residues on EGFR, FGFR1 and IGF1R. Mol Biosyst (2008) 1.19
An Improved Procedure for EI Nino Forecasting: Implications for Predictability. Science (1995) 1.15
Signaling flux redistribution at toll-like receptor pathway junctions. PLoS One (2008) 1.12
Epidermal growth factor receptor phosphorylation sites Ser991 and Tyr998 are implicated in the regulation of receptor endocytosis and phosphorylations at Ser1039 and Thr1041. Mol Cell Proteomics (2009) 1.07
Temporal perturbation of tyrosine phosphoproteome dynamics reveals the system-wide regulatory networks. Mol Cell Proteomics (2008) 1.07
Subsets of epidermal growth factor receptors during activation and endocytosis. J Biol Chem (1997) 1.03
Constructing biological pathway models with hybrid functional Petri nets. In Silico Biol (2004) 1.01
Tyrosine phosphorylation of ras GTPase-activating protein does not require association with the epidermal growth factor receptor. J Biol Chem (1993) 0.99
Receptor tyrosine kinase signaling: a view from quantitative proteomics. Mol Biosyst (2009) 0.97
A versatile petri net based architecture for modeling and simulation of complex biological processes. Genome Inform (2004) 0.94
Modeling and estimation of dynamic EGFR pathway by data assimilation approach using time series proteomic data. Genome Inform (2006) 0.93
An integrated comparative phosphoproteomic and bioinformatic approach reveals a novel class of MPM-2 motifs upregulated in EGFRvIII-expressing glioblastoma cells. Mol Biosyst (2008) 0.92
Parameter estimation of in silico biological pathways with particle filtering towards a petascale computing. Pac Symp Biocomput (2009) 0.91
AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction. BMC Bioinformatics (2007) 0.88
Genomic data assimilation for estimating hybrid functional Petri net from time-course gene expression data. Genome Inform (2006) 0.88
Epidermal growth factor receptor internalization rate is regulated by negative charges near the SH2 binding site Tyr992. Biochemistry (1999) 0.87
Bayesian learning of biological pathways on genomic data assimilation. Bioinformatics (2008) 0.82
Modeling and simulation with Hybrid Functional Petri Nets of the role of interleukin-6 in human early haematopoiesis. Pac Symp Biocomput (2006) 0.80
A carboxyl-terminal mutation of the epidermal growth factor receptor alters tyrosine kinase activity and substrate specificity as measured by a fluorescence polarization assay. J Biol Chem (2003) 0.80
International network of cancer genome projects. Nature (2010) 20.35
Frequent pathway mutations of splicing machinery in myelodysplasia. Nature (2011) 11.44
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res (2004) 9.18
Induction and activation of the transcription factor NFATc1 (NFAT2) integrate RANKL signaling in terminal differentiation of osteoclasts. Dev Cell (2002) 9.10
Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science (2003) 8.65
The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science (2007) 8.12
Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat Genet (2003) 7.98
Mapping human genetic diversity in Asia. Science (2009) 7.40
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
A cAMP-response element binding protein-induced microRNA regulates neuronal morphogenesis. Proc Natl Acad Sci U S A (2005) 6.61
A transcription factor response element for gene expression during circadian night. Nature (2002) 6.55
Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res (2011) 6.02
The medaka draft genome and insights into vertebrate genome evolution. Nature (2007) 5.77
Interferon-alpha induction through Toll-like receptors involves a direct interaction of IRF7 with MyD88 and TRAF6. Nat Immunol (2004) 5.71
Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome Res (2005) 5.22
Extensive feature detection of N-terminal protein sorting signals. Bioinformatics (2002) 5.16
Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature (2004) 5.08
Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators. Nat Genet (2012) 4.84
Curved EFC/F-BAR-domain dimers are joined end to end into a filament for membrane invagination in endocytosis. Cell (2007) 4.73
Integrated molecular analysis of clear-cell renal cell carcinoma. Nat Genet (2013) 4.61
DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs. Nucleic Acids Res (2002) 4.29
Human Proteinpedia enables sharing of human protein data. Nat Biotechnol (2008) 4.21
Phosphate-activated glutaminase (GLS2), a p53-inducible regulator of glutamine metabolism and reactive oxygen species. Proc Natl Acad Sci U S A (2010) 4.18
Gain-of-function of mutated C-CBL tumour suppressor in myeloid neoplasms. Nature (2009) 3.80
DBTSS, DataBase of Transcriptional Start Sites: progress report 2004. Nucleic Acids Res (2004) 3.73
Large-scale identification and characterization of human genes that activate NF-kappaB and MAPK signaling pathways. Oncogene (2003) 3.53
A vertebrate RNA-binding protein Fox-1 regulates tissue-specific splicing via the pentanucleotide GCAUG. EMBO J (2003) 3.44
Somatic Mutations and Clonal Hematopoiesis in Aplastic Anemia. N Engl J Med (2015) 3.42
The landscape of C. elegans 3'UTRs. Science (2010) 3.32
DBTSS: database of transcription start sites, progress report 2008. Nucleic Acids Res (2007) 3.11
Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites. Science (2008) 3.10
Clinical proteomics: A need to define the field and to begin to set adequate standards. Proteomics Clin Appl (2007) 2.84
Identification of genes upregulated in ALK-positive and EGFR/KRAS/ALK-negative lung adenocarcinomas. Cancer Res (2011) 2.81
DKK1, a negative regulator of Wnt signaling, is a target of the beta-catenin/TCF pathway. Oncogene (2004) 2.73
miRNA-mediated deadenylation is orchestrated by GW182 through two conserved motifs that interact with CCR4-NOT. Nat Struct Mol Biol (2011) 2.61
Thyrotrophin in the pars tuberalis triggers photoperiodic response. Nature (2008) 2.60
Prediction of transcriptional terminators in Bacillus subtilis and related species. PLoS Comput Biol (2005) 2.54
Phosphorylation by aurora B converts MgcRacGAP to a RhoGAP during cytokinesis. Dev Cell (2003) 2.54
Human Bub1 defines the persistent cohesion site along the mitotic chromosome by affecting Shugoshin localization. Curr Biol (2005) 2.53
DBTSS: DataBase of Human Transcription Start Sites, progress report 2006. Nucleic Acids Res (2006) 2.52
JNK promotes Bax translocation to mitochondria through phosphorylation of 14-3-3 proteins. EMBO J (2004) 2.50
The functional consequences of alternative promoter use in mammalian genomes. Trends Genet (2008) 2.47
Construction of a full-length enriched and a 5'-end enriched cDNA library using the oligo-capping method. Methods Mol Biol (2003) 2.45
The Plk1 target Kizuna stabilizes mitotic centrosomes to ensure spindle bipolarity. Nat Cell Biol (2006) 2.37
The human proteome project: current state and future direction. Mol Cell Proteomics (2011) 2.34
5'-end SAGE for the analysis of transcriptional start sites. Nat Biotechnol (2004) 2.34
Critical roles of c-Jun signaling in regulation of NFAT family and RANKL-regulated osteoclast differentiation. J Clin Invest (2004) 2.31
Estimation of genetic networks and functional structures between genes by using Bayesian networks and nonparametric regression. Pac Symp Biocomput (2002) 2.30
Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biol (2011) 2.18
Rice-based oral antibody fragment prophylaxis and therapy against rotavirus infection. J Clin Invest (2013) 2.15
Systemically injected exosomes targeted to EGFR deliver antitumor microRNA to breast cancer cells. Mol Ther (2012) 2.15
Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms. Nat Genet (2013) 2.14
Somatic SETBP1 mutations in myeloid malignancies. Nat Genet (2013) 2.12
Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing. Nat Genet (2010) 2.08
Promoter prediction analysis on the whole human genome. Nat Biotechnol (2004) 2.08
Inferring gene networks from time series microarray data using dynamic Bayesian networks. Brief Bioinform (2003) 2.08
The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res (2007) 2.07
NOTCH3 signaling pathway plays crucial roles in the proliferation of ErbB2-negative human breast cancer cells. Cancer Res (2008) 2.01
The Shigella flexneri effector OspI deamidates UBC13 to dampen the inflammatory response. Nature (2012) 1.99
Association of HTRA1 mutations and familial ischemic cerebral small-vessel disease. N Engl J Med (2009) 1.96
Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection. Bioinformatics (2003) 1.95
Dependence of self-tolerance on TRAF6-directed development of thymic stroma. Science (2005) 1.91
Fc{epsilon}RI-mediated mast cell degranulation requires calcium-independent microtubule-dependent translocation of granules to the plasma membrane. J Cell Biol (2005) 1.91
Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks. Proc IEEE Comput Soc Bioinform Conf (2003) 1.89
Rate of evolution in brain-expressed genes in humans and other primates. PLoS Biol (2007) 1.87
Variant ALDH2 is associated with accelerated progression of bone marrow failure in Japanese Fanconi anemia patients. Blood (2013) 1.79
Inhibition of angiogenesis and vascular leakiness by angiopoietin-related protein 4. Cancer Res (2003) 1.78
Exome sequencing identifies secondary mutations of SETBP1 and JAK3 in juvenile myelomonocytic leukemia. Nat Genet (2013) 1.71
Draft assembly of the Symbiodinium minutum nuclear genome reveals dinoflagellate gene structure. Curr Biol (2013) 1.69
Modeling gene expression regulatory networks with the sparse vector autoregressive model. BMC Syst Biol (2007) 1.69
The tumor-suppressive miR-497-195 cluster targets multiple cell-cycle regulators in hepatocellular carcinoma. PLoS One (2013) 1.69
NF-kappaB activation in development and progression of cancer. Cancer Sci (2007) 1.67
Activation of the IκB kinase complex by HTLV-1 Tax requires cytosolic factors involved in Tax-induced polyubiquitination. J Biochem (2011) 1.66
Functional gene screening system identified TRPV4 as a regulator of chondrogenic differentiation. J Biol Chem (2007) 1.66
Interaction of CagA with Crk plays an important role in Helicobacter pylori-induced loss of gastric epithelial cell adhesion. J Exp Med (2005) 1.66
BANK regulates BCR-induced calcium mobilization by promoting tyrosine phosphorylation of IP(3) receptor. EMBO J (2002) 1.64
Phosphoproteomics reveals new ERK MAP kinase targets and links ERK to nucleoporin-mediated nuclear transport. Nat Struct Mol Biol (2009) 1.64
Non-muscle myosin IIA is a functional entry receptor for herpes simplex virus-1. Nature (2010) 1.63
Analysis of small human proteins reveals the translation of upstream open reading frames of mRNAs. Genome Res (2004) 1.63
Two mechanistically and temporally distinct NF-kappaB activation pathways in IL-1 signaling. Sci Signal (2009) 1.61
Deletion of angiotensin-converting enzyme 2 accelerates pressure overload-induced cardiac dysfunction by increasing local angiotensin II. Hypertension (2006) 1.61
Massive transcriptional start site analysis of human genes in hypoxia cells. Nucleic Acids Res (2009) 1.60
Recommendations for biomarker identification and qualification in clinical proteomics. Sci Transl Med (2010) 1.59
Sustained activation of N-WASP through phosphorylation is essential for neurite extension. Dev Cell (2002) 1.58
Foreword: from the TRANSCRIPTOME conferences to the SYSTEMOSCOPE international consortium. C R Biol (2004) 1.58
Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity. Gene (2005) 1.57
Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis. Genome Res (2011) 1.57
Ezh2 augments leukemogenicity by reinforcing differentiation blockage in acute myeloid leukemia. Blood (2012) 1.56