Published in Wiley Interdiscip Rev Syst Biol Med on October 04, 2010
The PluriNetWork: an electronic representation of the network underlying pluripotency in mouse, and its applications. PLoS One (2010) 1.33
ExprEssence--revealing the essence of differential experimental data in the context of an interaction/regulation net-work. BMC Syst Biol (2010) 1.27
ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells. Database (Oxford) (2013) 1.10
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Sets2Networks: network inference from repeated observations of sets. BMC Syst Biol (2012) 0.95
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Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature (2007) 65.18
Genome-wide mapping of in vivo protein-DNA interactions. Science (2007) 64.92
Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet (2001) 63.36
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Combinatorial microRNA target predictions. Nat Genet (2005) 50.48
Core transcriptional regulatory circuitry in human embryonic stem cells. Cell (2005) 34.93
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Identifying biological themes within lists of genes with EASE. Genome Biol (2003) 31.72
TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res (2003) 29.26
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell (2008) 28.29
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics (2004) 26.64
Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature (2006) 25.90
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The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat Genet (2006) 20.76
A global map of p53 transcription-factor binding sites in the human genome. Cell (2006) 20.65
NCBI GEO: mining tens of millions of expression profiles--database and tools update. Nucleic Acids Res (2006) 19.42
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Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell (2008) 16.38
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A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell (2006) 14.70
An extended transcriptional network for pluripotency of embryonic stem cells. Cell (2008) 14.64
Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet (2003) 14.56
A stem cell molecular signature. Science (2002) 14.47
Selective blockade of microRNA processing by Lin28. Science (2008) 14.39
HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature (2008) 14.17
Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature (2009) 14.07
IntAct--open source resource for molecular interaction data. Nucleic Acids Res (2006) 13.82
TM4 microarray software suite. Methods Enzymol (2006) 13.78
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Reverse engineering of regulatory networks in human B cells. Nat Genet (2005) 13.16
WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res (2005) 12.88
Profiling gene expression using onto-express. Genomics (2002) 12.65
Network-based classification of breast cancer metastasis. Mol Syst Biol (2007) 12.18
Human protein reference database--2006 update. Nucleic Acids Res (2006) 12.16
Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes Dev (2005) 12.15
A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat Biotechnol (2006) 12.13
A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (2003) 12.07
MINT: the Molecular INTeraction database. Nucleic Acids Res (2006) 11.90
Dissecting self-renewal in stem cells with RNA interference. Nature (2006) 11.66
Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci U S A (2003) 10.82
Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol (2007) 10.46
Inferring cellular networks using probabilistic graphical models. Science (2004) 9.91
MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature (2008) 9.83
A protein interaction network for pluripotency of embryonic stem cells. Nature (2006) 9.63
A custom microarray platform for analysis of microRNA gene expression. Nat Methods (2004) 9.44
Characterization of human embryonic stem cell lines by the International Stem Cell Initiative. Nat Biotechnol (2007) 9.36
DGCR8 is essential for microRNA biogenesis and silencing of embryonic stem cell self-renewal. Nat Genet (2007) 9.25
GFINDer: genetic disease and phenotype location statistical analysis and mining of dynamically annotated gene lists. Nucleic Acids Res (2005) 9.05
miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res (2008) 8.97
ArrayExpress--a public database of microarray experiments and gene expression profiles. Nucleic Acids Res (2006) 8.92
Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol Cell Proteomics (2005) 8.92
Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J Mol Biol (1990) 8.75
TarBase: A comprehensive database of experimentally supported animal microRNA targets. RNA (2005) 8.40
Characterization of Dicer-deficient murine embryonic stem cells. Proc Natl Acad Sci U S A (2005) 8.35
The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res (2004) 8.23
MicroRNA-145 regulates OCT4, SOX2, and KLF4 and represses pluripotency in human embryonic stem cells. Cell (2009) 8.14
FunSpec: a web-based cluster interpreter for yeast. BMC Bioinformatics (2002) 8.01
Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics (2004) 7.76
RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res (2007) 7.64
Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. Genes Dev (2008) 7.07
Systematic discovery of in vivo phosphorylation networks. Cell (2007) 6.94
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res (2003) 6.86
Control, exploitation and tolerance of intracellular noise. Nature (2002) 6.81
Pluripotency governed by Sox2 via regulation of Oct3/4 expression in mouse embryonic stem cells. Nat Cell Biol (2007) 6.69
Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse cellular functions. Cell (2002) 6.62
g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Res (2007) 6.44
A resource for large-scale RNA-interference-based screens in mammals. Nature (2004) 6.36
Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC Bioinformatics (2007) 6.21
miRBase: the microRNA sequence database. Methods Mol Biol (2006) 6.17
Variability and memory of protein levels in human cells. Nature (2006) 6.15
ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res (2006) 6.13
The 20 years of PROSITE. Nucleic Acids Res (2007) 6.06
An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets. Nat Biotechnol (2005) 5.93
STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res (2000) 5.68
Network component analysis: reconstruction of regulatory signals in biological systems. Proc Natl Acad Sci U S A (2003) 5.64
PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation. Proteomics (2004) 5.55
Reverse engineering gene networks using singular value decomposition and robust regression. Proc Natl Acad Sci U S A (2002) 5.29
Embryonic stem cell-specific microRNAs regulate the G1-S transition and promote rapid proliferation. Nat Genet (2008) 5.26
Mining literature for protein-protein interactions. Bioinformatics (2001) 5.18
A biochemical approach to identifying microRNA targets. Proc Natl Acad Sci U S A (2007) 5.16
GeneTrail--advanced gene set enrichment analysis. Nucleic Acids Res (2007) 5.10
Regulatory networks define phenotypic classes of human stem cell lines. Nature (2008) 4.98
Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics (2007) 4.91
miRGen: a database for the study of animal microRNA genomic organization and function. Nucleic Acids Res (2006) 4.91
Tcf3 is an integral component of the core regulatory circuitry of embryonic stem cells. Genes Dev (2008) 4.77
Mesenchymal and haematopoietic stem cells form a unique bone marrow niche. Nature (2010) 15.28
A stem cell molecular signature. Science (2002) 14.47
Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature (2012) 13.71
Dissecting self-renewal in stem cells with RNA interference. Nature (2006) 11.66
Stem cells and their niches. Science (2006) 7.86
Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages. Nat Immunol (2012) 7.32
Functional atlas of the integrin adhesome. Nat Cell Biol (2007) 6.89
Synaptic, transcriptional and chromatin genes disrupted in autism. Nature (2014) 5.30
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics (2013) 4.73
The timing of cortical neurogenesis is encoded within lineages of individual progenitor cells. Nat Neurosci (2006) 4.49
Patient-specific induced pluripotent stem-cell-derived models of LEOPARD syndrome. Nature (2010) 4.38
Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network. Cell (2011) 4.04
Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases. BMC Bioinformatics (2007) 3.44
ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinformatics (2010) 3.42
shRNA knockdown of Bmi-1 reveals a critical role for p21-Rb pathway in NSC self-renewal during development. Cell Stem Cell (2007) 3.40
Systems biology of stem cell fate and cellular reprogramming. Nat Rev Mol Cell Biol (2009) 2.93
Induction of a hemogenic program in mouse fibroblasts. Cell Stem Cell (2013) 2.71
Systems-level dynamic analyses of fate change in murine embryonic stem cells. Nature (2009) 2.70
Minimal differentiation of classical monocytes as they survey steady-state tissues and transport antigen to lymph nodes. Immunity (2013) 2.61
Mutation of SHOC2 promotes aberrant protein N-myristoylation and causes Noonan-like syndrome with loose anagen hair. Nat Genet (2009) 2.57
KrasG12D-induced IKK2/β/NF-κB activation by IL-1α and p62 feedforward loops is required for development of pancreatic ductal adenocarcinoma. Cancer Cell (2012) 2.55
A genomewide functional network for the laboratory mouse. PLoS Comput Biol (2008) 2.25
Generation of anterior foregut endoderm from human embryonic and induced pluripotent stem cells. Nat Biotechnol (2011) 2.22
KEA: kinase enrichment analysis. Bioinformatics (2009) 1.94
Prdm16 is a physiologic regulator of hematopoietic stem cells. Blood (2011) 1.86
A systems approach identifies HIPK2 as a key regulator of kidney fibrosis. Nat Med (2012) 1.83
Design logic of a cannabinoid receptor signaling network that triggers neurite outgrowth. Science (2008) 1.82
Wnt-inhibitory factor 1 dysregulation of the bone marrow niche exhausts hematopoietic stem cells. Blood (2011) 1.76
Krüppel-like factor 6 regulates mitochondrial function in the kidney. J Clin Invest (2015) 1.72
Smarcc1/Baf155 couples self-renewal gene repression with changes in chromatin structure in mouse embryonic stem cells. Stem Cells (2009) 1.72
Systems pharmacology of arrhythmias. Sci Signal (2010) 1.72
Oct4 links multiple epigenetic pathways to the pluripotency network. Cell Res (2011) 1.69
Global phosphorylation analysis of beta-arrestin-mediated signaling downstream of a seven transmembrane receptor (7TMR). Proc Natl Acad Sci U S A (2010) 1.64
Systems approach to explore components and interactions in the presynapse. Proteomics (2009) 1.61
Nanog-dependent feedback loops regulate murine embryonic stem cell heterogeneity. Nat Cell Biol (2012) 1.56
Regulation of embryonic and induced pluripotency by aurora kinase-p53 signaling. Cell Stem Cell (2012) 1.54
A molecular profile of a hematopoietic stem cell niche. Proc Natl Acad Sci U S A (2002) 1.53
Stem cells: interactive niches. Nature (2003) 1.42
MacroH2A histone variants act as a barrier upon reprogramming towards pluripotency. Nat Commun (2013) 1.39
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder. Am J Hum Genet (2013) 1.39
Bmi-1 cooperates with Foxg1 to maintain neural stem cell self-renewal in the forebrain. Genes Dev (2009) 1.39
Alternative induced pluripotent stem cell characterization criteria for in vitro applications. Cell Stem Cell (2009) 1.36
Genomewide gain-of-function genetic screen identifies functionally active genes in mouse embryonic stem cells. Proc Natl Acad Sci U S A (2006) 1.35
Sox2 in the dermal papilla niche controls hair growth by fine-tuning BMP signaling in differentiating hair shaft progenitors. Dev Cell (2012) 1.34
Lists2Networks: integrated analysis of gene/protein lists. BMC Bioinformatics (2010) 1.33
Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers. Bioinformatics (2011) 1.31
Diversification of stem cell molecular repertoire by alternative splicing. Proc Natl Acad Sci U S A (2005) 1.27
Zfp281 mediates Nanog autorepression through recruitment of the NuRD complex and inhibits somatic cell reprogramming. Proc Natl Acad Sci U S A (2012) 1.26
Single transcription factor reprogramming of hair follicle dermal papilla cells to induced pluripotent stem cells. Stem Cells (2011) 1.22
Kruppel-like factor 15 (KLF15) is a key regulator of podocyte differentiation. J Biol Chem (2012) 1.21
Epigenetic roles of MLL oncoproteins are dependent on NF-κB. Cancer Cell (2013) 1.20
Network2Canvas: network visualization on a canvas with enrichment analysis. Bioinformatics (2013) 1.20
DAWN: a framework to identify autism genes and subnetworks using gene expression and genetics. Mol Autism (2014) 1.20
AVIS: AJAX viewer of interactive signaling networks. Bioinformatics (2007) 1.19
Statistical mechanics of pluripotency. Cell (2013) 1.16
A genetic and genomic analysis identifies a cluster of genes associated with hematopoietic cell turnover. Blood (2002) 1.13
Stem cells and reprogramming: breaking the epigenetic barrier? Trends Pharmacol Sci (2011) 1.12
ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells. Database (Oxford) (2013) 1.10
Epigenetic reprogramming induces the expansion of cord blood stem cells. J Clin Invest (2014) 1.09
t4 workshop report: Pathways of Toxicity. ALTEX (2013) 1.06
GATE: software for the analysis and visualization of high-dimensional time series expression data. Bioinformatics (2009) 1.05
Delivery of short hairpin RNAs--triggers of gene silencing--into mouse embryonic stem cells. Nat Methods (2006) 1.05
Systems biology of kidney diseases. Kidney Int (2011) 1.05
Expression of HIV transgene aggravates kidney injury in diabetic mice. Kidney Int (2013) 1.00
Flotillin-mediated endocytic events dictate cell type-specific responses to semaphorin 3A. J Neurosci (2010) 0.99
Genes2FANs: connecting genes through functional association networks. BMC Bioinformatics (2012) 0.99
"Tie-ing" down the hematopoietic niche. Cell (2004) 0.95
Sets2Networks: network inference from repeated observations of sets. BMC Syst Biol (2012) 0.95
Reprogramming cell fates: insights from combinatorial approaches. Ann N Y Acad Sci (2012) 0.93
Systems pharmacology meets predictive, preventive, personalized and participatory medicine. Pharmacogenomics (2013) 0.93
A new paradigm for the closed-loop intraoperative administration of analgesics in humans. IEEE Trans Biomed Eng (2002) 0.93
Induced pluripotent stem cell-derived cardiomyocytes as models for genetic cardiovascular disorders. Curr Opin Cardiol (2011) 0.92
Combining competition assays with genetic complementation strategies to dissect mouse embryonic stem cell self-renewal and pluripotency. Nat Protoc (2012) 0.91
Receptor heteromerization expands the repertoire of cannabinoid signaling in rodent neurons. PLoS One (2012) 0.91
Genes2WordCloud: a quick way to identify biological themes from gene lists and free text. Source Code Biol Med (2011) 0.91
SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells. BMC Syst Biol (2010) 0.90
Introduction to statistical methods to analyze large data sets: principal components analysis. Sci Signal (2011) 0.89
Genomic editing tools to model human diseases with isogenic pluripotent stem cells. Stem Cells Dev (2014) 0.89
Network- and attribute-based classifiers can prioritize genes and pathways for autism spectrum disorders and intellectual disability. Am J Med Genet C Semin Med Genet (2012) 0.88
Chronic morphine alters the presynaptic protein profile: identification of novel molecular targets using proteomics and network analysis. PLoS One (2011) 0.88
Functions of bifans in context of multiple regulatory motifs in signaling networks. Biophys J (2008) 0.87
ELK1 transcription factor linked to dysregulated striatal mu opioid receptor signaling network and OPRM1 polymorphism in human heroin abusers. Biol Psychiatry (2013) 0.87
Interconnected network motifs control podocyte morphology and kidney function. Sci Signal (2014) 0.87
Renoprotective effect of combined inhibition of angiotensin-converting enzyme and histone deacetylase. J Am Soc Nephrol (2013) 0.87