Published in Stem Cells on February 01, 2005
Core transcriptional regulatory circuitry in human embryonic stem cells. Cell (2005) 34.93
A chromatin landmark and transcription initiation at most promoters in human cells. Cell (2007) 23.41
An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors. Nat Genet (2008) 17.67
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet (2008) 11.17
Reciprocal transcriptional regulation of Pou5f1 and Sox2 via the Oct4/Sox2 complex in embryonic stem cells. Mol Cell Biol (2005) 4.54
A meta-analysis of human embryonic stem cells transcriptome integrated into a web-based expression atlas. Stem Cells (2007) 3.62
Klf4 cooperates with Oct3/4 and Sox2 to activate the Lefty1 core promoter in embryonic stem cells. Mol Cell Biol (2006) 2.59
Histone h3 lysine 56 acetylation is linked to the core transcriptional network in human embryonic stem cells. Mol Cell (2009) 2.27
Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. Genome Res (2007) 2.16
Pluripotency and nuclear reprogramming. Philos Trans R Soc Lond B Biol Sci (2008) 1.82
Zic3 is required for maintenance of pluripotency in embryonic stem cells. Mol Biol Cell (2007) 1.77
FOXO1 is an essential regulator of pluripotency in human embryonic stem cells. Nat Cell Biol (2011) 1.70
MicroRNA expression pattern of undifferentiated and differentiated human embryonic stem cells. Stem Cells Dev (2007) 1.65
Global gene expression profiling reveals similarities and differences among mouse pluripotent stem cells of different origins and strains. Dev Biol (2007) 1.61
Engineering the embryoid body microenvironment to direct embryonic stem cell differentiation. Biotechnol Prog (2009) 1.61
Genome wide profiling of human embryonic stem cells (hESCs), their derivatives and embryonal carcinoma cells to develop base profiles of U.S. Federal government approved hESC lines. BMC Dev Biol (2006) 1.58
Assessing self-renewal and differentiation in human embryonic stem cell lines. Stem Cells (2005) 1.58
JNK-induced apoptosis, compensatory growth, and cancer stem cells. Cancer Res (2012) 1.52
Transcriptional analysis of early lineage commitment in human embryonic stem cells. BMC Dev Biol (2007) 1.31
Dynamic changes in gene expression during human early embryo development: from fundamental aspects to clinical applications. Hum Reprod Update (2010) 1.28
Evolutionarily conserved transcriptional co-expression guiding embryonic stem cell differentiation. PLoS One (2008) 1.24
Soft microenvironments promote the early neurogenic differentiation but not self-renewal of human pluripotent stem cells. Integr Biol (Camb) (2012) 1.20
Expression profiling of nuclear receptors in human and mouse embryonic stem cells. Mol Endocrinol (2009) 1.16
The FunGenES database: a genomics resource for mouse embryonic stem cell differentiation. PLoS One (2009) 1.15
Nodal signaling via an autocrine pathway promotes proliferation of mouse spermatogonial stem/progenitor cells through Smad2/3 and Oct-4 activation. Stem Cells (2009) 1.15
The abbreviated pluripotent cell cycle. J Cell Physiol (2013) 1.09
Role of Cripto-1 in stem cell maintenance and malignant progression. Am J Pathol (2010) 1.09
A conserved mechanism for control of human and mouse embryonic stem cell pluripotency and differentiation by shp2 tyrosine phosphatase. PLoS One (2009) 1.08
Combinatorial extracellular matrices for human embryonic stem cell differentiation in 3D. Biomacromolecules (2010) 1.08
Toward a complete in silico, multi-layered embryonic stem cell regulatory network. Wiley Interdiscip Rev Syst Biol Med (2010) 1.06
Genome-wide profiling reveals stimulus-specific functions of p53 during differentiation and DNA damage of human embryonic stem cells. Nucleic Acids Res (2013) 1.02
Comparative transcriptional profiling of the limbal epithelial crypt demonstrates its putative stem cell niche characteristics. BMC Genomics (2010) 0.99
Non-canonical TAF complexes regulate active promoters in human embryonic stem cells. Elife (2012) 0.97
Zfp281 functions as a transcriptional repressor for pluripotency of mouse embryonic stem cells. Stem Cells (2011) 0.97
A UTF1-based selection system for stable homogeneously pluripotent human embryonic stem cell cultures. Nucleic Acids Res (2007) 0.96
Designer blood: creating hematopoietic lineages from embryonic stem cells. Blood (2005) 0.93
Stem cells and calcium signaling. Adv Exp Med Biol (2012) 0.92
Initial colony morphology-based selection for iPS cells derived from adult fibroblasts is substantially improved by temporary UTF1-based selection. PLoS One (2010) 0.90
A specific and quick gene expression study in mouse ES cells. J Assist Reprod Genet (2007) 0.90
Periodontal-ligament-derived stem cells exhibit the capacity for long-term survival, self-renewal, and regeneration of multiple tissue types in vivo. Stem Cells Dev (2014) 0.90
Embryonic stem cells are redirected to non-tumorigenic epithelial cell fate by interaction with the mammary microenvironment. PLoS One (2013) 0.87
Detailed characterization of the mouse embryonic stem cell transcriptome reveals novel genes and intergenic splicing associated with pluripotency. BMC Genomics (2008) 0.86
The evolving biology of small molecules: controlling cell fate and identity. Philos Trans R Soc Lond B Biol Sci (2011) 0.85
Expression profiling of the mouse early embryo: reflections and perspectives. Dev Dyn (2006) 0.84
Wnt and Frizzled RNA expression in human mesenchymal and embryonic (H7) stem cells. J Mol Signal (2008) 0.84
Regulation of human Cripto-1 expression by nuclear receptors and DNA promoter methylation in human embryonal and breast cancer cells. J Cell Physiol (2013) 0.82
Molecular basis of Mammalian embryonic stem cell pluripotency and self-renewal. Acta Naturae (2010) 0.81
Current progress with primate embryonic stem cells. Curr Stem Cell Res Ther (2006) 0.79
Maintenance in the chicken genome of the retroviral-like cENS gene family specifically expressed in early embryos. J Mol Evol (2007) 0.79
Cross-species comparison of biological themes and underlying genes on a global gene expression scale in a mouse model of colorectal liver metastasis and in clinical specimens. BMC Genomics (2008) 0.79
Transient RUNX1 Expression during Early Mesendodermal Differentiation of hESCs Promotes Epithelial to Mesenchymal Transition through TGFB2 Signaling. Stem Cell Reports (2016) 0.78
Gene targeting and Calcium handling efficiencies in mouse embryonic stem cell lines. World J Stem Cells (2010) 0.78
Establishing clonal cell lines with endothelial-like potential from CD9(hi), SSEA-1(-) cells in embryonic stem cell-derived embryoid bodies. PLoS One (2006) 0.77
Using biomarker signature patterns for an mRNA molecular diagnostic of mouse embryonic stem cell differentiation state. BMC Genomics (2007) 0.76
The architectural organization of human stem cell cycle regulatory machinery. Curr Pharm Des (2012) 0.76
Precocious Phenotypic Transcription-Factor Expression during Early Development. J Cell Biochem (2016) 0.75
Transcriptional differences between rhesus embryonic stem cells generated from in vitro and in vivo derived embryos. PLoS One (2012) 0.75
Derivation of Porcine Embryonic Stem-Like Cells from In Vitro-Produced Blastocyst-Stage Embryos. Sci Rep (2016) 0.75
Transcriptional Regulation of Human NANOG by Alternate Promoters in Embryonic Stem Cells. J Stem Cell Res Ther (2012) 0.75
Beta-catenin does not show nuclear location in undifferentiated murine embryonic stem cells. Dokl Biol Sci (2007) 0.75
Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20
A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39
Scalable molecular dynamics with NAMD. J Comput Chem (2005) 59.49
Alternative isoform regulation in human tissue transcriptomes. Nature (2008) 52.76
The diploid genome sequence of an Asian individual. Nature (2008) 46.29
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet (2007) 32.41
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
International network of cancer genome projects. Nature (2010) 20.35
Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27
Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet (2006) 17.19
A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell (2006) 14.70
An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proc Natl Acad Sci U S A (2005) 13.54
Breast cancer classification and prognosis based on gene expression profiles from a population-based study. Proc Natl Acad Sci U S A (2003) 13.00
Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. Nat Genet (2008) 12.51
An oestrogen-receptor-alpha-bound human chromatin interactome. Nature (2009) 12.16
piggyBac transposition reprograms fibroblasts to induced pluripotent stem cells. Nature (2009) 11.27
Sequencing of 50 human exomes reveals adaptation to high altitude. Science (2010) 11.27
MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature (2008) 9.83
Comment on " 'Stemness': transcriptional profiling of embryonic and adult stem cells" and "a stem cell molecular signature". Science (2003) 8.79
Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell (2010) 8.74
Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts. Breast Cancer Res (2005) 8.73
Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer. Cancer Res (2006) 8.08
A two-gene expression ratio predicts clinical outcome in breast cancer patients treated with tamoxifen. Cancer Cell (2004) 8.06
Automatic atom type and bond type perception in molecular mechanical calculations. J Mol Graph Model (2006) 7.93
Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nat Methods (2005) 7.87
Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat Biotechnol (2009) 7.59
The BATTLE trial: personalizing therapy for lung cancer. Cancer Discov (2011) 7.57
Mapping human genetic diversity in Asia. Science (2009) 7.40
Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat Biotechnol (2012) 7.37
Oncogenic Kras maintains pancreatic tumors through regulation of anabolic glucose metabolism. Cell (2012) 7.36
Acute renal failure and sepsis. N Engl J Med (2004) 7.18
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol (2010) 7.08
A core Klf circuitry regulates self-renewal of embryonic stem cells. Nat Cell Biol (2008) 6.90
Expansion of cancer care and control in countries of low and middle income: a call to action. Lancet (2010) 6.84
Pharmacologic disruption of Polycomb-repressive complex 2-mediated gene repression selectively induces apoptosis in cancer cells. Genes Dev (2007) 6.71
High-performance neuroprosthetic control by an individual with tetraplegia. Lancet (2012) 6.66
Resolution of cell fate decisions revealed by single-cell gene expression analysis from zygote to blastocyst. Dev Cell (2010) 6.24
Transcriptional regulation of nanog by OCT4 and SOX2. J Biol Chem (2005) 6.05
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci U S A (2009) 6.01
Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection. Lancet (2003) 5.99
Whole-genome cartography of estrogen receptor alpha binding sites. PLoS Genet (2007) 5.85
The dog genome: survey sequencing and comparative analysis. Science (2003) 5.84
Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res (2005) 5.71
New loci associated with kidney function and chronic kidney disease. Nat Genet (2010) 5.58
Antitumor activity of rapamycin in a Phase I trial for patients with recurrent PTEN-deficient glioblastoma. PLoS Med (2008) 5.54
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature (2008) 5.54
Predictive value for the Chinese population of the Framingham CHD risk assessment tool compared with the Chinese Multi-Provincial Cohort Study. JAMA (2004) 5.34
Chimeric transcript discovery by paired-end transcriptome sequencing. Proc Natl Acad Sci U S A (2009) 5.30
The oyster genome reveals stress adaptation and complexity of shell formation. Nature (2012) 5.30
De novo mutations in histone-modifying genes in congenital heart disease. Nature (2013) 5.15
Evidence for HIV-associated B cell exhaustion in a dysfunctional memory B cell compartment in HIV-infected viremic individuals. J Exp Med (2008) 5.14
MicroRNA-34b and MicroRNA-34c are targets of p53 and cooperate in control of cell proliferation and adhesion-independent growth. Cancer Res (2007) 4.95
RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol (2006) 4.93
Sall4 modulates embryonic stem cell pluripotency and early embryonic development by the transcriptional regulation of Pou5f1. Nat Cell Biol (2006) 4.81
Reciprocal transcriptional regulation of Pou5f1 and Sox2 via the Oct4/Sox2 complex in embryonic stem cells. Mol Cell Biol (2005) 4.54
SOX2, a persistent marker for multipotential neural stem cells derived from embryonic stem cells, the embryo or the adult. Dev Neurosci (2005) 4.48
Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res (2009) 4.47
MicroRNA-125b is a novel negative regulator of p53. Genes Dev (2009) 4.43
Reprogramming of fibroblasts into induced pluripotent stem cells with orphan nuclear receptor Esrrb. Nat Cell Biol (2009) 4.32
Hepatocyte growth factor induces gefitinib resistance of lung adenocarcinoma with epidermal growth factor receptor-activating mutations. Cancer Res (2008) 4.30
Relapse risk after discontinuation of risperidone in Alzheimer's disease. N Engl J Med (2012) 4.22
Probable limited person-to-person transmission of highly pathogenic avian influenza A (H5N1) virus in China. Lancet (2008) 4.17
EpCAM and alpha-fetoprotein expression defines novel prognostic subtypes of hepatocellular carcinoma. Cancer Res (2008) 4.17
Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage. Nat Biotechnol (2011) 3.97
Glycine decarboxylase activity drives non-small cell lung cancer tumor-initiating cells and tumorigenesis. Cell (2012) 3.92
Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis. Nature (2010) 3.90
Genomic alterations in cultured human embryonic stem cells. Nat Genet (2005) 3.89
Efficacy of RAD001 (everolimus) and octreotide LAR in advanced low- to intermediate-grade neuroendocrine tumors: results of a phase II study. J Clin Oncol (2008) 3.85
Pelvic Organ Support Study (POSST): the distribution, clinical definition, and epidemiologic condition of pelvic organ support defects. Am J Obstet Gynecol (2005) 3.85
A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Nature (2010) 3.84
Association between adverse clinical outcome in human disease caused by novel influenza A H7N9 virus and sustained viral shedding and emergence of antiviral resistance. Lancet (2013) 3.83
Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell (2013) 3.81
Epidemiological transition of stroke in China: twenty-one-year observational study from the Sino-MONICA-Beijing Project. Stroke (2008) 3.81
Natural selection on EPAS1 (HIF2alpha) associated with low hemoglobin concentration in Tibetan highlanders. Proc Natl Acad Sci U S A (2010) 3.78
Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res (2008) 3.76
Acute renal failure: definitions, diagnosis, pathogenesis, and therapy. J Clin Invest (2004) 3.75
Gene expression in human embryonic stem cell lines: unique molecular signature. Blood (2003) 3.73
Monitoring chronic lymphocytic leukemia progression by whole genome sequencing reveals heterogeneous clonal evolution patterns. Blood (2012) 3.63
Discovery and annotation of functional chromatin signatures in the human genome. PLoS Comput Biol (2009) 3.61
Residential proximity to naturally occurring asbestos and mesothelioma risk in California. Am J Respir Crit Care Med (2005) 3.55
Clinical application of massively parallel sequencing-based prenatal noninvasive fetal trisomy test for trisomies 21 and 18 in 11,105 pregnancies with mixed risk factors. Prenat Diagn (2012) 3.54
Surgical treatment of giant coronary artery aneurysm. J Thorac Cardiovasc Surg (2005) 3.53
ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome. PLoS Comput Biol (2008) 3.46
Gene expression profiles of BRCA1-linked, BRCA2-linked, and sporadic ovarian cancers. J Natl Cancer Inst (2002) 3.40
A proprotein convertase subtilisin/kexin type 9 neutralizing antibody reduces serum cholesterol in mice and nonhuman primates. Proc Natl Acad Sci U S A (2009) 3.39
Retinoic acid increases Foxp3+ regulatory T cells and inhibits development of Th17 cells by enhancing TGF-beta-driven Smad3 signaling and inhibiting IL-6 and IL-23 receptor expression. J Immunol (2008) 3.37
Characteristics associated with differences in survival among black and white women with breast cancer. JAMA (2013) 3.35
Effects of acupuncture on pregnancy rates in women undergoing in vitro fertilization: a systematic review and meta-analysis. Fertil Steril (2012) 3.33
Differences between human and mouse embryonic stem cells. Dev Biol (2004) 3.30