Published in PLoS Comput Biol on November 24, 2006
Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature (2011) 9.33
Reprogramming in vivo produces teratomas and iPS cells with totipotency features. Nature (2013) 2.47
Identification of Pou5f1, Sox2, and Nanog downstream target genes with statistical confidence by applying a novel algorithm to time course microarray and genome-wide chromatin immunoprecipitation data. BMC Genomics (2008) 2.27
Reprogramming DNA methylation in the mammalian life cycle: building and breaking epigenetic barriers. Philos Trans R Soc Lond B Biol Sci (2013) 1.70
Metastatic progression of prostate cancer and e-cadherin regulation by zeb1 and SRC family kinases. Am J Pathol (2011) 1.33
Acute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity. Nucleic Acids Res (2011) 1.10
Pluripotency-related, valproic acid (VPA)-induced genome-wide histone H3 lysine 9 (H3K9) acetylation patterns in embryonic stem cells. J Biol Chem (2011) 1.05
Do all roads lead to Oct4? the emerging concepts of induced pluripotency. Trends Cell Biol (2013) 0.98
Non-polyadenylated transcription in embryonic stem cells reveals novel non-coding RNA related to pluripotency and differentiation. Nucleic Acids Res (2013) 0.94
Functional analysis of Tcl1 using Tcl1-deficient mouse embryonic stem cells. PLoS One (2013) 0.79
Using biomarker signature patterns for an mRNA molecular diagnostic of mouse embryonic stem cell differentiation state. BMC Genomics (2007) 0.76
Metabolic remodeling during the loss and acquisition of pluripotency. Development (2017) 0.75
Manganese Superoxide Dismutase Gene Expression Is Induced by Nanog and Oct4, Essential Pluripotent Stem Cells' Transcription Factors. PLoS One (2015) 0.75
Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods (2001) 414.27
Bioconductor: open software development for computational biology and bioinformatics. Genome Biol (2004) 143.19
Statistical significance for genomewide studies. Proc Natl Acad Sci U S A (2003) 88.64
DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol (2003) 84.79
Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res (2003) 52.74
affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics (2004) 32.08
Establishment in culture of pluripotential cells from mouse embryos. Nature (1981) 30.49
Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell (1992) 27.80
Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells. Nat Genet (2000) 21.52
Derivation of completely cell culture-derived mice from early-passage embryonic stem cells. Proc Natl Acad Sci U S A (1993) 20.33
Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells. Cell (2003) 20.16
Isolation of a pluripotent cell line from early mouse embryos cultured in medium conditioned by teratocarcinoma stem cells. Proc Natl Acad Sci U S A (1981) 18.96
"Stemness": transcriptional profiling of embryonic and adult stem cells. Science (2002) 15.55
A stem cell molecular signature. Science (2002) 14.47
Multipotent cell lineages in early mouse development depend on SOX2 function. Genes Dev (2003) 12.38
Comment on " 'Stemness': transcriptional profiling of embryonic and adult stem cells" and "a stem cell molecular signature". Science (2003) 8.79
Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Res (2002) 7.29
Hybrid vigor, fetal overgrowth, and viability of mice derived by nuclear cloning and tetraploid embryo complementation. Proc Natl Acad Sci U S A (2001) 5.76
Expression pattern of the mouse T gene and its role in mesoderm formation. Nature (1990) 4.97
RESOURCERER: a database for annotating and linking microarray resources within and across species. Genome Biol (2001) 4.79
Gene expression patterns in human embryonic stem cells and human pluripotent germ cell tumors. Proc Natl Acad Sci U S A (2003) 4.67
Development of definitive endoderm from embryonic stem cells in culture. Development (2004) 4.61
Combining multiple microarray studies and modeling interstudy variation. Bioinformatics (2003) 4.38
Molecular signature of human embryonic stem cells and its comparison with the mouse. Dev Biol (2003) 3.95
Gene expression in human embryonic stem cell lines: unique molecular signature. Blood (2003) 3.73
Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis. PLoS Biol (2006) 3.52
Differences between human and mouse embryonic stem cells. Dev Biol (2004) 3.30
Incomplete reactivation of Oct4-related genes in mouse embryos cloned from somatic nuclei. Development (2003) 3.22
Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation. Nat Biotechnol (2004) 2.60
Ascorbic acid enhances differentiation of embryonic stem cells into cardiac myocytes. Circulation (2003) 2.54
Fbx15 is a novel target of Oct3/4 but is dispensable for embryonic stem cell self-renewal and mouse development. Mol Cell Biol (2003) 2.40
Murine embryonic stem cell differentiation is promoted by SOCS-3 and inhibited by the zinc finger transcription factor Klf4. Blood (2004) 2.35
Study of stem cell function using microarray experiments. FEBS Lett (2005) 2.28
Nestin mRNA expression correlates with the central nervous system progenitor cell state in many, but not all, regions of developing central nervous system. Brain Res Dev Brain Res (1995) 2.22
Specific expression of a retinoic acid-regulated, zinc-finger gene, Rex-1, in preimplantation embryos, trophoblast and spermatocytes. Development (1991) 2.11
Dax1 antagonizes Sry action in mammalian sex determination. Nature (1998) 1.88
Gene expression profiling of embryo-derived stem cells reveals candidate genes associated with pluripotency and lineage specificity. Genome Res (2002) 1.77
Statistical issues and methods for meta-analysis of microarray data: a case study in prostate cancer. Funct Integr Genomics (2003) 1.77
Transcriptome analysis of mouse stem cells and early embryos. PLoS Biol (2003) 1.75
Differences in gene expression between B-cell chronic lymphocytic leukemia and normal B cells: a meta-analysis of three microarray studies. Bioinformatics (2004) 1.72
Correlation of murine embryonic stem cell gene expression profiles with functional measures of pluripotency. Stem Cells (2005) 1.52
An integrated strategy for analyzing the unique developmental programs of different myoblast subtypes. PLoS Genet (2006) 1.51
Cell and tissue requirements for the gene eed during mouse gastrulation and organogenesis. Genesis (2001) 1.49
Gene expression analysis with the parametric bootstrap. Biostatistics (2001) 1.42
Expression of the fibroblast growth factor-5 gene in the mouse embryo. Development (1991) 1.39
Identifying differentially expressed genes from microarray experiments via statistic synthesis. Bioinformatics (2004) 1.39
Combining Affymetrix microarray results. BMC Bioinformatics (2005) 1.36
Functional and biochemical association of Hck with the LIF/IL-6 receptor signal transducing subunit gp130 in embryonic stem cells. EMBO J (1994) 1.27
Comment on " 'Stemness': transcriptional profiling of embryonic and adult stem cells" and "a stem cell molecular signature". Science (2003) 1.25
TCL1 participates in early embryonic development and is overexpressed in human seminomas. Proc Natl Acad Sci U S A (2002) 1.19
Stem cell bioengineering. Annu Rev Biomed Eng (2001) 1.17
Integrative analysis of multiple gene expression profiles with quality-adjusted effect size models. BMC Bioinformatics (2005) 1.17
Unique gene expression signature by human embryonic stem cells cultured under serum-free conditions correlates with their enhanced and prolonged growth in an undifferentiated stage. Stem Cells (2005) 0.97
Stem cell assays: something old, something new, something borrowed. Stem Cells (2004) 0.96
Cancer stem cells--perspectives on current status and future directions: AACR Workshop on cancer stem cells. Cancer Res (2006) 17.42
Purification and unique properties of mammary epithelial stem cells. Nature (2006) 15.98
The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature (2012) 11.91
Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res (2008) 10.18
Cancer stem cells: an evolving concept. Nat Rev Cancer (2012) 4.57
Steroid hormone receptor status of mouse mammary stem cells. J Natl Cancer Inst (2006) 4.47
A method for quantifying normal human mammary epithelial stem cells with in vivo regenerative ability. Nat Med (2008) 3.64
Rapid behavior-based identification of neuroactive small molecules in the zebrafish. Nat Chem Biol (2010) 2.87
Hematopoietic stem cells proliferate until after birth and show a reversible phase-specific engraftment defect. J Clin Invest (2006) 2.79
The hematopoietic stem compartment consists of a limited number of discrete stem cell subsets. Blood (2005) 2.79
Inhibition of mitochondrial translation as a therapeutic strategy for human acute myeloid leukemia. Cancer Cell (2011) 2.68
Differential expression of Hox, Meis1, and Pbx1 genes in primitive cells throughout murine hematopoietic ontogeny. Exp Hematol (2002) 2.53
Prospective isolation and molecular characterization of hematopoietic stem cells with durable self-renewal potential. Blood (2009) 2.41
A mouse atlas of gene expression: large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells. Proc Natl Acad Sci U S A (2005) 2.35
ZNF703 is a common Luminal B breast cancer oncogene that differentially regulates luminal and basal progenitors in human mammary epithelium. EMBO Mol Med (2011) 2.07
Hematopoietic stem cell heterogeneity takes center stage. Cell Stem Cell (2012) 1.94
High-throughput analysis of single hematopoietic stem cell proliferation in microfluidic cell culture arrays. Nat Methods (2011) 1.93
Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver. Genome Res (2010) 1.90
Loss-of-function Additional sex combs like 1 mutations disrupt hematopoiesis but do not cause severe myelodysplasia or leukemia. Blood (2009) 1.90
Targeting YB-1 in HER-2 overexpressing breast cancer cells induces apoptosis via the mTOR/STAT3 pathway and suppresses tumor growth in mice. Cancer Res (2008) 1.88
Targeting primitive chronic myeloid leukemia cells by effective inhibition of a new AHI-1-BCR-ABL-JAK2 complex. J Natl Cancer Inst (2013) 1.75
Epithelial progenitors in the normal human mammary gland. J Mammary Gland Biol Neoplasia (2005) 1.74
IVIg-mediated amelioration of murine ITP via FcgammaRIIB is independent of SHIP1, SHP-1, and Btk activity. Blood (2003) 1.73
SHIP-deficient mice are severely osteoporotic due to increased numbers of hyper-resorptive osteoclasts. Nat Med (2002) 1.71
Hematopoietic stem cell subtypes expand differentially during development and display distinct lymphopoietic programs. Cell Stem Cell (2012) 1.71
Alkaline phosphatase-positive colony formation is a sensitive, specific, and quantitative indicator of undifferentiated human embryonic stem cells. Stem Cells (2008) 1.69
Different in vivo repopulating activities of purified hematopoietic stem cells before and after being stimulated to divide in vitro with the same kinetics. Exp Hematol (2003) 1.69
Identification of a new intrinsically timed developmental checkpoint that reprograms key hematopoietic stem cell properties. Proc Natl Acad Sci U S A (2007) 1.68
The Lin28b-let-7-Hmga2 axis determines the higher self-renewal potential of fetal haematopoietic stem cells. Nat Cell Biol (2013) 1.67
Lessons learned from the analysis of gender effect on risk factors and procedural outcomes of lower extremity arterial disease. J Vasc Surg (2010) 1.61
Permanent and panerythroid correction of murine beta thalassemia by multiple lentiviral integration in hematopoietic stem cells. Proc Natl Acad Sci U S A (2002) 1.61
Quantitative profiling of ubiquitylated proteins reveals proteasome substrates and the substrate repertoire influenced by the Rpn10 receptor pathway. Mol Cell Proteomics (2007) 1.53
Correlation of murine embryonic stem cell gene expression profiles with functional measures of pluripotency. Stem Cells (2005) 1.52
Comprehensive analysis of mammalian miRNA* species and their role in myeloid cells. Blood (2011) 1.44
Ischemic colitis after endovascular aortoiliac aneurysm repair: a 10-year retrospective study. Arch Surg (2009) 1.43
Y-box binding protein-1 induces the expression of CD44 and CD49f leading to enhanced self-renewal, mammosphere growth, and drug resistance. Cancer Res (2010) 1.38
Identification of a long non-coding RNA as a novel biomarker and potential therapeutic target for metastatic prostate cancer. Oncotarget (2014) 1.38
Assessing differentiation status of human embryonic stem cells noninvasively using Raman microspectroscopy. Anal Chem (2010) 1.37
High-level beta-globin expression and preferred intragenic integration after lentiviral transduction of human cord blood stem cells. J Clin Invest (2004) 1.35
Deciphering the mammary epithelial cell hierarchy. Cell Cycle (2006) 1.34
Dynamics of the yeast transcriptome during wine fermentation reveals a novel fermentation stress response. FEMS Yeast Res (2008) 1.32
Cancer stem cells: Here, there, everywhere? Nature (2008) 1.32
Deregulated expression of HOXB4 enhances the primitive growth activity of human hematopoietic cells. Blood (2002) 1.30
Steel factor responsiveness regulates the high self-renewal phenotype of fetal hematopoietic stem cells. Blood (2007) 1.26
Aldehyde dehydrogenase activity is a biomarker of primitive normal human mammary luminal cells. Stem Cells (2012) 1.25
Characterization of mouse hematopoietic stem and progenitor cells. Curr Protoc Immunol (2008) 1.21
BCR/ABL and other kinases from chronic myeloproliferative disorders stimulate single-strand annealing, an unfaithful DNA double-strand break repair. Cancer Res (2008) 1.17
Rac2-MRC-cIII-generated ROS cause genomic instability in chronic myeloid leukemia stem cells and primitive progenitors. Blood (2012) 1.16
LongSAGE profiling of nine human embryonic stem cell lines. Genome Biol (2007) 1.15
Overexpression of a dominant negative form of STAT3 selectively impairs hematopoietic stem cell activity. Oncogene (2002) 1.15
Maturation of adult beta-cells revealed using a Pdx1/insulin dual-reporter lentivirus. Endocrinology (2008) 1.14
Near-maximal expansions of hematopoietic stem cells in culture using NUP98-HOX fusions. Exp Hematol (2007) 1.13
Analysis of the clonal growth and differentiation dynamics of primitive barcoded human cord blood cells in NSG mice. Blood (2013) 1.13
Enzymatic dissociation and culture of normal human mammary tissue to detect progenitor activity. Methods Mol Biol (2005) 1.12
The inositol 5'-phosphatase SHIP-1 and the Src kinase Lyn negatively regulate macrophage colony-stimulating factor-induced Akt activity. J Biol Chem (2003) 1.12
Open versus endovascular stent graft repair of abdominal aortic aneurysms: a meta-analysis of randomized trials. JACC Cardiovasc Interv (2012) 1.09
Unique effects of Stat3 on the early phase of hematopoietic stem cell regeneration. Blood (2006) 1.07
A yeast phenomic model for the gene interaction network modulating CFTR-ΔF508 protein biogenesis. Genome Med (2012) 1.06
Identification of transcripts with enriched expression in the developing and adult pancreas. Genome Biol (2008) 1.06
Steel factor coordinately regulates the molecular signature and biologic function of hematopoietic stem cells. Blood (2008) 1.05
Plasma miRNAs as biomarkers to identify patients with castration-resistant metastatic prostate cancer. Int J Mol Sci (2013) 1.04
Characterization of primitive hematopoietic cells from patients with dyskeratosis congenita. Blood (2008) 1.04
SAGE reveals expression of Wnt signalling pathway members during mouse prostate development. Gene Expr Patterns (2005) 1.03
Genomic instability of human mammary epithelial cells overexpressing a truncated form of EMSY. J Natl Cancer Inst (2005) 1.03
In situ analysis of living embryonic stem cells by coherent anti-stokes Raman microscopy. Anal Chem (2007) 1.02
Site-1 protease is essential for endochondral bone formation in mice. J Cell Biol (2007) 1.02
Analysis of gender-related differences in lower extremity peripheral arterial disease. J Vasc Surg (2010) 1.01
Anemia, thrombocytopenia, leukocytosis, extramedullary hematopoiesis, and impaired progenitor function in Pten+/-SHIP-/- mice: a novel model of myelodysplasia. Blood (2004) 1.01
Parallel assessment of globin lentiviral transfer in induced pluripotent stem cells and adult hematopoietic stem cells derived from the same transplanted β-thalassemia patient. Stem Cells (2013) 1.01
Expression of Groucho/TLE proteins during pancreas development. BMC Dev Biol (2008) 1.00
Common and distinct features of cytokine effects on hematopoietic stem and progenitor cells revealed by dose-response surface analysis. Biotechnol Bioeng (2002) 1.00
Synthetic lethal genetic interactions that decrease somatic cell proliferation in Caenorhabditis elegans identify the alternative RFC CTF18 as a candidate cancer drug target. Mol Biol Cell (2009) 0.97
Liver and marrow of adult mdr-1a/1b(-/-) mice show normal generation, function, and multi-tissue trafficking of primitive hematopoietic cells. Exp Hematol (2002) 0.97
Antagonistic effects of Grg6 and Groucho/TLE on the transcription repression activity of brain factor 1/FoxG1 and cortical neuron differentiation. Mol Cell Biol (2005) 0.97
The marrow homing efficiency of murine hematopoietic stem cells remains constant during ontogeny. Exp Hematol (2003) 0.97
Type IIB procollagen NH(2)-propeptide induces death of tumor cells via interaction with integrins alpha(V)beta(3) and alpha(V)beta(5). J Biol Chem (2010) 0.96
Enhanced generation of hematopoietic cells from human hepatocarcinoma cell-stimulated human embryonic and induced pluripotent stem cells. Exp Hematol (2009) 0.95
Synthetic lethality of cohesins with PARPs and replication fork mediators. PLoS Genet (2012) 0.95
Probing the mitotic history and developmental stage of hematopoietic cells using single telomere length analysis (STELA). Blood (2009) 0.95
The BRG1 chromatin remodeler protects against ovarian cysts, uterine tumors, and mammary tumors in a lineage-specific manner. PLoS One (2012) 0.94
Heterogeneity in hematopoietic stem cell populations: implications for transplantation. Curr Opin Hematol (2013) 0.93
Enhanced normal short-term human myelopoiesis in mice engineered to express human-specific myeloid growth factors. Blood (2012) 0.93
Spontaneous tibioperoneal trunk and anterior tibial artery pseudoaneurysms. Vasc Med (2012) 0.91
Quantitation of human mammary epithelial stem cells with in vivo regenerative properties using a subrenal capsule xenotransplantation assay. Nat Protoc (2010) 0.91
The emerging role of histone lysine demethylases in prostate cancer. Mol Cancer (2012) 0.91
Kinetics and genomic profiling of adult human and mouse β-cell maturation. Islets (2011) 0.90
Global analysis of yeast endosomal transport identifies the vps55/68 sorting complex. Mol Biol Cell (2008) 0.90
The non-coding transcriptome as a dynamic regulator of cancer metastasis. Cancer Metastasis Rev (2014) 0.89
Developmental changes in hematopoietic stem cell properties. Exp Mol Med (2013) 0.89
Developmental changes in the in vitro activated regenerative activity of primitive mammary epithelial cells. PLoS Biol (2013) 0.89
Modeling human hematopoietic cell development from pluripotent stem cells. Exp Hematol (2012) 0.88
Logistic equations effectively model Mammalian cell batch and fed-batch kinetics by logically constraining the fit. Biotechnol Prog (2005) 0.88
The future of mammary stem cell biology: the power of in vivo transplants. Breast Cancer Res (2008) 0.88