Published in BMC Genomics on July 20, 2009
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Rare coding variants in the phospholipase D3 gene confer risk for Alzheimer's disease. Nature (2013) 2.79
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Systems analysis of human brain gene expression: mechanisms for HIV-associated neurocognitive impairment and common pathways with Alzheimer's disease. BMC Med Genomics (2013) 0.86
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Integrating mRNA and miRNA Weighted Gene Co-Expression Networks with eQTLs in the Nucleus Accumbens of Subjects with Alcohol Dependence. PLoS One (2015) 0.77
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Module Based Differential Coexpression Analysis Method for Type 2 Diabetes. Biomed Res Int (2015) 0.76
Differential gene network analysis for the identification of asthma-associated therapeutic targets in allergen-specific T-helper memory responses. BMC Med Genomics (2016) 0.76
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Analysis of time-resolved gene expression measurements across individuals. PLoS One (2013) 0.76
Transcriptomic analysis reveals abnormal muscle repair and remodeling in survivors of critical illness with sustained weakness. Sci Rep (2016) 0.75
Integrated analysis of genetic, behavioral, and biochemical data implicates neural stem cell-induced changes in immunity, neurotransmission and mitochondrial function in Dementia with Lewy Body mice. Acta Neuropathol Commun (2017) 0.75
An evolutionary game approach for determination of the structural conflicts in signed networks. Sci Rep (2016) 0.75
Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction. Nucleic Acids Res (2016) 0.75
Identification of prognostic markers of high grade prostate cancer through an integrated bioinformatics approach. J Cancer Res Clin Oncol (2017) 0.75
Screening of Critical Genes and MicroRNAs in Blood Samples of Patients with Ruptured Intracranial Aneurysms by Bioinformatic Analysis of Gene Expression Data. Med Sci Monit (2017) 0.75
Comparing brain graphs in which nodes are regions of interest or independent components: a simulation study. J Neurosci Methods (2017) 0.75
Overexpression of Topoisomerase 2-Alpha Confers a Poor Prognosis in Pancreatic Adenocarcinoma Identified by Co-Expression Analysis. Dig Dis Sci (2017) 0.75
Excavation of attractor modules for nasopharyngeal carcinoma via integrating systemic module inference with attract method. Braz J Med Biol Res (2017) 0.75
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Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell (2007) 101.42
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Induced pluripotent stem cell lines derived from human somatic cells. Science (2007) 71.50
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature (2007) 65.18
A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell (2006) 48.80
Reprogramming of human somatic cells to pluripotency with defined factors. Nature (2007) 30.84
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell (2008) 28.29
Control of developmental regulators by Polycomb in human embryonic stem cells. Cell (2006) 28.21
Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature (2006) 25.90
A chromatin landmark and transcription initiation at most promoters in human cells. Cell (2007) 23.41
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Generation of induced pluripotent stem cells without Myc from mouse and human fibroblasts. Nat Biotechnol (2007) 21.93
Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution. Cell Stem Cell (2007) 21.58
The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat Genet (2006) 20.76
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The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells. Cell (2003) 17.72
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An extended transcriptional network for pluripotency of embryonic stem cells. Cell (2008) 14.64
Selective blockade of microRNA processing by Lin28. Science (2008) 14.39
Generation of human induced pluripotent stem cells from dermal fibroblasts. Proc Natl Acad Sci U S A (2008) 13.09
Dissecting self-renewal in stem cells with RNA interference. Nature (2006) 11.66
Loss of cyclophilin D reveals a critical role for mitochondrial permeability transition in cell death. Nature (2005) 11.22
Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. Bioinformatics (2007) 7.72
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Functional organization of the transcriptome in human brain. Nat Neurosci (2008) 7.02
A core Klf circuitry regulates self-renewal of embryonic stem cells. Nat Cell Biol (2008) 6.90
Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target. Proc Natl Acad Sci U S A (2006) 6.33
Integrating genetic and network analysis to characterize genes related to mouse weight. PLoS Genet (2006) 5.82
Conservation and evolution of gene coexpression networks in human and chimpanzee brains. Proc Natl Acad Sci U S A (2006) 5.69
Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation. Cell Stem Cell (2008) 5.40
Two supporting factors greatly improve the efficiency of human iPSC generation. Cell Stem Cell (2008) 5.04
Regulatory networks define phenotypic classes of human stem cell lines. Nature (2008) 4.98
Geometric interpretation of gene coexpression network analysis. PLoS Comput Biol (2008) 4.57
Stem-cell-based therapy and lessons from the heart. Nature (2008) 4.54
A gene expression network model of type 2 diabetes links cell cycle regulation in islets with diabetes susceptibility. Genome Res (2008) 4.33
Eigengene networks for studying the relationships between co-expression modules. BMC Syst Biol (2007) 4.06
Gene connectivity, function, and sequence conservation: predictions from modular yeast co-expression networks. BMC Genomics (2006) 3.87
Gene network interconnectedness and the generalized topological overlap measure. BMC Bioinformatics (2007) 3.83
Weighted gene coexpression network analysis strategies applied to mouse weight. Mamm Genome (2007) 3.59
Understanding network concepts in modules. BMC Syst Biol (2007) 3.28
Cathepsin L proteolytically processes histone H3 during mouse embryonic stem cell differentiation. Cell (2008) 3.09
A gene regulatory network in mouse embryonic stem cells. Proc Natl Acad Sci U S A (2007) 2.94
Cell cycle control of embryonic stem cells. Stem Cell Rev (2005) 2.64
Transcriptional coordination of the metabolic network in Arabidopsis. Plant Physiol (2006) 2.36
Network neighborhood analysis with the multi-node topological overlap measure. Bioinformatics (2006) 2.35
Orphan nuclear receptor LRH-1 is required to maintain Oct4 expression at the epiblast stage of embryonic development. Mol Cell Biol (2005) 2.32
Dynamic changes in mitochondrial biogenesis and antioxidant enzymes during the spontaneous differentiation of human embryonic stem cells. Biochem Biophys Res Commun (2006) 2.15
Downregulation of multiple stress defense mechanisms during differentiation of human embryonic stem cells. Stem Cells (2007) 2.07
Integrated weighted gene co-expression network analysis with an application to chronic fatigue syndrome. BMC Syst Biol (2008) 1.93
Proteomic analysis of the mouse liver mitochondrial inner membrane. J Biol Chem (2003) 1.86
Interaction of the metalloprotease disintegrins MDC9 and MDC15 with two SH3 domain-containing proteins, endophilin I and SH3PX1. J Biol Chem (1999) 1.85
Transcriptome analysis of mouse stem cells and early embryos. PLoS Biol (2003) 1.75
Connecting genes, coexpression modules, and molecular signatures to environmental stress phenotypes in plants. BMC Syst Biol (2008) 1.64
Systematic discovery of functional modules and context-specific functional annotation of human genome. Bioinformatics (2007) 1.61
Prediction and testing of novel transcriptional networks regulating embryonic stem cell self-renewal and commitment. Cell Stem Cell (2007) 1.56
A nonclassical bHLH Rbpj transcription factor complex is required for specification of GABAergic neurons independent of Notch signaling. Genes Dev (2008) 1.54
Nuclear pore composition regulates neural stem/progenitor cell differentiation in the mouse embryo. Dev Cell (2008) 1.46
Oct4 RNA interference induces trophectoderm differentiation in mouse embryonic stem cells. Genesis (2003) 1.30
UTF1 is a chromatin-associated protein involved in ES cell differentiation. J Cell Biol (2007) 1.24
Mitochondria in stem cells. Mitochondrion (2007) 1.22
Deficiency of the G-protein alpha-subunit G(s)alpha in osteoblasts leads to differential effects on trabecular and cortical bone. J Biol Chem (2005) 1.19
NRAGE mediates p38 activation and neural progenitor apoptosis via the bone morphogenetic protein signaling cascade. Mol Cell Biol (2005) 1.14
Oct-3/4 maintains the proliferative embryonic stem cell state via specific binding to a variant octamer sequence in the regulatory region of the UTF1 locus. Mol Cell Biol (2005) 1.14
Expression of a mouse zinc finger protein gene in both spermatocytes and oocytes during meiosis. Dev Biol (1992) 1.06
Regenerative medicine and human models of human disease. Nature (2008) 1.06
Inferring transcriptional compensation interactions in yeast via stepwise structure equation modeling. BMC Bioinformatics (2008) 1.03
Expression and roles of connective tissue growth factor in Meckel's cartilage development. Dev Dyn (2004) 0.93
The associated contributions of p53 and the DNA mismatch repair protein Msh6 to spontaneous tumorigenesis. Carcinogenesis (2007) 0.84
Mitochondrial benzodiazepine receptors regulate oxygen homeostasis in the early mouse embryo. Reprod Toxicol (2003) 0.81
A search engine to identify pathway genes from expression data on multiple organisms. BMC Syst Biol (2007) 0.79
A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell (2006) 48.80
Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature (2006) 25.90
Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution. Cell Stem Cell (2007) 21.58
WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics (2008) 18.58
A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol (2005) 17.23
Molecular determinants of the response of glioblastomas to EGFR kinase inhibitors. N Engl J Med (2005) 15.42
Variations in DNA elucidate molecular networks that cause disease. Nature (2008) 12.04
Transcriptomic analysis of autistic brain reveals convergent molecular pathology. Nature (2011) 10.16
DNA methylation-related chromatin remodeling in activity-dependent BDNF gene regulation. Science (2003) 8.81
Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures. Cell Stem Cell (2009) 8.62
Gene expression profiling of gliomas strongly predicts survival. Cancer Res (2004) 7.79
Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. Bioinformatics (2007) 7.72
DNA methylation age of human tissues and cell types. Genome Biol (2013) 7.48
Role of the murine reprogramming factors in the induction of pluripotency. Cell (2009) 7.46
Identification and classification of chromosomal aberrations in human induced pluripotent stem cells. Cell Stem Cell (2010) 7.16
Global histone modification patterns predict risk of prostate cancer recurrence. Nature (2005) 7.03
Functional organization of the transcriptome in human brain. Nat Neurosci (2008) 7.02
Efficient method to generate single-copy transgenic mice by site-specific integration in embryonic stem cells. Genesis (2006) 6.64
Integrating genetic and network analysis to characterize genes related to mouse weight. PLoS Genet (2006) 5.82
Conservation and evolution of gene coexpression networks in human and chimpanzee brains. Proc Natl Acad Sci U S A (2006) 5.69
Antitumor activity of rapamycin in a Phase I trial for patients with recurrent PTEN-deficient glioblastoma. PLoS Med (2008) 5.54
Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation. Cell Stem Cell (2008) 5.40
Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons. Nat Neurosci (2010) 5.12
Epigenetic reprogramming and induced pluripotency. Development (2009) 4.90
Chd1 regulates open chromatin and pluripotency of embryonic stem cells. Nature (2009) 4.13
The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science (2013) 4.12
Eigengene networks for studying the relationships between co-expression modules. BMC Syst Biol (2007) 4.06
Retinoic acid regulates sex-specific timing of meiotic initiation in mice. Proc Natl Acad Sci U S A (2006) 3.94
Gene connectivity, function, and sequence conservation: predictions from modular yeast co-expression networks. BMC Genomics (2006) 3.87
Gene network interconnectedness and the generalized topological overlap measure. BMC Bioinformatics (2007) 3.83
Identification of molecular subtypes of glioblastoma by gene expression profiling. Oncogene (2003) 3.83
Weighted gene coexpression network analysis strategies applied to mouse weight. Mamm Genome (2007) 3.59
Epigenetic predictor of age. PLoS One (2011) 3.46
Elucidating the role of gonadal hormones in sexually dimorphic gene coexpression networks. Endocrinology (2008) 3.38
Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis. Genome Res (2009) 3.36
Analysis of the phosphatidylinositol 3'-kinase signaling pathway in glioblastoma patients in vivo. Cancer Res (2003) 3.36
Optimizing the detection of lung cancer patients harboring anaplastic lymphoma kinase (ALK) gene rearrangements potentially suitable for ALK inhibitor treatment. Clin Cancer Res (2010) 3.30
Understanding network concepts in modules. BMC Syst Biol (2007) 3.28
Carbonic anhydrase IX is an independent predictor of survival in advanced renal clear cell carcinoma: implications for prognosis and therapy. Clin Cancer Res (2003) 3.25
Gene expression profiling identifies molecular subtypes of gliomas. Oncogene (2003) 3.13
Fusion of EML4 and ALK is associated with development of lung adenocarcinomas lacking EGFR and KRAS mutations and is correlated with ALK expression. Mol Cancer (2010) 3.06
Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing. Nature (2013) 3.06
Aging effects on DNA methylation modules in human brain and blood tissue. Genome Biol (2012) 3.05
Relations among positive parenting, children's effortful control, and externalizing problems: a three-wave longitudinal study. Child Dev (2005) 3.03
Broader implications of defining standards for the pluripotency of iPSCs. Cell Stem Cell (2009) 3.03
Identification of inflammatory gene modules based on variations of human endothelial cell responses to oxidized lipids. Proc Natl Acad Sci U S A (2006) 3.03
ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells. Proc Natl Acad Sci U S A (2009) 2.96
Is my network module preserved and reproducible? PLoS Comput Biol (2011) 2.91
Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism. Cell (2013) 2.87
Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways. Proc Natl Acad Sci U S A (2010) 2.85
Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors. Proc Natl Acad Sci U S A (2010) 2.81
Transcriptional competence and the active marking of tissue-specific enhancers by defined transcription factors in embryonic and induced pluripotent stem cells. Genes Dev (2009) 2.70
Retracted Mutations in CLCN2 encoding a voltage-gated chloride channel are associated with idiopathic generalized epilepsies. Nat Genet (2003) 2.70
Differential sensitivity of glioma- versus lung cancer-specific EGFR mutations to EGFR kinase inhibitors. Cancer Discov (2012) 2.61
Female human iPSCs retain an inactive X chromosome. Cell Stem Cell (2010) 2.59
ERM is required for transcriptional control of the spermatogonial stem cell niche. Nature (2005) 2.58
X-inactivation in female human embryonic stem cells is in a nonrandom pattern and prone to epigenetic alterations. Proc Natl Acad Sci U S A (2008) 2.53
Understanding mother-adolescent conflict discussions: concurrent and across-time prediction from youths' dispositions and parenting. Monogr Soc Res Child Dev (2008) 2.53
Using genetic markers to orient the edges in quantitative trait networks: the NEO software. BMC Syst Biol (2008) 2.51
Directed differentiation of human-induced pluripotent stem cells generates active motor neurons. Stem Cells (2009) 2.51
Pancreatic β cell identity is maintained by DNA methylation-mediated repression of Arx. Dev Cell (2011) 2.49
Dynamic expression of de novo DNA methyltransferases Dnmt3a and Dnmt3b in the central nervous system. J Neurosci Res (2005) 2.42
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Network neighborhood analysis with the multi-node topological overlap measure. Bioinformatics (2006) 2.35
Kidney transplant rejection and tissue injury by gene profiling of biopsies and peripheral blood lymphocytes. Am J Transplant (2004) 2.35
A positive autoregulatory loop of Jak-STAT signaling controls the onset of astrogliogenesis. Nat Neurosci (2005) 2.30
Gene expression analysis of glioblastomas identifies the major molecular basis for the prognostic benefit of younger age. BMC Med Genomics (2008) 2.29
Global levels of histone modifications predict prognosis in different cancers. Am J Pathol (2009) 2.28
Abnormal CpG island methylation occurs during in vitro differentiation of human embryonic stem cells. Hum Mol Genet (2006) 2.27
Histone h3 lysine 56 acetylation is linked to the core transcriptional network in human embryonic stem cells. Mol Cell (2009) 2.27
A systems genetics approach implicates USF1, FADS3, and other causal candidate genes for familial combined hyperlipidemia. PLoS Genet (2009) 2.24
EGFR signaling through an Akt-SREBP-1-dependent, rapamycin-resistant pathway sensitizes glioblastomas to antilipogenic therapy. Sci Signal (2009) 2.23
IFN-gamma mediates CD4+ T-cell loss and impairs secondary antitumor responses after successful initial immunotherapy. Nat Med (2007) 2.23
Longitudinal relations of children's effortful control, impulsivity, and negative emotionality to their externalizing, internalizing, and co-occurring behavior problems. Dev Psychol (2009) 2.20
Epidermal growth factor receptor mutations and their correlation with gefitinib therapy in patients with non-small cell lung cancer: a meta-analysis based on updated individual patient data from six medical centers in mainland China. J Thorac Oncol (2007) 2.15
A heterozygous moth genome provides insights into herbivory and detoxification. Nat Genet (2013) 2.13
Neurosphere formation is an independent predictor of clinical outcome in malignant glioma. Stem Cells (2009) 2.10
MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data. Nucleic Acids Res (2012) 2.09
BCOR regulates mesenchymal stem cell function by epigenetic mechanisms. Nat Cell Biol (2009) 2.04
Arabidopsis hapless mutations define essential gametophytic functions. Genetics (2004) 2.04
Molecular characterization of meiotic recombination across the 140-kb multigenic a1-sh2 interval of maize. Proc Natl Acad Sci U S A (2002) 1.98
Maternal embryonic leucine zipper kinase is a key regulator of the proliferation of malignant brain tumors, including brain tumor stem cells. J Neurosci Res (2008) 1.96
Strategies for aggregating gene expression data: the collapseRows R function. BMC Bioinformatics (2011) 1.96
Derivation of primordial germ cells from human embryonic and induced pluripotent stem cells is significantly improved by coculture with human fetal gonadal cells. Stem Cells (2009) 1.94
Integrated weighted gene co-expression network analysis with an application to chronic fatigue syndrome. BMC Syst Biol (2008) 1.93
Sexually dimorphic gene expression in mouse brain precedes gonadal differentiation. Brain Res Mol Brain Res (2003) 1.93
Tumor classification by tissue microarray profiling: random forest clustering applied to renal cell carcinoma. Mod Pathol (2005) 1.89
The role of DNA methylation in the central nervous system and neuropsychiatric disorders. Int Rev Neurobiol (2009) 1.89
Gain-of-function mutation S422L in the KCNJ8-encoded cardiac K(ATP) channel Kir6.1 as a pathogenic substrate for J-wave syndromes. Heart Rhythm (2010) 1.89
Reprogrammed mouse fibroblasts differentiate into cells of the cardiovascular and hematopoietic lineages. Stem Cells (2008) 1.83
Identification of enriched driver gene alterations in subgroups of non-small cell lung cancer patients based on histology and smoking status. PLoS One (2012) 1.82
Molecular analyses of human induced pluripotent stem cells and embryonic stem cells. Cell Stem Cell (2010) 1.81
DNA methylation and its basic function. Neuropsychopharmacology (2012) 1.76
The organization of the transcriptional network in specific neuronal classes. Mol Syst Biol (2009) 1.74
Epigenetics of reprogramming to induced pluripotency. Cell (2013) 1.73
Fast R Functions for Robust Correlations and Hierarchical Clustering. J Stat Softw (2012) 1.72