Published in Nat Biotechnol on March 29, 2009
Human DNA methylomes at base resolution show widespread epigenomic differences. Nature (2009) 34.27
Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics (2010) 17.53
Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature (2011) 13.94
Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet (2010) 10.71
Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat Genet (2009) 10.54
Somatic coding mutations in human induced pluripotent stem cells. Nature (2011) 9.50
Increased methylation variation in epigenetic domains across cancer types. Nat Genet (2011) 8.92
Target-enrichment strategies for next-generation sequencing. Nat Methods (2010) 8.78
Dynamic changes in the human methylome during differentiation. Genome Res (2010) 7.96
Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders. Science (2012) 6.21
Induced pluripotency: history, mechanisms, and applications. Genes Dev (2010) 4.89
Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells. Mol Cell (2011) 4.89
Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells. Nat Cell Biol (2011) 4.77
Polycomb group proteins: navigators of lineage pathways led astray in cancer. Nat Rev Cancer (2009) 4.40
Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human. Nat Methods (2009) 4.38
Finding the fifth base: genome-wide sequencing of cytosine methylation. Genome Res (2009) 4.16
Recapitulation of premature ageing with iPSCs from Hutchinson-Gilford progeria syndrome. Nature (2011) 3.56
Exome sequencing: the sweet spot before whole genomes. Hum Mol Genet (2010) 3.50
Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. Genome Res (2010) 3.17
High-throughput bisulfite sequencing in mammalian genomes. Methods (2009) 3.14
High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Res (2009) 3.08
Contribution of intragenic DNA methylation in mouse gametic DNA methylomes to establish oocyte-specific heritable marks. PLoS Genet (2012) 2.89
DNA methylation of the first exon is tightly linked to transcriptional silencing. PLoS One (2011) 2.80
Harnessing the potential of induced pluripotent stem cells for regenerative medicine. Nat Cell Biol (2011) 2.74
Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process. Nucleic Acids Res (2010) 2.72
Energy metabolism in human pluripotent stem cells and their differentiated counterparts. PLoS One (2011) 2.64
Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage. Genome Res (2010) 2.61
The expanding scope of DNA sequencing. Nat Biotechnol (2012) 2.57
Cell type-specific DNA methylation at intragenic CpG islands in the immune system. Genome Res (2011) 2.51
Multiplex padlock targeted sequencing reveals human hypermutable CpG variations. Genome Res (2009) 2.38
Generation of endoderm-derived human induced pluripotent stem cells from primary hepatocytes. Hepatology (2010) 2.31
The metabolome of induced pluripotent stem cells reveals metabolic changes occurring in somatic cell reprogramming. Cell Res (2011) 2.30
Induced pluripotent stem cells: opportunities and challenges. Philos Trans R Soc Lond B Biol Sci (2011) 2.09
Tackling the epigenome: challenges and opportunities for collaboration. Nat Biotechnol (2010) 2.04
Molecular analyses of human induced pluripotent stem cells and embryonic stem cells. Cell Stem Cell (2010) 1.81
DNA methylation and cellular reprogramming. Trends Cell Biol (2010) 1.77
Induced pluripotent stem cells: developmental biology to regenerative medicine. Nat Rev Cardiol (2010) 1.71
Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells. Proc Natl Acad Sci U S A (2012) 1.69
Epigenomics reveals a functional genome anatomy and a new approach to common disease. Nat Biotechnol (2010) 1.56
Genome-wide survey reveals dynamic widespread tissue-specific changes in DNA methylation during development. BMC Genomics (2011) 1.56
Large-scale de novo DNA synthesis: technologies and applications. Nat Methods (2014) 1.51
Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing. Genome Res (2012) 1.50
Reprogramming within hours following nuclear transfer into mouse but not human zygotes. Nat Commun (2011) 1.49
Developing safe therapies from human pluripotent stem cells. Nat Biotechnol (2009) 1.48
Epigenome mapping in normal and disease States. Circ Res (2010) 1.47
The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells. Mol Syst Biol (2011) 1.44
A novel and well-defined benchmarking method for second generation read mapping. BMC Bioinformatics (2011) 1.44
Applications of targeted gene capture and next-generation sequencing technologies in studies of human deafness and other genetic disabilities. Hear Res (2012) 1.43
High-quality DNA sequence capture of 524 disease candidate genes. Proc Natl Acad Sci U S A (2011) 1.41
Methylation Markers for the Identification of Body Fluids and Tissues from Forensic Trace Evidence. PLoS One (2016) 1.40
The DNA methylome. FEBS Lett (2010) 1.38
Genetic and epigenetic stability of human pluripotent stem cells. Nat Rev Genet (2012) 1.38
20 years of Nature Biotechnology research tools. Nat Biotechnol (2016) 1.38
Library-free methylation sequencing with bisulfite padlock probes. Nat Methods (2012) 1.37
Allele-specific methylation in the human genome: implications for genetic studies of complex disease. Epigenetics (2010) 1.37
Epigenetic regulation of oligodendrocyte identity. Trends Neurosci (2010) 1.36
De novo DNA methylation by Dnmt3a and Dnmt3b is dispensable for nuclear reprogramming of somatic cells to a pluripotent state. Genes Dev (2011) 1.32
Differentiation-defective phenotypes revealed by large-scale analyses of human pluripotent stem cells. Proc Natl Acad Sci U S A (2013) 1.32
Different binding properties and function of CXXC zinc finger domains in Dnmt1 and Tet1. PLoS One (2011) 1.30
Rapid identification of heterozygous mutations in Drosophila melanogaster using genomic capture sequencing. Genome Res (2010) 1.26
Epigenetic regulation in pluripotent stem cells: a key to breaking the epigenetic barrier. Philos Trans R Soc Lond B Biol Sci (2013) 1.26
A sensitive mass spectrometry method for simultaneous quantification of DNA methylation and hydroxymethylation levels in biological samples. Anal Biochem (2011) 1.26
Methods in DNA methylation profiling. Epigenomics (2009) 1.25
MIPgen: optimized modeling and design of molecular inversion probes for targeted resequencing. Bioinformatics (2014) 1.23
Cytosine DNA methylation is found in Drosophila melanogaster but absent in Saccharomyces cerevisiae, Schizosaccharomyces pombe, and other yeast species. Anal Chem (2014) 1.23
Production of embryonic and fetal-like red blood cells from human induced pluripotent stem cells. PLoS One (2011) 1.19
Tissue-specific variation in DNA methylation levels along human chromosome 1. Epigenetics Chromatin (2009) 1.19
Profiling DNA methylomes from microarray to genome-scale sequencing. Technol Cancer Res Treat (2010) 1.17
A decade of transcription factor-mediated reprogramming to pluripotency. Nat Rev Mol Cell Biol (2016) 1.16
Dedifferentiation and reprogramming: origins of cancer stem cells. EMBO Rep (2014) 1.16
The 22q11.2 microdeletion: fifteen years of insights into the genetic and neural complexity of psychiatric disorders. Int J Dev Neurosci (2010) 1.16
Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing. Nucleic Acids Res (2011) 1.15
Pre-B cell to macrophage transdifferentiation without significant promoter DNA methylation changes. Nucleic Acids Res (2011) 1.15
DNA synthesis is required for reprogramming mediated by stem cell fusion. Cell (2013) 1.14
Defining hypo-methylated regions of stem cell-specific promoters in human iPS cells derived from extra-embryonic amnions and lung fibroblasts. PLoS One (2010) 1.11
DNA methylation in embryonic stem cells. J Cell Biochem (2010) 1.11
High-throughput method for analyzing methylation of CpGs in targeted genomic regions. Proc Natl Acad Sci U S A (2010) 1.08
Induced pluripotent mesenchymal stromal cell clones retain donor-derived differences in DNA methylation profiles. Mol Ther (2012) 1.07
Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples. Genome Res (2010) 1.07
Genomic approaches to deconstruct pluripotency. Annu Rev Genomics Hum Genet (2011) 1.06
Genome-wide DNA methylation maps in follicular lymphoma cells determined by methylation-enriched bisulfite sequencing. PLoS One (2010) 1.06
Pluripotent stem cell energy metabolism: an update. EMBO J (2014) 1.05
Oxidative stress and DNA methylation in prostate cancer. Obstet Gynecol Int (2010) 1.03
Application of microdroplet PCR for large-scale targeted bisulfite sequencing. Genome Res (2011) 1.01
Contribution of hepatic lineage stage-specific donor memory to the differential potential of induced mouse pluripotent stem cells. Stem Cells (2012) 1.00
DNA methylation programming and reprogramming in primate embryonic stem cells. Genome Res (2009) 0.99
Dissecting DNA hypermethylation in cancer. FEBS Lett (2010) 0.98
Analyzing the cancer methylome through targeted bisulfite sequencing. Cancer Lett (2012) 0.96
Strategies for discovery and validation of methylated and hydroxymethylated DNA biomarkers. Cancer Med (2012) 0.96
Next generation sequencing based approaches to epigenomics. Brief Funct Genomics (2010) 0.95
Diametrically opposite methylome-transcriptome relationships in high- and low-CpG promoter genes in postmitotic neural rat tissue. Epigenetics (2012) 0.95
Epigenetic mechanisms involved in developmental nutritional programming. World J Diabetes (2011) 0.95
Insulin-producing surrogate β-cells from embryonic stem cells: are we there yet? Mol Ther (2011) 0.94
The case for induced pluripotent stem cell-derived cardiomyocytes in pharmacological screening. Br J Pharmacol (2013) 0.94
In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes. Nucleic Acids Res (2013) 0.94
Genome-wide epigenetic modifications in cancer. Prog Drug Res (2011) 0.93
The application of next generation sequencing in DNA methylation analysis. Genes (Basel) (2010) 0.93
Genome-wide genetic variations are highly correlated with proximal DNA methylation patterns. Genome Res (2012) 0.93
Comparison of the molecular profiles of human embryonic and induced pluripotent stem cells of isogenic origin. Stem Cell Res (2013) 0.92
Analysis of TET expression/activity and 5mC oxidation during normal and malignant germ cell development. PLoS One (2013) 0.92
DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol (2003) 84.79
Induced pluripotent stem cell lines derived from human somatic cells. Science (2007) 71.50
SOAP: short oligonucleotide alignment program. Bioinformatics (2008) 68.13
Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell (2008) 32.65
Reprogramming of human somatic cells to pluripotency with defined factors. Nature (2007) 30.84
Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature (2008) 30.29
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol (2009) 27.17
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature (2008) 26.78
CpG islands in vertebrate genomes. J Mol Biol (1987) 23.16
The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet (2009) 18.90
DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet (2006) 18.08
Dissecting direct reprogramming through integrative genomic analysis. Nature (2008) 16.47
A large genome center's improvements to the Illumina sequencing system. Nat Methods (2008) 15.56
DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet (2008) 15.45
Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell (2006) 15.24
Multiplex amplification of large sets of human exons. Nat Methods (2007) 15.11
Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol (2009) 11.18
Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res (2005) 8.69
Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res (2008) 8.62
High-throughput DNA methylation profiling using universal bead arrays. Genome Res (2006) 8.05
Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat Biotechnol (2003) 7.02
Gene body-specific methylation on the active X chromosome. Science (2007) 6.33
Nuclear reprogramming of somatic cells after fusion with human embryonic stem cells. Science (2005) 6.14
A high-efficiency system for the generation and study of human induced pluripotent stem cells. Cell Stem Cell (2008) 5.99
Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res (2006) 5.99
Regulatory networks define phenotypic classes of human stem cell lines. Nature (2008) 4.98
DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project. PLoS Biol (2004) 4.96
The DNA methylation paradox. Trends Genet (1999) 4.40
Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. Cancer Res (2007) 3.40
Human embryonic stem cells have a unique epigenetic signature. Genome Res (2006) 2.89
Genome-wide analysis of DNA methylation patterns. Development (2007) 2.13
A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39
Induced pluripotent stem cell lines derived from human somatic cells. Science (2007) 71.50
Scalable molecular dynamics with NAMD. J Comput Chem (2005) 59.49
The diploid genome sequence of an Asian individual. Nature (2008) 46.29
Human DNA methylomes at base resolution show widespread epigenomic differences. Nature (2009) 34.27
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet (2007) 32.41
Reprogramming of human somatic cells to pluripotency with defined factors. Nature (2007) 30.84
In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state. Nature (2007) 28.24
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol (2009) 27.17
Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution. Cell Stem Cell (2007) 21.58
Accurate multiplex polony sequencing of an evolved bacterial genome. Science (2005) 20.91
Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27
Disease-specific induced pluripotent stem cells. Cell (2008) 16.95
Multiplex amplification of large sets of human exons. Nat Methods (2007) 15.11
Selective blockade of microRNA processing by Lin28. Science (2008) 14.39
Induced pluripotent stem cells generated from patients with ALS can be differentiated into motor neurons. Science (2008) 14.26
Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA. Cell Stem Cell (2010) 14.18
Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature (2011) 13.94
MOM: maximum oligonucleotide mapping. Bioinformatics (2009) 13.75
Induced pluripotent stem cells generated without viral integration. Science (2008) 13.38
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
Defining molecular cornerstones during fibroblast to iPS cell reprogramming in mouse. Cell Stem Cell (2008) 12.45
Induced pluripotent stem cells from a spinal muscular atrophy patient. Nature (2008) 12.21
The DNA-encoded nucleosome organization of a eukaryotic genome. Nature (2008) 11.41
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
Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol (2009) 11.18
Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat Genet (2009) 10.54
Interrogating a high-density SNP map for signatures of natural selection. Genome Res (2002) 10.33
Somatic coding mutations in human induced pluripotent stem cells. Nature (2011) 9.50
Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells. Nat Biotechnol (2010) 9.24
Gene targeting of a disease-related gene in human induced pluripotent stem and embryonic stem cells. Cell Stem Cell (2009) 8.97
Increased methylation variation in epigenetic domains across cancer types. Nat Genet (2011) 8.92
Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell (2010) 8.74
Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines. Cell (2011) 8.21
A two-gene expression ratio predicts clinical outcome in breast cancer patients treated with tamoxifen. Cancer Cell (2004) 8.06
Characterization of AMN107, a selective inhibitor of native and mutant Bcr-Abl. Cancer Cell (2005) 7.99
Automatic atom type and bond type perception in molecular mechanical calculations. J Mol Graph Model (2006) 7.93
Feeder-independent culture of human embryonic stem cells. Nat Methods (2006) 7.61
Guidelines and techniques for the generation of induced pluripotent stem cells. Cell Stem Cell (2008) 7.57
Prostaglandin E2 regulates vertebrate haematopoietic stem cell homeostasis. Nature (2007) 7.55
Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature (2011) 7.43
Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells. Cell Stem Cell (2011) 7.41
Oncogenic Kras maintains pancreatic tumors through regulation of anabolic glucose metabolism. Cell (2012) 7.36
Neural differentiation of human induced pluripotent stem cells follows developmental principles but with variable potency. Proc Natl Acad Sci U S A (2010) 7.31
Acute renal failure and sepsis. N Engl J Med (2004) 7.18
Functional cardiomyocytes derived from human induced pluripotent stem cells. Circ Res (2009) 7.09
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
Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells. Nature (2010) 7.05
Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science (2009) 6.96
Immortalization eliminates a roadblock during cellular reprogramming into iPS cells. Nature (2009) 6.85
Live cell imaging distinguishes bona fide human iPS cells from partially reprogrammed cells. Nat Biotechnol (2009) 6.76
High-performance neuroprosthetic control by an individual with tetraplegia. Lancet (2012) 6.66
Efficient method to generate single-copy transgenic mice by site-specific integration in embryonic stem cells. Genesis (2006) 6.64
Lin28 promotes transformation and is associated with advanced human malignancies. Nat Genet (2009) 6.35
Nuclear reprogramming of somatic cells after fusion with human embryonic stem cells. Science (2005) 6.14
Non-cell autonomous effect of glia on motor neurons in an embryonic stem cell-based ALS model. Nat Neurosci (2007) 6.08
Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature (2010) 6.06
A high-efficiency system for the generation and study of human induced pluripotent stem cells. Cell Stem Cell (2008) 5.99
Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma. Proc Natl Acad Sci U S A (2008) 5.94
The dog genome: survey sequencing and comparative analysis. Science (2003) 5.84
Chemically defined conditions for human iPSC derivation and culture. Nat Methods (2011) 5.84
HoxB4 confers definitive lymphoid-myeloid engraftment potential on embryonic stem cell and yolk sac hematopoietic progenitors. Cell (2002) 5.71
Mechanisms of autoinhibition and STI-571/imatinib resistance revealed by mutagenesis of BCR-ABL. Cell (2003) 5.71
Induced pluripotent stem cell generation using a single lentiviral stem cell cassette. Stem Cells (2009) 5.69
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
Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. Nat Genet (2010) 5.37
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
The oyster genome reveals stress adaptation and complexity of shell formation. Nature (2012) 5.30
Oct4 expression is not required for mouse somatic stem cell self-renewal. Cell Stem Cell (2007) 5.29
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
The promise of induced pluripotent stem cells in research and therapy. Nature (2012) 5.05
Regulatory networks define phenotypic classes of human stem cell lines. Nature (2008) 4.98
A functionally characterized test set of human induced pluripotent stem cells. Nat Biotechnol (2011) 4.95
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