Recurrent variations in DNA methylation in human pluripotent stem cells and their differentiated derivatives.
- Authors
- Nazor, Kristopher L; Altun, Gulsah; Lynch, Candace; Tran, Ha; Harness, Julie V; Slavin, Ileana; Garitaonandia, Ibon; MΓΌller, Franz-Josef; Wang, Yu-Chieh; Boscolo, Francesca S; Fakunle, Eyitayo; Dumevska, Biljana; Lee, Sunray; Park, Hyun Sook; Olee, Tsaiwei; D'Lima, Darryl D; Semechkin, Ruslan; Parast, Mana M; Galat, Vasiliy; Laslett, Andrew L; Schmidt, Uli; Keirstead, Hans S; Loring, Jeanne F; Laurent, Louise C
- Year
- 2012
- Journal
- Cell stem cell
- PMID
- 22560082
- DOI
- 10.1016/j.stem.2012.02.013
- PMCID
- PMC3348513
Human pluripotent stem cells (hPSCs) are potential sources of cells for modeling disease and development, drug discovery, and regenerative medicine. However, it is important to identify factors that may impact the utility of hPSCs for these applications. In an unbiased analysis of 205 hPSC and 130 somatic samples, we identified hPSC-specific epigenetic and transcriptional aberrations in genes subject to X chromosome inactivation (XCI) and genomic imprinting, which were not corrected during directed differentiation. We also found that specific tissue types were distinguished by unique patterns of DNA hypomethylation, which were recapitulated by DNA demethylation during in vitro directed differentiation. Our results suggest that verification of baseline epigenetic status is critical for hPSC-based disease models in which the observed phenotype depends on proper XCI or imprinting and that tissue-specific DNA methylation patterns can be accurately modeled during directed differentiation of hPSCs, even in the presence of variations in XCI or imprinting.
Differential DNA methylation in pluripotent and somatic cellsData for CpG sites differentially methylated between pluripotent and somatic cells (ΞΞ² > 0.2) on the 27K DNA Methylation array are shown. A. PluripotentLowVar/SomaticLowVar: 1432 CpGs for 1282 genes with low variation (s.d. < 0.2) within both the pluripotent and somatic sample groups. The seven clusters of CpGs that were examined using the GREAT algorithm are shaded on the left. B. PluripotentHighVar/SomaticLowVar: 303 CpGs for 234 genes with variable methylation only in the pluripotent group (s.d. > 0.2). C. PluripotentLowVar/SomaticHighVar: 1691 CpGs for 1442 genes with variable methylation only in the somatic group. The color scale for the Ξ² values is shown. The distribution of sample types are indicated below each heatmap, with hESCs in black, hiPSCs in yellow, and somatic cells in red. See also Figure S1 and Table S2.
LLM interpretation
This figure consists of three heatmaps (A, B, and C) showing DNA methylation levels ($\beta$ values) across pluripotent and somatic cells, with a color scale ranging from green (unmethylated) to red (methylated). Each panel compares different groups of CpG sites based on methylation variation: (A) low variation in both groups, (B) high variation in pluripotent cells only, and (C) high variation in somatic cells only. The heatmaps include hierarchical clustering, sample distribution bars (hESCs in black, hiPSCs in yellow, and somatic cells in red), and text boxes listing enriched biological processes with associated fold-change and FDR values.
Tissue-specific patterns of DNA methylationData for CpG sites on the 450K DNA Methylation array that were differentially methylated between samples from a given tissue and all other samples (ΞΞ² > 0.5) are shown. A. The histogram shows the fold difference in total number of uniquely hypomethylated and hypermethylated CpGs for a given tissue (listed in Table S3). If hypomethylated CpGs predominate, the bar is green; if hypermethylated CpGs predominate, the bar is red. The total number of unique CpGs that were differentially methylated in the given tissue type is shown above each bar, and the total number of samples per tissue type is shown on the X-axis. B. 12,254 CpGs on the 450K DNA Methylation array with uniquely hypomethylated CpGs in specific tissue types. Functional enrichments for tissue-specific hypomethylated clusters are identified with boxes. Samples are grouped according to hierarchical clustering and CpGs are rank-ordered for each tissue (see also Table S3). C. DNA methylation of pluripotency- and neural-specific transcription factor genes.
LLM interpretation
This figure presents tissue-specific DNA methylation patterns across three panels. Panel A is a bar chart showing the fold difference between uniquely hypomethylated (green) and hypermethylated (red) CpGs for various tissues, with the total number of differentially methylated CpGs labeled above each bar. Panel B features a hierarchical clustering heatmap of 12,254 hypomethylated CpGs across hPSC and somatic samples, with call-out boxes detailing functional enrichments and FDR values for specific tissue clusters. Panel C is a heatmap showing the DNA methylation levels of specific pluripotency and neural transcription factor genes across hPSCs, brain tissue, and other tissues.
Directed differentiation of hPSCs recapitulates epigenetic hallmarks of human tissuesA. Immunocytochemistry showing NESTIN and PAX6 staining in WA07-derived neural progenitor cells (NPCs) on day 22 of NPC differentiation. B. Immunostaining of A2B5 and OLIG1 in WA07-derived oligodendroctye precursor cells (OPCs) on day 42 of OPC differentiation. C. Immunostaining of GALC in WA07-derived oligodendrocytes on day 42 of OPC differentiation. Magnifications are indicated. D. DNA methylation (using the 450K DNA Methylation array) of select oligodendrocyte and neuronal genes in NPCs, OPCs, hPSCs and tissues. E. Diagram of DNA methylation patterns of PAX6 in NPCs, OPCs and brain samples corresponding to the chromosomal regions listed to the right of the heatmap in Figure 3D. Segments that are green are unmethylated and those that are red are methylated in the samples listed on the left. See also Figure S2 and Table S4.
LLM interpretation
This figure consists of immunocytochemistry images (A-C), a heatmap (D), and a genomic diagram (E) illustrating the differentiation of hPSCs into neural lineages. Panels A-C show positive staining for lineage-specific markers (NESTIN, PAX6, A2B5, OLIG1, and GALC) in NPCs, OPCs, and oligodendrocytes. The heatmap in panel D compares DNA methylation levels across hPSCs, NPCs, OPCs, and various human tissues for select genes, while panel E maps the specific unmethylated (green) and methylated (red) regions of the *PAX6* gene across different cell types and brain samples.
DNA methylation of imprinted genesGene names highlighted in blue are paternally imprinted, pink are maternally imprinted and green are isoform dependent. Hierarachical clustering was performed for each group of samples (gynogenetic/androgenetic, hESCs, hiPSCs, somatic) independently. For each gene, CpG probes are ordered according to chromosomal position. A. DNA methylation (27K DNA Methylation array) of 49 imprinted CpG sites showing a gametic imprint pattern in parthenogenetic, androgenetic and tissue samples. B. DNA methylation (450K DNA Methylation array) of 214 gametic imprinted CpG sites in source fibroblasts and chondrocytes, early passage hiPSCs, and late passage hiPSCs. CβD. Allele-specific expression of PEG10 and PEG3 in hPSC and somatic samples. hPSC samples are represented as squares, somatic samples as triangles, and each data point is colored according to the average beta value for that gene shown in the heatmap to the right. Genomic DNA and no template (NT) controls are plotted as blue diamonds. Error bars indicate the standard error. See also Figure S3.
LLM interpretation
This figure consists of two heatmaps and two scatter plots analyzing DNA methylation and allele-specific expression of imprinted genes. Panels A and B are heatmaps showing DNA methylation levels (green for unmethylated, red for methylated) across various sample groups (androgenetic, gynogenetic, hESC, hiPSC, and somatic), with genes color-coded by imprinting pattern. Panels C and D are scatter plots showing the allele-specific expression of *PEG10* and *PEG3* in hPSC and somatic samples, accompanied by small heatmaps indicating average methylation values for the corresponding genes.
DNA methylation on the X chromosomeCpGs are ordered by chromosomal location, with the cytobands indicated to the left of the heatmaps. AβB. Hierarchical clustering of all samples according to 27K DNA Methylation array data. Cluster assignments are shown on the enlarged dendrogram above the heatmaps. XIST expression is shown below the heatmap. C. Box and whisker plot of chrX Ξ² values in 106 female hPSC samples ordered according to decreasing XIST expression. D. XIST expression in parental fibroblasts and 11 hiPSC clones at early, intermediate, and late passages shows an increase in XIST expression following reprogramming and a subsequent tendency for loss of XIST expression over time in culture. E. DNA methylation (450K DNA Methylation array) for fibroblast, early passage hiPSC, and late passage hiPSC samples. See also Figure S4β5.
LLM interpretation
This figure presents DNA methylation patterns on the X chromosome across various samples. Panels A and B show hierarchical clustering and heatmaps of 27K DNA methylation array data, where samples are grouped into five clusters and correlated with XIST expression levels. Panel C uses a box-and-whisker plot to show chrX $\beta$ values across 106 female hPSC samples ordered by decreasing XIST expression. Panel D is a line graph showing XIST mRNA expression across passages in fibroblasts and hiPSC clones, while Panel E provides a 450K DNA methylation array heatmap comparing fibroblasts to early and late passage hiPSCs.
Allele-specific expression of genes subject to XCIAllele-specific expression of RPGR, MAMLD1, SLC25A43, USP51 and DDX26B in hPSC samples. hPSC samples are represented as squares and each data point is colored according to the average beta value for that gene shown in the heatmap to the right; data points without corresponding DNA methylation data are white. Red arrows identify HDF51 iPSC lines that switched from monoallelic expression at early passages to biallelic expression at late passages. Genomic DNA and no template (NT) controls are plotted as blue triangles. Error bars indicate the standard error.
LLM interpretation
This figure consists of five panels (A-E), each featuring a scatter plot paired with a DNA methylation heatmap for a specific gene (RPGR, MAMLD1, SLC25A43, USP51, and DDX26B). The scatter plots compare Allele A expression versus Allele B expression (in RFUs) for hPSC samples (squares) and controls (blue triangles), with data points color-coded by average methylation levels. Red arrows highlight specific HDF51 iPSC lines transitioning from monoallelic to biallelic expression across different passages.
Implications of aberrations in XCI and genomic imprints on disease modelingA. DNA methylation (450K DNA Methylation array) of 214 gametic imprinted CpG sites at imprinted loci for control androgenetic and gynogenetic samples, undifferentiated (labeled with green text) and differentiated (labeled with red text) hPSC samples. Arrows indicate direction of differentiation. B. The heatmap shows DNA methylation (450K DNA Methylation array) on the X chromosome for control male tissue samples, control female tissue samples, undifferentiated samples (labeled with green text) and differentiated samples (labeled with red text) hPSC samples. Arrows indicate direction of differentiation. CpGs are ordered by chromosomal location, with the cytobands indicated to the left of the heatmap. C. Diagram indicating the frequency of loss of XCI at X-linked disease genes among 11 hiPSC clones reprogrammed from the same fibroblast culture. The number of clones showing loss of XCI at each locus is listed to the right of the gene name. Genes with loss of XCI in 1β3 clones are shown in black, in 4β5 clones in orange, and in 6β8 clones in red.
LLM interpretation
This figure consists of two heatmaps and a diagram analyzing DNA methylation and X-chromosome inactivation (XCI). Panel A shows a heatmap of 214 gametic imprinted CpG sites across androgenetic, gynogenetic, undifferentiated (green), and differentiated (red) hPSC samples. Panel B displays a heatmap of 3,279 CpGs on the X chromosome for male and female tissue controls and hPSC samples, with cytobands labeled on the left. Panel C is a diagram listing X-linked disease genes and the frequency of XCI loss across 11 hiPSC clones, color-coded by frequency (black: 1β3, orange: 4β5, red: 6β8 clones).
| Name | Type |
|---|---|
| 15 week fetal brain local | anatomy |
| 18β20 week fetal brain local | anatomy |
| 27K DNA Methylation array local | drug |
| 450K DNA Methylation array local | drug |
| A2B5 local | drug |
| A2B5 local | gene |
| aberrant_methylation local | phenotype |
| accutase | drug |
| adult bladder sample local | cohort |
| AFP local | gene |
| Agilent 2100 Bioanalyzer | drug |
| Agilent DNA1000 Kit local | drug |
| androgenetic samples local | cohort |
| Androgenetic samples local | cohort |
| ANKRD11 local | gene |
| Beckwith-Wiedemann syndrome local | phenotype |
| bFGF | drug |
| BIORAD local | drug |
| bisection local | drug |
| blood | drug |
| BRACHYURY local | gene |
| brain | anatomy |
| brain local | cohort |
| BSA | drug |
| C.B-17-Prkdcscid mouse local | cohort |
| cellular differentiation local | phenotype |
| CFX-96 Real-Time PCR Detection System local | drug |
| chondrocyte local | cohort |
| chondrocyte hiPSC clones local | cohort |
| Cluster 1 | cohort |
| CM8 local | cohort |
| collagenase local | drug |
| Complete hydatidiform mole local | phenotype |
| CpG cluster local | variant |
| CpG probes local | drug |
| CpG site local | drug |
| CpG site local | variant |
| current hPSC media local | drug |
| DDX26B local | gene |
| defense response local | phenotype |
| differentiation potential local | phenotype |
| DIRAS3 local | gene |
| DIRAS3 aberrations local | variant |
| Dlgap2 | gene |
| DMEM | drug |
| DMEM/F12 | drug |
| DNA hypomethylation local | drug |
| DNA methylation | drug |
| DNA methylation loss local | phenotype |
| DNA methylation variability local | phenotype |
| earlier D.P.F local | phenotype |
| energy homeostasis | phenotype |
| ESI051p37 hPSC sample local | cohort |
| EZ DNA methylation kit | drug |
| FBS | drug |
| female hESC local | cohort |
| female hiPSCs local | cohort |
| female hPSCs local | cohort |
| female hPSC samples local | cohort |
| female somatic samples local | cohort |
| fetal bovine serum | drug |
| fetal brain | anatomy |
| FGF2 | drug |
| fibroblast local | cohort |
| fibroblast-derived clones local | cohort |
| fibroblast-derived hiPSC clones local | cohort |
| GALC local | gene |
| gametic imprinting local | phenotype |
| gelatin | drug |
| gene expression | phenotype |
| genomic imprinting | phenotype |
| Glutamax | drug |
| Gnas | gene |
| GRB10 | gene |
| gynogenetic samples local | cohort |
| Gynogenetic samples local | cohort |
| H19 local | gene |
| HDF51 hiPSC clones local | cohort |
| HDF51iPS cells local | cohort |
| heart | anatomy |
| hESC medium local | drug |
| hESCs | cohort |
| hESC samples local | cohort |
| hiPSC | cohort |
| hiPSC clones local | cohort |
| hiPSC samples local | cohort |
| histone modifications local | drug |
| HPRT1 | gene |
| hPSC local | cohort |
| hPSC-based X-linked disease models local | cohort |
| hPSC lines local | cohort |
| hPSCs | cohort |
| Human cancers local | phenotype |
| human embryonic stem cell lines local | cohort |
| human embryonic stem cells | cohort |
| human fibroblasts | cohort |
| Hydatidiform mole local | phenotype |
| hydatidiform moles local | phenotype |
| HYMA1 local | gene |
| hypermethylation local | phenotype |
| Illumina GenomeStudio local | drug |
| Illumina HT12v3 Gene Expression BeadArray local | drug |
| Illumina Infinium 27K local | drug |
| Illumina Infinium 27K DNA Methylation array local | drug |
| Illumina Infinium 450K DNA Methylation array local | drug |
| Illumina iScan | drug |
| immune response | phenotype |
| immune system process local | phenotype |
| imprinted genes | gene |
| Imprinted genes local | phenotype |
| imprinted loci local | phenotype |
| imprinting local | phenotype |
| imprinting aberrations local | phenotype |
| Imprinting defects local | phenotype |
| Infinium 450K BeadChips local | drug |
| Infinium HumanMethylation27K local | drug |
| iPS201B7 local | cohort |
| iPS3 local | cohort |
| iPS414C.2 local | cohort |
| iPS7 local | cohort |
| KCNK9 local | gene |
| Kcnq1 | gene |
| Keirstead lab local | cohort |
| kidney local | cohort |
| KLF2 local | gene |
| Klf4 | gene |
| knockout serum replacement | drug |
| L3MBTL local | gene |
| L3MBTL aberrations local | variant |
| large and diverse collection of pluripotent and somatic samples local | cohort |
| Laslett lab local | cohort |
| late passage samples local | cohort |
| Lesch-Nyhan Syndrome local | phenotype |
| LIF | drug |
| Life Technologies | drug |
| Lipofectamine 2000 | drug |
| LLC15 local | cohort |
| Loring lab local | cohort |
| loss_of_DNA_methylation local | phenotype |
| loss of XCI local | phenotype |
| low fat milk local | drug |
| lymph node local | cohort |
| male hPSC samples local | cohort |
| male somatic samples local | cohort |
| MAMLD1 local | gene |
| MAP2 | gene |
| maternal imprints local | phenotype |
| Maternal imprints local | phenotype |
| matrigel | drug |
| MEFs local | drug |
| MEG3 | gene |
| MEST local | gene |
| Mkrn3 | gene |
| mouse ESC-like phenotype local | phenotype |
| mRNA expression local | drug |
| mRNA transcript local | drug |
| Myc | gene |
| myelin | phenotype |
| MYT1 | gene |
| Myt1l | gene |
| Nanog | gene |
| NAP1L5 | gene |
| nestin | gene |
| New England Biolabs | drug |
| nicotine dependence | phenotype |
| NNAT | gene |
| non-coding RNA expression local | drug |
| non-essential amino acids | drug |
| NPCs | cohort |
| OLIG1 | gene |
| Olig2 | gene |
| oligodendrocyte differentiation local | phenotype |
| OPCs | anatomy |
| originalES local | drug |
| originalES medium local | drug |
| original hESC medium local | drug |
| ovarian teratoma local | phenotype |
| Ovarian teratoma local | phenotype |
| paraformaldehyde | drug |
| parental chondrocyte local | cohort |
| parental fibroblast local | cohort |
| parental fibroblasts local | cohort |
| parthenogenetic hESCs local | cohort |
| Parthenotes local | phenotype |
| paternal imprints local | phenotype |
| Paternal imprints local | phenotype |
| Pax6 | gene |
| PEG10 local | gene |
| PEG3 local | gene |
| PEG3 aberrations local | variant |
| PLAGL1 local | gene |
| PLP1 | gene |
| pluripotency | phenotype |
| Pluripotent local | phenotype |
| pluripotent cells | drug |
| PluripotentHighVar/SomaticLowVar local | variant |
| PluripotentLowVar/SomaticHighVar local | cohort |
| PluripotentLowVar/SomaticHighVar local | variant |
| PluripotentLowVar/SomaticLowVar local | variant |
| PluripotentLowVar/SomaticLowVar category local | cohort |
| pluripotent state local | phenotype |
| PMP22 local | gene |
| polybrene | drug |
| poly-D-lysine | drug |
| POU3F2 | gene |
| POU3F3 local | gene |
| POU5F1 | gene |
| Prader-Willi syndrome | phenotype |
| primary cell lines local | cohort |
| Primary cell lines local | cohort |
| Primary cell line samples local | cohort |
| Purinergic nucleotide receptor activity local | phenotype |
| Qiagen DNeasy Blood and Tissue Kit | drug |
| QKI local | gene |
| Quantitect Reverse Transcription Kit local | drug |
| Qubit dsDNA BR Assay Kit local | drug |
| reprogramming local | phenotype |
| RNA | drug |
| RPGR local | gene |
| schizophrenia | phenotype |
| self-renewal local | phenotype |
| sex | phenotype |
| Silver-Russell syndrome local | phenotype |
| SIVF024 local | cohort |
| SIVF028 local | cohort |
| SIVF029 local | cohort |
| SKI local | gene |
| SLC25A43 local | gene |
| SMA local | gene |
| small molecules | drug |
| SNRPN local | gene |
| somatic | phenotype |
| somatic samples local | cohort |
| Somatic samples local | cohort |
| SOX1 | gene |
| Sox2 | gene |
| spleen local | cohort |
| SSI DNA methyltransferase local | drug |
| Taqman qPCR SNP genotyping array local | drug |
| three hPSC lines local | cohort |
| tissue | anatomy |
| tissue samples local | cohort |
| Tissue samples local | cohort |
| TRA1-81 local | drug |
| Triton X-100 | drug |
| UCSC hg18 local | drug |
| USP51 local | gene |
| Valproic acid | drug |
| WA07 local | cohort |
| WA09 local | cohort |
| WA09-derived hiPSC lines local | cohort |
| WA09 hESC local | cohort |
| whole embryo plating local | drug |
| Wicell-conditioned medium local | drug |
| Wicell medium local | drug |
| X chromosome | drug |
| X chromosome local | phenotype |
| X chromosome CpG methylation local | phenotype |
| X chromosome DNA methylation local | phenotype |
| X chromosome inactivation (XCI) local | phenotype |
| XCI local | phenotype |
| X-Cluster 1 local | cohort |
| X-Cluster 2 local | cohort |
| X-Cluster 3 local | cohort |
| X-Cluster 4 local | cohort |
| X-Cluster 5 local | cohort |
| XIST | gene |
| XIST expression local | phenotype |
| X-linked disease genes local | gene |
| XO genotype local | phenotype |
| XX genotype local | phenotype |
| ZIM2 local | gene |
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| DNA methylation changes during long-term in vitro cell culture are caused by epigenetic drift. | Franzen J et al. | β | 2021 | β |
| Epigenetic clocks reveal a rejuvenation event during embryogenesis followed by aging. | Kerepesi C et al. | β | 2021 | β |
| Epigenetic Mechanisms of ART-Related Imprinting Disorders: Lessons From iPSC and Mouse Models. | HorΓ‘nszky A et al. | β | 2021 | β |
| Extracellular laminin regulates hematopoietic potential of pluripotent stem cells through integrin Ξ²1-ILK-Ξ²-catenin-JUN axis. | Yuzuriha A et al. | β | 2021 | β |
| Induced pluripotent stem cells from subjects with Lesch-Nyhan disease. | Sutcliffe DJ et al. | β | 2021 | β |
| Induced pluripotent stem cell technology: trends in molecular biology, from genetics to epigenetics. | Maali A et al. | β | 2021 | β |
| Inherent genomic properties underlie the epigenomic heterogeneity of human induced pluripotent stem cells. | Yokobayashi S et al. | β | 2021 | β |
| <i>STK31</i> upregulation is associated with chromatin remodeling in gastric cancer and induction of tumorigenicity in a xenograft mouse model. | Bae DH et al. | β | 2021 | β |
| Large-scale analysis of imprinting in naive human pluripotent stem cells reveals recurrent aberrations and a potential link to FGF signaling. | Keshet G et al. | β | 2021 | β |
| Modeling preeclampsia using human induced pluripotent stem cells. | Horii M et al. | β | 2021 | β |
| Novel epigenetic clock for fetal brain development predicts prenatal age for cellular stem cell models and derived neurons. | Steg LC et al. | β | 2021 | β |
| Pan-cancer network disorders revealed by overall and local signaling entropy. | Feng L et al. | β | 2021 | β |
| Pseudoautosomal Region 1 Overdosage Affects the Global Transcriptome in iPSCs From Patients With Klinefelter Syndrome and High-Grade X Chromosome Aneuploidies. | Astro V et al. | β | 2021 | β |
| Single cell heterogeneity in human pluripotent stem cells. | Yang S et al. | β | 2021 | β |
| Sperm DNA methylation mediates the association of male age on reproductive outcomes among couples undergoing infertility treatment. | Oluwayiose OA et al. | β | 2021 | β |
| The Application of Induced Pluripotent Stem Cells Against Liver Diseases: An Update and a Review. | Zhang L et al. | β | 2021 | β |
| The genomic loci of specific human tRNA genes exhibit ageing-related DNA hypermethylation. | Acton RJ et al. | β | 2021 | β |
| The X chromosome dosage compensation program during the development of cynomolgus monkeys. | Okamoto I et al. | β | 2021 | β |
| A comparison of epigenetic mitotic-like clocks for cancer risk prediction. | Teschendorff AE | β | 2020 | β |
| Association between sperm mitochondarial DNA copy number and nuclear DNA methylation. | Oluwayiose OA et al. | β | 2020 | β |
| DNA G-quadruplex stability, position and chromatin accessibility are associated with CpG island methylation. | Jara-Espejo M et al. | β | 2020 | β |
| EPISCORE: cell type deconvolution of bulk tissue DNA methylomes from single-cell RNA-Seq data. | Teschendorff AE et al. | β | 2020 | β |
| Identification of potential transcription factors that enhance human iPSC generation. | Swaidan NT et al. | β | 2020 | β |
| IMPLICON: an ultra-deep sequencing method to uncover DNA methylation at imprinted regions. | KlobuΔar T et al. | β | 2020 | β |
| MethylResolver-a method for deconvoluting bulk DNA methylation profiles into known and unknown cell contents. | Arneson D et al. | β | 2020 | β |
| Naive Pluripotent Stem Cells Exhibit Phenotypic Variability that Is Driven by Genetic Variation. | Ortmann D et al. | β | 2020 | β |
| ONECUT2 upregulation is associated with CpG hypomethylation at promoter-proximal DNA in gastric cancer and triggers ACSL5. | Seo EH et al. | β | 2020 | β |
| Progress and Challenges of Amniotic Fluid Derived Stem Cells in Therapy of Ischemic Heart Disease. | Fang YH et al. | β | 2020 | β |
| Strategies for Cancer Immunotherapy Using Induced Pluripotency Stem Cells-Based Vaccines. | Bernardes de Jesus B et al. | β | 2020 | β |
| Transcriptome and epigenome diversity and plasticity of muscle stem cells following transplantation. | Evano B et al. | β | 2020 | β |
| X chromosome inactivation in human development. | Patrat C et al. | β | 2020 | β |
| De Novo DNA Methylation at Imprinted Loci during Reprogramming intoΒ Naive and Primed Pluripotency. | Yagi M et al. | β | 2019 | β |
| Effects of reprogramming on genomic imprinting and the application of pluripotent stem cells. | Li X et al. | β | 2019 | β |
| Epigenetic aberrations in human pluripotent stem cells. | Bar S et al. | β | 2019 | β |
| Expression of miRNAs from the Imprinted <i>DLK1/DIO3</i> Locus Signals the Osteogenic Potential of Human Pluripotent Stem Cells. | Barrault L et al. | β | 2019 | β |
| Genome-wide Screen for Culture Adaptation and Tumorigenicity-Related Genes in Human Pluripotent Stem Cells. | Weissbein U et al. | β | 2019 | β |
| Global Characterization of X Chromosome Inactivation in Human Pluripotent Stem Cells. | Bar S et al. | β | 2019 | β |
| How Does Reprogramming to Pluripotency Affect Genomic Imprinting? | Perrera V et al. | β | 2019 | β |
| Induced Pluripotent Stem Cells and Their Use in Human Models of Disease and Development. | Karagiannis P et al. | β | 2019 | β |
| LncRNAs regulating stemness in aging. | Sousa-Franco A et al. | β | 2019 | β |
| New considerations for hiPSC-based models of neuropsychiatric disorders. | Hoffman GE et al. | β | 2019 | β |
| Pluripotent Stem Cell Heterogeneity. | Hayashi Y et al. | β | 2019 | β |
| Polyamine supplementation reduces DNA damage in adipose stem cells cultured in 3-D. | Minguzzi M et al. | β | 2019 | β |
| Reproducibility and staging of 3D human retinal organoids across multiple pluripotent stem cell lines. | Capowski EE et al. | β | 2019 | β |
| Two decades of embryonic stem cells: a historical overview. | Eguizabal C et al. | β | 2019 | β |
| Up-regulation of FAM64A promotes epithelial-to-mesenchymal transition and enhances stemness features in breast cancer cells. | Zhang J et al. | β | 2019 | β |
| Acquired Genetic and Epigenetic Variation in Human Pluripotent Stem Cells. | Kyriakides O et al. | β | 2018 | β |
| A novel cell-type deconvolution algorithm reveals substantial contamination by immune cells in saliva, buccal and cervix. | Zheng SC et al. | β | 2018 | β |
| Comparative molecular characterization of typical and exceptional responders in glioblastoma. | Wipfler K et al. | β | 2018 | β |
| Corneal cell therapy: with iPSCs, it is no more a far-sight. | Chakrabarty K et al. | β | 2018 | β |
| Direct Control of Stem Cell Behavior Using Biomaterials and Genetic Factors. | Yoon JK et al. | β | 2018 | β |
| DNA Methylation Patterns in Normal Tissue Correlate more Strongly with Breast Cancer Status than Copy-Number Variants. | Gao Y et al. | β | 2018 | β |
| Epigenetic-scale comparison of human iPSCs generated by retrovirus, Sendai virus or episomal vectors. | Nishino K et al. | β | 2018 | β |
| GATA2 deficiency and human hematopoietic development modeled using induced pluripotent stem cells. | Jung M et al. | β | 2018 | β |
| Generation of Fabry cardiomyopathy model for drug screening using induced pluripotent stem cell-derived cardiomyocytes from a female Fabry patient. | Kuramoto Y et al. | β | 2018 | β |
| Genetics of Alcohol Use Disorder: A Role for Induced Pluripotent Stem Cells? | Prytkova I et al. | β | 2018 | β |
| Identification of differentially methylated cell types in epigenome-wide association studies. | Zheng SC et al. | β | 2018 | β |
| Immunomethylomics: A Novel Cancer Risk Prediction Tool. | Kelsey KT et al. | β | 2018 | β |
| Improving Cell Survival in Injected Embryos Allows Primed Pluripotent Stem Cells to Generate Chimeric Cynomolgus Monkeys. | Kang Y et al. | β | 2018 | β |
| Loss of hierarchical imprinting regulation at the Prader-Willi/Angelman syndrome locus in human iPSCs. | PΓ³lvora-BrandΓ£o D et al. | β | 2018 | β |
| Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation. | Malta TM et al. | β | 2018 | β |
| Paracrine mechanisms in early differentiation of human pluripotent stem cells: Insights from a mathematical model. | Gaspari E et al. | β | 2018 | β |
| Pluripotent stem cell-based therapy for Parkinson's disease: Current status and future prospects. | Sonntag KC et al. | β | 2018 | β |
| Recent advances in lineage differentiation from stem cells: hurdles and opportunities? | Terryn J et al. | β | 2018 | β |
| The MiAge Calculator: a DNA methylation-based mitotic age calculator of human tissue types. | Youn A et al. | β | 2018 | β |
| The role of the reprogramming method and pluripotency state in gamete differentiation from patient-specific human pluripotent stem cells. | Mishra S et al. | β | 2018 | β |
| The Role of Xist in X-Chromosome Dosage Compensation. | Sahakyan A et al. | β | 2018 | β |
| Tissue-specific DNA methylation loss during ageing and carcinogenesis is linked to chromosome structure, replication timing and cell division rates. | Dmitrijeva M et al. | β | 2018 | β |
| Tracing human stem cell lineage during development using DNA methylation. | Salas LA et al. | β | 2018 | β |
| Trisomy silencing by XIST normalizes Down syndrome cell pathogenesis demonstrated for hematopoietic defects in vitro. | Chiang JC et al. | β | 2018 | β |
| Who Will Win: Induced Pluripotent Stem Cells Versus Embryonic Stem Cells for Ξ² Cell Replacement and Diabetes Disease Modeling? | Jacobson EF et al. | β | 2018 | β |
| Aberrant DNA Methylation in Human iPSCs Associates with MYC-Binding Motifs in a Clone-Specific Manner Independent of Genetics. | Panopoulos AD et al. | β | 2017 | β |
| A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies. | Teschendorff AE et al. | β | 2017 | β |
| Allele-specific analysis of cell fusion-mediated pluripotent reprograming reveals distinct and predictive susceptibilities of human X-linked genes to reactivation. | Cantone I et al. | β | 2017 | β |
| Analysis of Transcriptional Variability in a Large Human iPSC Library Reveals Genetic and Non-genetic Determinants of Heterogeneity. | Carcamo-Orive I et al. | β | 2017 | β |
| Assessment of imprinting- and genetic variation-dependent monoallelic expression using reciprocal allele descendants between human family trios. | Chuang TJ et al. | β | 2017 | β |
| Changeability of the fully methylated status of the 15q11.2 region in induced pluripotent stem cells derived from a patient with Prader-Willi syndrome. | Okuno H et al. | β | 2017 | β |
| Common genetic variation drives molecular heterogeneity in human iPSCs. | Kilpinen H et al. | β | 2017 | β |
| Concise Review: Embryonic Stem Cells Derived by Somatic Cell Nuclear Transfer: A Horse in the Race? | Wolf DP et al. | β | 2017 | β |
| Culture-induced recurrent epigenetic aberrations in human pluripotent stem cells. | Weissbein U et al. | β | 2017 | β |
| Derivation of Human Induced Pluripotent Stem Cell (iPSC) Lines and Mechanism of Pluripotency: Historical Perspective and Recent Advances. | Chhabra A | β | 2017 | β |
| Differential X Chromosome Inactivation Patterns during the Propagation of Human Induced Pluripotent Stem Cells. | Andoh-Noda T et al. | β | 2017 | β |
| Divergent Levels of Marker Chromosomes in an hiPSC-Based Model ofΒ Psychosis. | Tcw J et al. | β | 2017 | β |
| Diverse Non-genetic, Allele-Specific Expression Effects Shape Genetic Architecture at the Cellular Level in the Mammalian Brain. | Huang WC et al. | β | 2017 | β |
| DNA methylation and transcriptional trajectories during human development and reprogramming of isogenic pluripotent stem cells. | Roost MS et al. | β | 2017 | β |
| Epigenetic resetting of human pluripotency. | Guo G et al. | β | 2017 | β |
| Epigenetics of cell fate reprogramming and its implications for neurological disorders modelling. | Grzybek M et al. | β | 2017 | β |
| Evaluating Synthetic Activation and Repression of Neuropsychiatric-Related Genes in hiPSC-Derived NPCs, Neurons, and Astrocytes. | Ho SM et al. | β | 2017 | β |
| Faithful SGCE imprinting in iPSC-derived cortical neurons: an endogenous cellular model of myoclonus-dystonia. | GrΓΌtz K et al. | β | 2017 | β |
| GATA4 loss of function in liver cancer impedes precursor to hepatocyte transition. | Enane FO et al. | β | 2017 | β |
| Genome-wide identification of inter-individually variable DNA methylation sites improves the efficacy of epigenetic association studies. | Hachiya T et al. | β | 2017 | β |
| Higher-Level Pathway Objectives of Epigenetic Therapy: A Solution to the p53 Problem in Cancer. | Velcheti V et al. | β | 2017 | β |
| Human Embryonic Stem Cells Do Not Change Their X Inactivation Status during Differentiation. | Patel S et al. | β | 2017 | β |
| Human Naive Pluripotent Stem Cells Model X Chromosome Dampening and X Inactivation. | Sahakyan A et al. | β | 2017 | β |
| Human X chromosome inactivation and reactivation: implications for cell reprogramming and disease. | Cantone I et al. | β | 2017 | β |
| Induced Pluripotent Stem Cells 10 Years Later: For Cardiac Applications. | Yoshida Y et al. | β | 2017 | β |
| iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types. | Panopoulos AD et al. | β | 2017 | β |
| Large-Scale Analysis of Loss of Imprinting in Human Pluripotent Stem Cells. | Bar S et al. | β | 2017 | β |
| Molecular analyses of neurogenic defects in a human pluripotent stem cell model of fragile X syndrome. | Boland MJ et al. | β | 2017 | β |
| Preconception urinary phthalate concentrations and sperm DNA methylation profiles among men undergoing IVF treatment: a cross-sectional study. | Wu H et al. | β | 2017 | β |
| Preparation, characterization, and banking of clinical-grade cells for neural transplantation: Scale up, fingerprinting, and genomic stability of stem cell lines. | Natalwala A et al. | β | 2017 | β |
| Regulation of X-chromosome dosage compensation in human: mechanisms and model systems. | Sahakyan A et al. | β | 2017 | β |
| Sirt1 Regulates DNA Methylation and Differentiation Potential of Embryonic Stem Cells by Antagonizing Dnmt3l. | Heo J et al. | β | 2017 | β |
| Systems-epigenomics inference of transcription factor activity implicates aryl-hydrocarbon-receptor inactivation as a key event in lung cancer development. | Chen Y et al. | β | 2017 | β |
| The human-induced pluripotent stem cell initiative-data resources for cellular genetics. | Streeter I et al. | β | 2017 | β |
| Usage of Human Mesenchymal Stem Cells in Cell-based Therapy: Advantages and Disadvantages. | Kim HJ et al. | β | 2017 | β |
| Variability of human pluripotent stem cell lines. | Ortmann D et al. | β | 2017 | β |
| XACT Noncoding RNA Competes with XIST in the Control of X Chromosome Activity during Human Early Development. | Vallot C et al. | β | 2017 | β |
| X chromosome inactivation in human pluripotent stem cells as a model for human development: back to the drawing board? | Geens M et al. | β | 2017 | β |
| Achilles' heel of pluripotent stem cells: genetic, genomic and epigenetic variations during prolonged culture. | Rebuzzini P et al. | β | 2016 | β |
| An integrative analysis of reprogramming in human isogenic system identified a clone selection criterion. | Shutova MV et al. | β | 2016 | β |
| Bone Tissue Engineering: Past-Present-Future. | Quarto R et al. | β | 2016 | β |
| Correlation of an epigenetic mitotic clock with cancer risk. | Yang Z et al. | β | 2016 | β |
| Describing the Stem Cell Potency: The Various Methods of Functional Assessment and <i>In silico</i> Diagnostics. | Singh VK et al. | β | 2016 | β |
| DNA methylation dynamics in cellular commitment and differentiation. | Suelves M et al. | β | 2016 | β |
| DNA Methylation in Skeletal Muscle Stem Cell Specification, Proliferation, and Differentiation. | Laker RC et al. | β | 2016 | β |
| DNA methylation outliers in normal breast tissue identify field defects that are enriched in cancer. | Teschendorff AE et al. | β | 2016 | β |
| Epigenetic Reprogramming of Muscle Progenitors: Inspiration for Clinical Therapies. | Consalvi S et al. | β | 2016 | β |
| Epigenetic status of H19/IGF2 and SNRPN imprinted genes in aborted and successfully derived embryonic stem cell lines in non-human primates. | Wianny F et al. | β | 2016 | β |
| Epigenetic Variation between Human Induced Pluripotent Stem Cell Lines Is an Indicator of Differentiation Capacity. | Nishizawa M et al. | β | 2016 | β |
| Female human pluripotent stem cells rapidly lose X chromosome inactivation marks and progress to a skewed methylation pattern during culture. | Geens M et al. | β | 2016 | β |
| Genome engineering tools for building cellular models of disease. | Lin J et al. | β | 2016 | β |
| Human Inducible Pluripotent Stem Cells and Autism Spectrum Disorder: Emerging Technologies. | Nestor MW et al. | β | 2016 | β |
| Human pluripotent stem cells as a model of trophoblast differentiation in both normal development and disease. | Horii M et al. | β | 2016 | β |
| Imprints and DPPA3 are bypassed during pluripotency- and differentiation-coupled methylation reprogramming in testicular germ cell tumors. | Killian JK et al. | β | 2016 | β |
| In Pursuit of Authenticity: Induced Pluripotent Stem Cell-Derived Retinal Pigment Epithelium for Clinical Applications. | Miyagishima KJ et al. | β | 2016 | β |
| Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium. | Salomonis N et al. | β | 2016 | β |
| Minireview: Genome Editing of Human Pluripotent Stem Cells for Modeling Metabolic Disease. | Yu H et al. | β | 2016 | β |
| Modeling Alzheimer's disease with human induced pluripotent stem (iPS) cells. | Mungenast AE et al. | β | 2016 | β |
| Ordered chromatin changes and human X chromosome reactivation by cell fusion-mediated pluripotent reprogramming. | Cantone I et al. | β | 2016 | β |
| Profiling placental and fetal DNA methylation in human neural tube defects. | Price EM et al. | β | 2016 | β |
| Rewinding the process of mammalian extinction. | Saragusty J et al. | β | 2016 | β |
| Specific expression and methylation of SLIT1, SLIT2, SLIT3, and miR-218 in gastric cancer subtypes. | Kim M et al. | β | 2016 | β |
| The Aberrant DNA Methylation Profile of Human Induced Pluripotent Stem Cells Is Connected to the Reprogramming Process and Is Normalized During In Vitro Culture. | Tesarova L et al. | β | 2016 | β |
| The Effect of Culture on Human Bone Marrow Mesenchymal Stem Cells: Focus on DNA Methylation Profiles. | Bentivegna A et al. | β | 2016 | β |
| The multi-omic landscape of transcription factor inactivation in cancer. | Teschendorff AE et al. | β | 2016 | β |
| The Role of Stem Cell DNA Methylation in Colorectal Carcinogenesis. | Song L et al. | β | 2016 | β |
| Tissue-independent and tissue-specific patterns of DNA methylation alteration in cancer. | Chen Y et al. | β | 2016 | β |
| Transgene Reactivation in Induced Pluripotent Stem Cell Derivatives and Reversion to Pluripotency of Induced Pluripotent Stem Cell-Derived Mesenchymal Stem Cells. | Galat V et al. | β | 2016 | β |
| Validation of SCT Methylation as a Hallmark Biomarker for Lung Cancers. | Zhang YA et al. | β | 2016 | β |
| What Signatures Dominantly Associate with Gene Age? | Yin H et al. | β | 2016 | β |
| Advances in reprogramming-based study of neurologic disorders. | Nityanandam A et al. | β | 2015 | β |
| An integrative multi-scale analysis of the dynamic DNA methylation landscape in aging. | Yuan T et al. | β | 2015 | β |
| A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics. | Gallego Romero I et al. | β | 2015 | β |
| Cultural relativism: maintenance of genomic imprints in pluripotent stem cell culture systems. | Greenberg MV et al. | β | 2015 | β |
| DNA methylation dynamics in muscle development and disease. | CarriΓ³ E et al. | β | 2015 | β |
| DNA methylation fingerprint of neuroblastoma reveals new biological and clinical insights. | GΓ³mez S et al. | β | 2015 | β |
| DNA Methylation Landscapes of Human Fetal Development. | Slieker RC et al. | β | 2015 | β |
| Epigenetic biomarker to support classification into pluripotent and non-pluripotent cells. | Lenz M et al. | β | 2015 | β |
| Epigenetic mechanisms in heart development and disease. | Martinez SR et al. | β | 2015 | β |
| Epigenetic profile of human adventitial progenitor cells correlates with therapeutic outcomes in a mouse model of limb ischemia. | Gubernator M et al. | β | 2015 | β |
| Erosion of X Chromosome Inactivation in Human Pluripotent Cells Initiates with XACT Coating and Depends on a Specific Heterochromatin Landscape. | Vallot C et al. | β | 2015 | β |
| From "directed differentiation" to "neuronal induction": modeling neuropsychiatric disease. | Ho SM et al. | β | 2015 | β |
| Generation of embryonic stem cells from mouse adipose-tissue derived cells via somatic cell nuclear transfer. | Qin Y et al. | β | 2015 | β |
| [Genetic Cell Reprogramming: A New Technology for Basic Research and Applied Usage]. | Bogomazova AN et al. | β | 2015 | β |
| Genetic Evaluation of Copy Number Variations, Loss of Heterozygosity, and Single-Nucleotide Variant Levels in Human Embryonic Stem Cells With or Without Skewed X Chromosome Inactivation. | Liu WQ et al. | β | 2015 | β |
| Human stem cells from single blastomeres reveal pathways of embryonic or trophoblast fate specification. | Zdravkovic T et al. | β | 2015 | β |
| Increased risk of genetic and epigenetic instability in human embryonic stem cells associated with specific culture conditions. | Garitaonandia I et al. | β | 2015 | β |
| Investigating DNA methylation dynamics and safety of human embryonic stem cell differentiation toward striatal neurons. | Baronchelli S et al. | β | 2015 | β |
| KeyGenes, a Tool to Probe Tissue Differentiation Using a Human Fetal Transcriptional Atlas. | Roost MS et al. | β | 2015 | β |
| Methylation analysis of the DAPK1 gene in imatinib-resistant chronic myeloid leukemia patients. | Celik S et al. | β | 2015 | β |
| Neural Differentiation of Human Pluripotent Stem Cells for Nontherapeutic Applications: Toxicology, Pharmacology, and In Vitro Disease Modeling. | Yap MS et al. | β | 2015 | β |
| Points to consider in the development of seed stocks of pluripotent stem cells for clinical applications: International Stem Cell Banking Initiative (ISCBI). | Andrews PW et al. | β | 2015 | β |
| Stem cell reprogramming: basic implications and future perspective for movement disorders. | BrΓ€ndl B et al. | β | 2015 | β |
| Tapping Stem Cells to Target AMD: Challenges and Prospects. | Brandl C et al. | β | 2015 | β |
| The safety of human pluripotent stem cells in clinical treatment. | Simonson OE et al. | β | 2015 | β |
| The 'sweet' spot of cellular pluripotency: protein glycosylation in human pluripotent stem cells and its applications in regenerative medicine. | Wang YC et al. | β | 2015 | β |
| Variations in the Intragene Methylation Profiles Hallmark Induced Pluripotency. | Druzhkov P et al. | β | 2015 | β |
| X chromosome reactivation in reprogramming and in development. | Pasque V et al. | β | 2015 | β |
| Aberrant DNA methylation reprogramming during induced pluripotent stem cell generation is dependent on the choice of reprogramming factors. | Planello AC et al. | β | 2014 | β |
| Aberrant patterns of X chromosome inactivation in a new line of human embryonic stem cells established in physiological oxygen concentrations. | de Oliveira Georges JA et al. | β | 2014 | β |
| Abnormalities in human pluripotent cells due to reprogramming mechanisms. | Ma H et al. | β | 2014 | β |
| Aged iPSCs display an uncommon mitochondrial appearance and fail to undergo in vitro neurogenesis. | Masotti A et al. | β | 2014 | β |
| A panel of CpG methylation sites distinguishes human embryonic stem cells and induced pluripotent stem cells. | Huang K et al. | β | 2014 | β |
| Application of a low cost array-based technique - TAB-Array - for quantifying and mapping both 5mC and 5hmC at single base resolution in human pluripotent stem cells. | Nazor KL et al. | β | 2014 | β |
| Array-based assay detects genome-wide 5-mC and 5-hmC in the brains of humans, non-human primates, and mice. | Chopra P et al. | β | 2014 | β |
| Cancer-like epigenetic derangements of human pluripotent stem cells and their impact on applications in regeneration and repair. | Huo JS et al. | β | 2014 | β |
| Comparable frequencies of coding mutations and loss of imprinting in human pluripotent cells derived by nuclear transfer and defined factors. | Johannesson B et al. | β | 2014 | β |
| Disease modeling and cell based therapy with iPSC: future therapeutic option with fast and safe application. | Kim C | β | 2014 | β |
| DNA methylation and evolution of duplicate genes. | Keller TE et al. | β | 2014 | β |
| Epigenetic heredity of human height. | Simeone P et al. | β | 2014 | β |
| Epigenetic regulation of pluripotency and differentiation. | Boland MJ et al. | β | 2014 | β |
| Genomic instability in pluripotent stem cells: implications for clinical applications. | Peterson SE et al. | β | 2014 | β |
| Getting off the ground state: X chromosome inactivation knocks down barriers to differentiation. | Morey R et al. | β | 2014 | β |
| Human iPS Cell-Derived Germ Cells: Current Status and Clinical Potential. | Ishii T | β | 2014 | β |
| Methylation and transcripts expression at the imprinted GNAS locus in human embryonic and induced pluripotent stem cells and their derivatives. | Grybek V et al. | β | 2014 | β |
| Micro-environment causes reversible changes in DNA methylation and mRNA expression profiles in patient-derived glioma stem cells. | Baysan M et al. | β | 2014 | β |
| Novel insights into embryonic stem cell self-renewal revealed through comparative human and mouse systems biology networks. | Dowell KG et al. | β | 2014 | β |
| Opportunities and Limitations of Modelling Alzheimer's Disease with Induced Pluripotent Stem Cells. | Ovchinnikov DA et al. | β | 2014 | β |
| Origin-dependent neural cell identities in differentiated human iPSCs in vitro and after transplantation into the mouse brain. | Hargus G et al. | β | 2014 | β |
| Physiological oxygen prevents frequent silencing of the DLK1-DIO3 cluster during human embryonic stem cells culture. | Xie P et al. | β | 2014 | β |
| Preclinical studies for induced pluripotent stem cell-based therapeutics. | Harding J et al. | β | 2014 | β |
| Protein post-translational modifications and regulation of pluripotency in human stem cells. | Wang YC et al. | β | 2014 | β |
| Sex-dependent gene expression in human pluripotent stem cells. | Ronen D et al. | β | 2014 | β |
| The epigenome in pluripotency and differentiation. | Thiagarajan RD et al. | β | 2014 | β |
| Tissue engineering and regenerative medicine: a year in review. | Harrison RH et al. | β | 2014 | β |
| Totipotency and lineage segregation in the human embryo. | De Paepe C et al. | β | 2014 | β |
| Variable allelic expression of imprinted genes in human pluripotent stem cells during differentiation into specialized cell types in vitro. | Park SW et al. | β | 2014 | β |
| Xist deficiency and disorders of X-inactivation in rabbit embryonic stem cells can be rescued by transcription-factor-mediated conversion. | Jiang Y et al. | β | 2014 | β |
| Abnormal neuronal differentiation and mitochondrial dysfunction in hair follicle-derived induced pluripotent stem cells of schizophrenia patients. | Robicsek O et al. | β | 2013 | β |
| A cellular star atlas: using astrocytes from human pluripotent stem cells for disease studies. | Krencik R et al. | β | 2013 | β |
| A quantitative system for discriminating induced pluripotent stem cells, embryonic stem cells and somatic cells. | Wang A et al. | β | 2013 | β |
| Cellular network entropy as the energy potential in Waddington's differentiation landscape. | Banerji CR et al. | β | 2013 | β |
| Charting a dynamic DNA methylation landscape of the human genome. | Ziller MJ et al. | β | 2013 | β |
| Correlation between miRNA-targeted-gene promoter methylation and miRNA regulation of target genes | Taguchi Y | β | 2013 | β |
| Cyclooxygenase, cancer stem cells and DNA methylation play important roles in colorectal carcinogenesis. | Tsujii M | β | 2013 | β |
| DNA methylation age of human tissues and cell types. | Horvath S | β | 2013 | β |
| DNA methylation data analysis and its application to cancer research. | Ma X et al. | β | 2013 | β |
| DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes. | Aran D et al. | β | 2013 | β |
| Epigenetic basis of regeneration: analysis of genomic DNA methylation profiles in the MRL/MpJ mouse. | GΓ³rnikiewicz B et al. | β | 2013 | β |
| Epigenetics of reprogramming to induced pluripotency. | Papp B et al. | β | 2013 | β |
| Generation of human induced pluripotent stem cells using epigenetic regulators reveals a germ cell-like identity in partially reprogrammed colonies. | Goyal A et al. | β | 2013 | β |
| Genetic and epigenetic instability in human pluripotent stem cells. | Nguyen HT et al. | β | 2013 | β |
| Genetic and epigenetic variations in iPSCs: potential causes and implications for application. | Liang G et al. | β | 2013 | β |
| Genome editing of human pluripotent stem cells to generate human cellular disease models. | Musunuru K | β | 2013 | β |
| Genomic imprinting is variably lost during reprogramming of mouse iPS cells. | Takikawa S et al. | β | 2013 | β |
| Human embryonic stem cells derived by somatic cell nuclear transfer. | Tachibana M et al. | β | 2013 | β |
| Human kidney cell reprogramming: applications for disease modeling and personalized medicine. | O'Neill AC et al. | β | 2013 | β |
| Human pluripotent stem cells: an emerging model in developmental biology. | Zhu Z et al. | β | 2013 | β |
| Human pluripotent stem cells with distinct X inactivation status show molecular and cellular differences controlled by the X-Linked ELK-1 gene. | Bruck T et al. | β | 2013 | β |
| Identification of novel imprinted differentially methylated regions by global analysis of human-parthenogenetic-induced pluripotent stem cells. | Stelzer Y et al. | β | 2013 | β |
| Isogenic human pluripotent stem cell pairs reveal the role of a KCNH2 mutation in long-QT syndrome. | Bellin M et al. | β | 2013 | β |
| MicroRNAs in pluripotency, reprogramming and cell fate induction. | LΓΌningschrΓΆr P et al. | β | 2013 | β |
| -Oh no! hiPSCs misplace their 5hmCs. | Lowry WE | β | 2013 | β |
| Pivots of pluripotency: the roles of non-coding RNA in regulating embryonic and induced pluripotent stem cells. | Huo JS et al. | β | 2013 | β |
| Pluripotent stem cells escape from senescence-associated DNA methylation changes. | Koch CM et al. | β | 2013 | β |
| Return of results in translational iPS cell research: considerations for donor informed consent. | Lomax GP et al. | β | 2013 | β |
| Stability of DNA methylation patterns in mouse spermatogonia under conditions of MTHFR deficiency and methionine supplementation. | Garner JL et al. | β | 2013 | β |
| Standardization of human stem cell pluripotency using bioinformatics. | Nestor MW et al. | β | 2013 | β |
| To clone or not to clone? Induced pluripotent stem cells can be generated in bulk culture. | Willmann CA et al. | β | 2013 | β |
| Toward pluripotency by reprogramming: mechanisms and application. | Wang T et al. | β | 2013 | β |
| Translating dosage compensation to trisomy 21. | Jiang J et al. | β | 2013 | β |
| X chromosome inactivation and epigenetic responses to cellular reprogramming. | Lessing D et al. | β | 2013 | β |
| Does transcription factor induced pluripotency accurately mimic embryo derived pluripotency? | Lowry WE | β | 2012 | β |
| Epigenetic alterations in human pluripotent stem cells: a tale of two cultures. | Wutz A | β | 2012 | β |
| Equally potent? Does cellular reprogramming justify the abandonment of human embryonic stem cells? | Nazor KL et al. | β | 2012 | β |
| Erosion of dosage compensation impacts human iPSC disease modeling. | Mekhoubad S et al. | β | 2012 | β |
| Genetic and epigenetic stability of human pluripotent stem cells. | Lund RJ et al. | β | 2012 | β |
| Human disease modeling with induced pluripotent stem cells. | Trounson A et al. | β | 2012 | β |
| Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells. | Ruiz S et al. | β | 2012 | β |
| The directed differentiation of human iPS cells into kidney podocytes. | Song B et al. | β | 2012 | β |
| The functions of microRNAs in pluripotency and reprogramming. | Leonardo TR et al. | β | 2012 | β |
| Time to reconsider stem cell induction strategies. | Denker HW | β | 2012 | β |