A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs

EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering

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The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance

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Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells

(2014) Shanrong Zhao et al.   PLoS One

Genetic Background Drives Transcriptional Variation in Human Induced Pluripotent Stem Cells

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Refinement and Discovery of New Hotspots of Copy-Number Variation Associated with Autism Spectrum Disorder

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Ensembl 2014

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Differentiation-defective phenotypes revealed by large-scale analyses of human pluripotent stem cells

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Functional genomic screen of human stem cell differentiation reveals pathways involved in neurodevelopment and neurodegeneration

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Comparison of the molecular profiles of human embryonic and induced pluripotent stem cells of isogenic origin

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Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

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The Histone Deacetylase SIRT6 Is a Tumor Suppressor that Controls Cancer Metabolism

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Molecular Signatures of Human Induced Pluripotent Stem Cells Highlight Sex Differences and Cancer Genes

(2012) Montserrat C. Anguera et al.   Cell Stem Cell

HIF1α induced switch from bivalent to exclusively glycolytic metabolism during ESC-to-EpiSC/hESC transition

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Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells

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Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all–iPS cell mice from terminally differentiated B cells

(2012) Matthias Stadtfeld et al.   NATURE GENETICS

Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells

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Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling

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Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines

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Generation of Isogenic Pluripotent Stem Cells Differing Exclusively at Two Early Onset Parkinson Point Mutations

(2011) Frank Soldner et al.   CELL

Proteomic and phosphoproteomic comparison of human ES and iPS cells

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Modulation of Glucose Transporter 1 (GLUT1) Expression Levels Alters Mouse Mammary Tumor Cell Growth In Vitro and In Vivo

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Suppression of the Imprinted Gene NNAT and X-Chromosome Gene Activation in Isogenic Human iPS Cells

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The Histone Deacetylase Sirt6 Regulates Glucose Homeostasis via Hif1α

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Female Human iPSCs Retain an Inactive X Chromosome

(2010) Jason Tchieu et al.   Cell Stem Cell

Lab-Specific Gene Expression Signatures in Pluripotent Stem Cells

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Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells

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Pax6 Is a Human Neuroectoderm Cell Fate Determinant

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Molecular Analyses of Human Induced Pluripotent Stem Cells and Embryonic Stem Cells

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Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells

(2010) Matthias Stadtfeld et al.   NATURE

Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells

(2010) Sabine Loewer et al.   NATURE GENETICS

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Parkinson's Disease Patient-Derived Induced Pluripotent Stem Cells Free of Viral Reprogramming Factors

(2009) Frank Soldner et al.   CELL

Induced Pluripotent Stem Cells and Embryonic Stem Cells Are Distinguished by Gene Expression Signatures

(2009) Mark H. Chin et al.   Cell Stem Cell

Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling

(2009) Stuart M Chambers et al.   NATURE BIOTECHNOLOGY

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Structural Variation of Chromosomes in Autism Spectrum Disorder

(2008) Christian R. Marshall et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Disease-Specific Induced Pluripotent Stem Cells

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A High-Efficiency System for the Generation and Study of Human Induced Pluripotent Stem Cells

(2008) Nimet Maherali et al.   Cell Stem Cell

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

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