Selective demethylation and altered gene expression are associated with ICF syndrome in human-induced pluripotent stem cells and mesenchymal stem cells

Charting a dynamic DNA methylation landscape of the human genome

(2013) Michael J. Ziller et al.   NATURE

Large conserved domains of low DNA methylation maintained by Dnmt3a

(2013) Mira Jeong et al.   NATURE GENETICS

Global Epigenomic Reconfiguration During Mammalian Brain Development

(2013) R. Lister et al.   SCIENCE

Mouse Oocyte Methylomes at Base Resolution Reveal Genome-Wide Accumulation of Non-CpG Methylation and Role of DNA Methyltransferases

(2013) Kenjiro Shirane et al.   PLoS Genetics

A Panel of CpG Methylation Sites Distinguishes Human Embryonic Stem Cells and Induced Pluripotent Stem Cells

(2013) Kevin Huang et al.   Stem Cell Reports

A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells

(2012) Jose M. Polo et al.   CELL

Histone Demethylases KDM4B and KDM6B Promotes Osteogenic Differentiation of Human MSCs

(2012) Ling Ye et al.   Cell Stem Cell

Identification of novel molecular markers through transcriptomic analysis in human fetal and adult corneal endothelial cells

(2012) Yinyin Chen et al.   HUMAN MOLECULAR GENETICS

Accumulation and loss of asymmetric non-CpG methylation during male germ-cell development

(2012) Tomoko Ichiyanagi et al.   NUCLEIC ACIDS RESEARCH

A sensitive mass spectrometry method for simultaneous quantification of DNA methylation and hydroxymethylation levels in biological samples

(2011) Thuc Le et al.   ANALYTICAL BIOCHEMISTRY

Control of the Embryonic Stem Cell State

(2011) Richard A. Young   CELL

De novo DNA methylation by Dnmt3a and Dnmt3b is dispensable for nuclear reprogramming of somatic cells to a pluripotent state

(2011) M. Pawlak et al.   GENES & DEVELOPMENT

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

(2011) Ryan Lister et al.   NATURE

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

DNMT3A mutations in acute myeloid leukemia

(2011) Mrinal Y Shah et al.   NATURE GENETICS

Mutations in DNMT1 cause hereditary sensory neuropathy with dementia and hearing loss

(2011) Christopher J Klein et al.   NATURE GENETICS

Genomic Distribution and Inter-Sample Variation of Non-CpG Methylation across Human Cell Types

(2011) Michael J. Ziller et al.   PLoS Genetics

A comparative analysis of DNA methylation across human embryonic stem cell lines

(2011) Pao-Yang Chen et al.   GENOME BIOLOGY

BS Seeker: precise mapping for bisulfite sequencing

(2010) Pao-Yang Chen et al.   BMC BIOINFORMATICS

Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells

(2010) R. David Hawkins et al.   Cell Stem Cell

Repression of Retrotransposal Elements in Mouse Embryonic Stem Cells Is Primarily Mediated by a DNA Methylation-independent Mechanism

(2010) Leah K. Hutnick et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

DNMT3AMutations in Acute Myeloid Leukemia

(2010) Timothy J. Ley et al.   NEW ENGLAND JOURNAL OF MEDICINE

DNA methylation in cell differentiation and reprogramming: an emerging systematic view

(2010) Kevin Huang et al.   Regenerative Medicine

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Reprogramming towards pluripotency requires AID-dependent DNA demethylation

(2009) Nidhi Bhutani et al.   NATURE

Live cell imaging distinguishes bona fide human iPS cells from partially reprogrammed cells

(2009) Elayne M Chan et al.   NATURE BIOTECHNOLOGY

Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts

(2009) Akiko Doi et al.   NATURE GENETICS

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

(2009) Da Wei Huang et al.   Nature Protocols

ICF, an immunodeficiency syndrome: DNA methyltransferase 3B involvement, chromosome anomalies, and gene dysregulation

(2008) Melanie Ehrlich et al.   AUTOIMMUNITY

Defining Molecular Cornerstones during Fibroblast to iPS Cell Reprogramming in Mouse

(2008) Matthias Stadtfeld et al.   Cell Stem Cell

Unraveling Epigenetic Regulation in Embryonic Stem Cells

(2008) Marina Bibikova et al.   Cell Stem Cell

Promoter CpG Methylation Contributes to ES Cell Gene Regulation in Parallel with Oct4/Nanog, PcG Complex, and Histone H3 K4/K27 Trimethylation

(2008) Shaun D. Fouse et al.   Cell Stem Cell

Induction of Pluripotent Stem Cells from Mouse Embryonic Fibroblasts by Oct4 and Klf4 with Small-Molecule Compounds

(2008) Yan Shi et al.   Cell Stem Cell

Lineage-Specific Polycomb Targets and De Novo DNA Methylation Define Restriction and Potential of Neuronal Progenitors

(2008) Fabio Mohn et al.   MOLECULAR CELL

Dissecting direct reprogramming through integrative genomic analysis

(2008) Tarjei S. Mikkelsen et al.   NATURE

A drug-inducible transgenic system for direct reprogramming of multiple somatic cell types

(2008) Marius Wernig et al.   NATURE BIOTECHNOLOGY

Induction of pluripotent stem cells from primary human fibroblasts with only Oct4 and Sox2

(2008) Danwei Huangfu et al.   NATURE BIOTECHNOLOGY

Global Mapping of DNA Methylation in Mouse Promoters Reveals Epigenetic Reprogramming of Pluripotency Genes

(2008) Cassandra R. Farthing et al.   PLoS Genetics