Derivation of ground-state female ES cells maintaining gamete-derived DNA methylation

Naive Human Pluripotent Cells Feature a Methylation Landscape Devoid of Blastocyst or Germline Memory

(2016) William A. Pastor et al.   Cell Stem Cell

Molecular Criteria for Defining the Naive Human Pluripotent State

(2016) Thorold W. Theunissen et al.   Cell Stem Cell

Global Landscape and Regulatory Principles of DNA Methylation Reprogramming for Germ Cell Specification by Mouse Pluripotent Stem Cells

(2016) Kenjiro Shirane et al.   DEVELOPMENTAL CELL

Maternal DNA Methylation Regulates Early Trophoblast Development

(2016) Miguel R. Branco et al.   DEVELOPMENTAL CELL

Naive Pluripotent Stem Cells Derived Directly from Isolated Cells of the Human Inner Cell Mass

(2016) Ge Guo et al.   Stem Cell Reports

NIG_MoG: a mouse genome navigator for exploring intersubspecific genetic polymorphisms

(2015) Toyoyuki Takada et al.   MAMMALIAN GENOME

Premature Termination of Reprogramming In Vivo Leads to Cancer Development through Altered Epigenetic Regulation

(2014) Kotaro Ohnishi et al.   CELL

Regulatory Principles of Pluripotency: From the Ground State Up

(2014) Jamie A. Hackett et al.   Cell Stem Cell

The Two Active X Chromosomes in Female ESCs Block Exit from the Pluripotent State by Modulating the ESC Signaling Network

(2014) Edda G. Schulz et al.   Cell Stem Cell

Derivation and characterization of mouse embryonic stem cells from permissive and nonpermissive strains

(2014) Anne Czechanski et al.   Nature Protocols

The UCSC Genome Browser database: 2015 update

(2014) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

FGF Signaling Inhibition in ESCs Drives Rapid Genome-wide Demethylation to the Epigenetic Ground State of Pluripotency

(2013) Gabriella Ficz et al.   Cell Stem Cell

Whole-Genome Bisulfite Sequencing of Two Distinct Interconvertible DNA Methylomes of Mouse Embryonic Stem Cells

(2013) Ehsan Habibi et al.   Cell Stem Cell

The ancestor of extant Japanese fancy mice contributed to the mosaic genomes of classical inbred strains

(2013) T. Takada et al.   GENOME RESEARCH

Naive pluripotency is associated with global DNA hypomethylation

(2013) Harry G Leitch et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Latrunculin A Treatment Prevents Abnormal Chromosome Segregation for Successful Development of Cloned Embryos

(2013) Yukari Terashita et al.   PLoS One

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Synergistic Mechanisms of DNA Demethylation during Transition to Ground-State Pluripotency

(2013) Jamie A. Hackett et al.   Stem Cell Reports

Latrunculin A Can Improve the Birth Rate of Cloned Mice and Simplify the Nuclear Transfer Protocol by Gently Inhibiting Actin Polymerization1

(2012) Yukari Terashita et al.   BIOLOGY OF REPRODUCTION

The Transcriptional and Epigenomic Foundations of Ground State Pluripotency

(2012) Hendrik Marks et al.   CELL

A unique regulatory phase of DNA methylation in the early mammalian embryo

(2012) Zachary D. Smith et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Dual Inhibition of Src and GSK3 Maintains Mouse Embryonic Stem Cells, Whose Differentiation Is Mechanically Regulated by Src Signaling

(2012) Takeshi Shimizu et al.   STEM CELLS

Contribution of Intragenic DNA Methylation in Mouse Gametic DNA Methylomes to Establish Oocyte-Specific Heritable Marks

(2012) Hisato Kobayashi et al.   PLoS Genetics

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

Dynamic stage-specific changes in imprinted differentially methylated regions during early mammalian development and prevalence of non-CpG methylation in oocytes

(2011) S.-i. Tomizawa et al.   DEVELOPMENT

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

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

(2010) Matthias Stadtfeld et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome

(2010) Robert S. Illingworth et al.   PLoS Genetics

Naive and Primed Pluripotent States

(2009) Jennifer Nichols et al.   Cell Stem Cell

Capture of Authentic Embryonic Stem Cells from Rat Blastocysts

(2008) Mia Buehr et al.   CELL

The ground state of embryonic stem cell self-renewal

(2008) Qi-Long Ying et al.   NATURE