Prolonged Mek1/2 suppression impairs the developmental potential of embryonic stem cells

Next Generation Sequencing-Based Comprehensive Chromosome Screening in Mouse Polar Bodies, Oocytes, and Embryos1

(2016) Nathan R. Treff et al.   BIOLOGY OF REPRODUCTION

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

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

Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells

(2016) Ferdinand von Meyenn et al.   MOLECULAR CELL

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation

(2015) Aleksandra A. Kolodziejczyk et al.   Cell Stem Cell

Erk signaling is indispensable for genomic stability and self-renewal of mouse embryonic stem cells

(2015) Haixia Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Resetting Transcription Factor Control Circuitry toward Ground-State Pluripotency in Human

(2014) Yasuhiro Takashima et al.   CELL

Histone Variant H2A.X Deposition Pattern Serves as a Functional Epigenetic Mark for Distinguishing the Developmental Potentials of iPSCs

(2014) Tao Wu et al.   Cell Stem Cell

Systematic Identification of Culture Conditions for Induction and Maintenance of Naive Human Pluripotency

(2014) Thorold W. Theunissen 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

Genomic imprinting in development, growth, behavior and stem cells

(2014) Robert N. Plasschaert et al.   DEVELOPMENT

Beta-Catenin Is Vital for the Integrity of Mouse Embryonic Stem Cells

(2014) Angelo Raggioli et al.   PLoS One

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

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

(2013) Simon Anders et al.   Nature Protocols

Naive pluripotency is associated with global DNA hypomethylation

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

A Comparative Study of Protocols for Mouse Embryonic Stem Cell Culturing

(2013) Christoffer Tamm et al.   PLoS One

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

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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The Transcriptional and Epigenomic Foundations of Ground State Pluripotency

(2012) Hendrik Marks et al.   CELL

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

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

(2012) Patrick Boyle et al.   GENOME BIOLOGY

Identifying dispersed epigenomic domains from ChIP-Seq data

(2011) Qiang Song et al.   BIOINFORMATICS

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Inhibition of glycogen synthase kinase-3 alleviates Tcf3 repression of the pluripotency network and increases embryonic stem cell resistance to differentiation

(2011) Jason Wray et al.   NATURE CELL BIOLOGY

Self-Renewal Versus Lineage Commitment of Embryonic Stem Cells: Protein Kinase C Signaling Shifts the Balance

(2011) Debasree Dutta et al.   STEM CELLS

A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression

(2010) Edward L. Huttlin et al.   CELL

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

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

A reprogrammable mouse strain from gene-targeted embryonic stem cells

(2009) Matthias Stadtfeld et al.   NATURE METHODS

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

WSTF regulates the H2A.X DNA damage response via a novel tyrosine kinase activity

(2008) Andrew Xiao et al.   NATURE

The ground state of embryonic stem cell self-renewal

(2008) Qi-Long Ying et al.   NATURE