Establishment of mouse expanded potential stem cells

From the stem of the placental tree: trophoblast stem cells and their progeny

(2016) Paulina Anna Latos et al.   DEVELOPMENT

Tankyrase inhibition promotes a stable human naïve pluripotent state with improved functionality

(2016) Ludovic Zimmerlin et al.   DEVELOPMENT

Generating Cellular Diversity and Spatial Form: Wnt Signaling and the Evolution of Multicellular Animals

(2016) Kyle M. Loh et al.   DEVELOPMENTAL CELL

Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos

(2016) Xiaoyu Liu et al.   NATURE

Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition

(2016) John Arne Dahl et al.   NATURE

The landscape of accessible chromatin in mammalian preimplantation embryos

(2016) Jingyi Wu et al.   NATURE

A loss-of-function and H2B-Venus transcriptional reporter allele for Gata6 in mice

(2015) Laina Freyer et al.   BMC DEVELOPMENTAL BIOLOGY

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

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

FGF/MAPK signaling sets the switching threshold of a bistable circuit controlling cell fate decisions in embryonic stem cells

(2015) C. Schro ter et al.   DEVELOPMENT

Tankyrase Inhibitors Target YAP by Stabilizing Angiomotin Family Proteins

(2015) Wenqi Wang et al.   Cell Reports

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

(2014) S. Anders et al.   BIOINFORMATICS

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

(2014) Li Shen et al.   BMC GENOMICS

YAP/TAZ Incorporation in the β-Catenin Destruction Complex Orchestrates the Wnt Response

(2014) Luca Azzolin et al.   CELL

Yap1 Activation Enables Bypass of Oncogenic Kras Addiction in Pancreatic Cancer

(2014) Avnish Kapoor et al.   CELL

KRAS and YAP1 Converge to Regulate EMT and Tumor Survival

(2014) Diane D. Shao et al.   CELL

Reorganization of Enhancer Patterns in Transition from Naive to Primed Pluripotency

(2014) Christa Buecker et al.   Cell Stem Cell

Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells

(2014) Q. Deng et al.   SCIENCE

Derivation and Maintenance of Murine Trophoblast Stem Cells under Defined Conditions

(2014) Caroline Kubaczka et al.   Stem Cell Reports

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

Reprogramming in vivo produces teratomas and iPS cells with totipotency features

(2013) María Abad et al.   NATURE

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

Derivation of extraembryonic endoderm stem (XEN) cells from mouse embryos and embryonic stem cells

(2013) Kathy K Niakan et al.   Nature Protocols

Naive pluripotency is associated with global DNA hypomethylation

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

Totipotent Embryonic Stem Cells Arise in Ground-State Culture Conditions

(2013) Sophie M. Morgani et al.   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

Esrrb Is a Pivotal Target of the Gsk3/Tcf3 Axis Regulating Embryonic Stem Cell Self-Renewal

(2012) Graziano Martello et al.   Cell Stem Cell

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Calcineurin-NFAT Signaling Critically Regulates Early Lineage Specification in Mouse Embryonic Stem Cells and Embryos

(2011) Xiang Li et al.   Cell Stem Cell

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Histone H3K27 methyltransferase Ezh2 represses Wnt genes to facilitate adipogenesis

(2010) L. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Suppression of Erk signalling promotes ground state pluripotency in the mouse embryo

(2009) J. Nichols et al.   DEVELOPMENT

The Hippo Signaling Pathway Components Lats and Yap Pattern Tead4 Activity to Distinguish Mouse Trophectoderm from Inner Cell Mass

(2009) Noriyuki Nishioka et al.   DEVELOPMENTAL CELL

Tankyrase inhibition stabilizes axin and antagonizes Wnt signalling

(2009) Shih-Min A. Huang et al.   NATURE

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

(2009) Da Wei Huang et al.   Nature Protocols

The ground state of embryonic stem cell self-renewal

(2008) Qi-Long Ying et al.   NATURE

Epigenetic restriction of embryonic cell lineage fate by methylation of Elf5

(2008) Ray Kit Ng et al.   NATURE CELL BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY