From blastocyst to gastrula: gene regulatory networks of embryonic stem cells and early mouse embryogenesis

Lin28a Is Dormant, Functional, and Dispensable During Mouse Oocyte-to-Embryo Transition1

(2014) Matyas Flemr et al.   BIOLOGY OF REPRODUCTION

Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns

(2014) Zhenzhen Zheng et al.   BMC Systems Biology

Oct4 is required for lineage priming in the developing inner cell mass of the mouse blastocyst

(2014) G. C. Le Bin et al.   DEVELOPMENT

GATA6 Levels Modulate Primitive Endoderm Cell Fate Choice and Timing in the Mouse Blastocyst

(2014) Nadine Schrode et al.   DEVELOPMENTAL CELL

Two different network topologies yield bistability in models of mesoderm and anterior mesendoderm specification in amphibians

(2014) L.E. Brown et al.   JOURNAL OF THEORETICAL BIOLOGY

The ability of inner-cell-mass cells to self-renew as embryonic stem cells is acquired following epiblast specification

(2014) Thorsten Boroviak et al.   NATURE CELL BIOLOGY

Coordinated repressive chromatin-remodeling of Oct4 and Nanog genes in RA-induced differentiation of embryonic stem cells involves RIP140

(2014) Cheng-Ying Wu et al.   NUCLEIC ACIDS RESEARCH

Zfp322a Regulates Mouse ES Cell Pluripotency and Enhances Reprogramming Efficiency

(2014) Hui Ma et al.   PLoS Genetics

microRNA Control of Mouse and Human Pluripotent Stem Cell Behavior

(2013) Tobias S. Greve et al.   Annual Review of Cell and Developmental Biology

One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering

(2013) Haoyi Wang et al.   CELL

One-Step Generation of Mice Carrying Reporter and Conditional Alleles by CRISPR/Cas-Mediated Genome Engineering

(2013) Hui Yang et al.   CELL

Exit from Pluripotency Is Gated by Intracellular Redistribution of the bHLH Transcription Factor Tfe3

(2013) Joerg Betschinger et al.   CELL

The Hippo Pathway Member Nf2 Is Required for Inner Cell Mass Specification

(2013) Katie Cockburn et al.   CURRENT BIOLOGY

Polarity-Dependent Distribution of Angiomotin Localizes Hippo Signaling in Preimplantation Embryos

(2013) Yoshikazu Hirate et al.   CURRENT BIOLOGY

Wnt signalling in mouse gastrulation and anterior development: new players in the pathway and signal output

(2013) Ruth M Arkell et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The role of pluripotency gene regulatory network components in mediating transitions between pluripotent cell states

(2013) Nicola Festuccia et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Tcf7l1 prepares epiblast cells in the gastrulating mouse embryo for lineage specification

(2013) J. A. Hoffman et al.   DEVELOPMENT

Pax3 and Zic1 trigger the early neural crest gene regulatory network by the direct activation of multiple key neural crest specifiers

(2013) Jean-Louis Plouhinec et al.   DEVELOPMENTAL BIOLOGY

Oct4 Cell-Autonomously Promotes Primitive Endoderm Development in the Mouse Blastocyst

(2013) Tristan Frum et al.   DEVELOPMENTAL CELL

A genetic and developmental pathway from STAT3 to the OCT4-NANOG circuit is essential for maintenance of ICM lineages in vivo

(2013) D. V. Do et al.   GENES & DEVELOPMENT

A New Software Package for Predictive Gene Regulatory Network Modeling and Redesign

(2013) Emmanuel Faure et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Context-Dependent Wiring of Sox2 Regulatory Networks for Self-Renewal of Embryonic and Trophoblast Stem Cells

(2013) Kenjiro Adachi et al.   MOLECULAR CELL

A defined Oct4 level governs cell state transitions of pluripotency entry and differentiation into all embryonic lineages

(2013) Aliaksandra Radzisheuskaya et al.   NATURE CELL BIOLOGY

Systematic identification of transcriptional regulatory modules from protein–protein interaction networks

(2013) Diego Diez et al.   NUCLEIC ACIDS RESEARCH

In Vivo Function and Evolution of the Eutherian-Specific Pluripotency Marker UTF1

(2013) Masazumi Nishimoto et al.   PLoS One

Patterning pluripotency in embryonic stem cells

(2013) Yue Shelby Zhang et al.   STEM CELLS

Novel Insights into Embryonic Stem Cell Self-Renewal Revealed Through Comparative Human and Mouse Systems Biology Networks

(2013) Karen G. Dowell et al.   STEM CELLS

Signaling Roadmap Modulating Naive and Primed Pluripotency

(2013) Seyedeh-Nafiseh Hassani et al.   STEM CELLS AND DEVELOPMENT

Totipotent Embryonic Stem Cells Arise in Ground-State Culture Conditions

(2013) Sophie M. Morgani et al.   Cell Reports

Tcf15 Primes Pluripotent Cells for Differentiation

(2013) Owen R. Davies et al.   Cell Reports

The differential response to Fgf signalling in cells internalized at different times influences lineage segregation in preimplantation mouse embryos

(2013) S. A. Morris et al.   Open Biology

Wnt Signaling Regulates the Lineage Differentiation Potential of Mouse Embryonic Stem Cells through Tcf3 Down-Regulation

(2013) Yaser Atlasi et al.   PLoS Genetics

Single cell lineage analysis of mouse embryonic stem cells at the exit from pluripotency

(2013) J. Trott et al.   Biology Open

TBX3 Directs Cell-Fate Decision toward Mesendoderm

(2013) Clair E. Weidgang et al.   Stem Cell Reports

Lineage Specifiers: New Players in the Induction of Pluripotency

(2013) Jian Shu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Esrrb Is a Direct Nanog Target Gene that Can Substitute for Nanog Function in Pluripotent Cells

(2012) Nicola Festuccia et al.   Cell Stem 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

Transcriptional regulatory networks in epiblast cells and during anterior neural plate development as modeled in epiblast stem cells

(2012) M. Iwafuchi-Doi et al.   DEVELOPMENT

FGF4 is required for lineage restriction and salt-and-pepper distribution of primitive endoderm factors but not their initial expression in the mouse

(2012) M. Kang et al.   DEVELOPMENT

The developmental dismantling of pluripotency is reversed by ectopic Oct4 expression

(2012) R. Osorno et al.   DEVELOPMENT

Otx2 is an intrinsic determinant of the embryonic stem cell state and is required for transition to a stable epiblast stem cell condition

(2012) D. Acampora et al.   DEVELOPMENT

Direct and indirect control of oral ectoderm regulatory gene expression by Nodal signaling in the sea urchin embryo

(2012) Enhu Li et al.   DEVELOPMENTAL BIOLOGY

Experimental approaches for gene regulatory network construction: The chick as a model system

(2012) Andrea Streit et al.   GENESIS

Noise Propagation in Gene Regulation Networks Involving Interlinked Positive and Negative Feedback Loops

(2012) Hui Zhang et al.   PLoS One

Cross-Species Genome Wide Expression Analysis during Pluripotent Cell Determination in Mouse and Rat Preimplantation Embryos

(2012) Elisa A. Casanova et al.   PLoS One

Wdr5 Mediates Self-Renewal and Reprogramming via the Embryonic Stem Cell Core Transcriptional Network

(2011) Yen-Sin Ang et al.   CELL

Pluripotency Factors in Embryonic Stem Cells Regulate Differentiation into Germ Layers

(2011) Matt Thomson et al.   CELL

Control of the Embryonic Stem Cell State

(2011) Richard A. Young   CELL

A Precarious Balance: Pluripotency Factors as Lineage Specifiers

(2011) Kyle M. Loh et al.   Cell Stem Cell

Primitive Endoderm Differentiates via a Three-Step Mechanism Involving Nanog and RTK Signaling

(2011) Stephen Frankenberg et al.   DEVELOPMENTAL CELL

Pluripotency factors regulate definitive endoderm specification through eomesodermin

(2011) A. K. K. Teo et al.   GENES & DEVELOPMENT

The transcriptional and signalling networks of pluripotency

(2011) Huck-Hui Ng et al.   NATURE CELL BIOLOGY

The pleiotropic structure of the genotype–phenotype map: the evolvability of complex organisms

(2011) Günter P. Wagner et al.   NATURE REVIEWS GENETICS

Gene network inference and visualization tools for biologists: application to new human transcriptome datasets

(2011) Daniel Hurley et al.   NUCLEIC ACIDS RESEARCH

Mir-290-295 deficiency in mice results in partially penetrant embryonic lethality and germ cell defects

(2011) L. A. Medeiros et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The ground state of pluripotency

(2010) Jason Wray et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

An interaction-motif-based scoring function for protein-ligand docking

(2010) Zhong-Ru Xie et al.   BMC BIOINFORMATICS

Epiblast Stem Cell Subpopulations Represent Mouse Embryos of Distinct Pregastrulation Stages

(2010) Dong Wook Han et al.   CELL

An Oct4-Centered Protein Interaction Network in Embryonic Stem Cells

(2010) Debbie L.C. van den Berg et al.   Cell Stem Cell

Tracing the Derivation of Embryonic Stem Cells from the Inner Cell Mass by Single-Cell RNA-Seq Analysis

(2010) Fuchou Tang et al.   Cell Stem Cell

Gata3 regulates trophoblast development downstream of Tead4 and in parallel to Cdx2

(2010) A. Ralston et al.   DEVELOPMENT

FGF signal-dependent segregation of primitive endoderm and epiblast in the mouse blastocyst

(2010) Y. Yamanaka et al.   DEVELOPMENT

Maternal control of early mouse development

(2010) L. Li et al.   DEVELOPMENT

Klf5 regulates lineage formation in the pre-implantation mouse embryo

(2010) S.-C. J. Lin et al.   DEVELOPMENT

Nanog is required for primitive endoderm formation through a non-cell autonomous mechanism

(2010) Daniel M. Messerschmidt et al.   DEVELOPMENTAL BIOLOGY

The primitive endoderm lineage of the mouse blastocyst: Sequential transcription factor activation and regulation of differentiation by Sox17

(2010) Jérôme Artus et al.   DEVELOPMENTAL BIOLOGY

Resolution of Cell Fate Decisions Revealed by Single-Cell Gene Expression Analysis from Zygote to Blastocyst

(2010) Guoji Guo et al.   DEVELOPMENTAL CELL

Emerging properties of animal gene regulatory networks

(2010) Eric H. Davidson   NATURE

Tbx3 improves the germ-line competency of induced pluripotent stem cells

(2010) Jianyong Han et al.   NATURE

A Novel SALL4/OCT4 Transcriptional Feedback Network for Pluripotency of Embryonic Stem Cells

(2010) Jianchang Yang et al.   PLoS One

Origin and formation of the first two distinct cell types of the inner cell mass in the mouse embryo

(2010) S. A. Morris et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nanog Is the Gateway to the Pluripotent Ground State

(2009) Jose Silva et al.   CELL

Naive and Primed Pluripotent States

(2009) Jennifer Nichols et al.   Cell Stem Cell

Network design principles from the sea urchin embryo

(2009) Eric H Davidson   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

(2009) J. Nichols et al.   DEVELOPMENT

Klf4 reverts developmentally programmed restriction of ground state pluripotency

(2009) G. Guo et al.   DEVELOPMENT

Active cell movements coupled to positional induction are involved in lineage segregation in the mouse blastocyst

(2009) Sigolène M. Meilhac et al.   DEVELOPMENTAL BIOLOGY

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

Selective inactivation of Otx2 mRNA isoforms reveals isoform-specific requirement for visceral endoderm anteriorization and head morphogenesis and highlights cell diversity in the visceral endoderm

(2009) Dario Acampora et al.   MECHANISMS OF DEVELOPMENT

The Pluripotency-Associated Gene Dppa4 Is Dispensable for Embryonic Stem Cell Identity and Germ Cell Development but Essential for Embryogenesis

(2009) B. Madan et al.   MOLECULAR AND CELLULAR BIOLOGY

Genome-wide identification of post-translational modulators of transcription factor activity in human B cells

(2009) Kai Wang et al.   NATURE BIOTECHNOLOGY

Identification of Pou5f1, Sox2, and Nanog downstream target genes with statistical confidence by applying a novel algorithm to time course microarray and genome-wide chromatin immunoprecipitation data

(2008) Alexei A Sharov et al.   BMC GENOMICS

Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells

(2008) Alexander Marson et al.   CELL

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

Capturing Pluripotency

(2008) Jose Silva et al.   CELL

An Extended Transcriptional Network for Pluripotency of Embryonic Stem Cells

(2008) Jonghwan Kim et al.   CELL

Krüppel-like factor 5 Is Essential for Blastocyst Development and the Normal Self-Renewal of Mouse ESCs

(2008) Masatsugu Ema et al.   Cell Stem Cell

Sall4 Regulates Distinct Transcription Circuitries in Different Blastocyst-Derived Stem Cell Lineages

(2008) Chin Yan Lim et al.   Cell Stem Cell

Distinct sequential cell behaviours direct primitive endoderm formation in the mouse blastocyst

(2008) B. Plusa et al.   DEVELOPMENT

Tcf3 is an integral component of the core regulatory circuitry of embryonic stem cells

(2008) M. F. Cole et al.   GENES & DEVELOPMENT

REST maintains self-renewal and pluripotency of embryonic stem cells

(2008) Sanjay K. Singh et al.   NATURE

The ground state of embryonic stem cell self-renewal

(2008) Qi-Long Ying et al.   NATURE

MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation

(2008) Yvonne Tay et al.   NATURE

A core Klf circuitry regulates self-renewal of embryonic stem cells

(2008) Jianming Jiang et al.   NATURE CELL BIOLOGY

Ras-MAPK signaling promotes trophectoderm formation from embryonic stem cells and mouse embryos

(2008) Chi-Wei Lu et al.   NATURE GENETICS

Selective Blockade of MicroRNA Processing by Lin28

(2008) S. R. Viswanathan et al.   SCIENCE

The Transcription/Migration Interface in Heart Precursors of Ciona intestinalis

(2008) L. Christiaen et al.   SCIENCE

Small Increases in the Level of Sox2 Trigger the Differentiation of Mouse Embryonic Stem Cells

(2008) Janel L. Kopp et al.   STEM CELLS

Stage-Dependent Effect of TGF-β1 on Chondrogenic Differentiation of Human Embryonic Stem Cells

(2008) Zheng Yang et al.   STEM CELLS AND DEVELOPMENT

A spatially dynamic cohort of regulatory genes in the endomesodermal gene network of the sea urchin embryo

(2007) Joel Smith et al.   DEVELOPMENTAL BIOLOGY