Oct4 regulates the embryonic axis and coordinates exit from pluripotency and germ layer specification in the mouse embryo

Micropattern differentiation of mouse pluripotent stem cells recapitulates embryo regionalized cell fate patterning

(2018) Sophie M Morgani et al.   eLife

Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq

(2017) Jun Chen et al.   Nature Protocols

Spatial Transcriptome for the Molecular Annotation of Lineage Fates and Cell Identity in Mid-gastrula Mouse Embryo

(2016) Guangdun Peng et al.   DEVELOPMENTAL CELL

PathVisio 3: An Extendable Pathway Analysis Toolbox

(2015) Martina Kutmon et al.   PLoS Computational Biology

OCT4 Coordinates with WNT Signaling to Pre-pattern Chromatin at the SOX17 Locus during Human ES Cell Differentiation into Definitive Endoderm

(2015) Lei Ying et al.   Stem Cell Reports

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

(2014) S. Anders et al.   BIOINFORMATICS

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

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

SOX17 links gut endoderm morphogenesis and germ layer segregation

(2014) Manuel Viotti et al.   NATURE CELL BIOLOGY

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Reduced Oct4 Expression Directs a Robust Pluripotent State with Distinct Signaling Activity and Increased Enhancer Occupancy by Oct4 and Nanog

(2013) Violetta Karwacki-Neisius et al.   Cell Stem Cell

The Transcriptional and Functional Properties of Mouse Epiblast Stem Cells Resemble the Anterior Primitive Streak

(2013) Yoji Kojima et al.   Cell Stem Cell

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

(2013) Tristan Frum et al.   DEVELOPMENTAL 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

Epiblast Ground State Is Controlled by Canonical Wnt/β-Catenin Signaling in the Postimplantation Mouse Embryo and Epiblast Stem Cells

(2013) Tomoyuki Sumi et al.   PLoS One

Oct4 Is Required ∼E7.5 for Proliferation in the Primitive Streak

(2013) Brian DeVeale et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Distinct Lineage Specification Roles for NANOG, OCT4, and SOX2 in Human Embryonic Stem Cells

(2012) Zheng Wang et al.   Cell Stem Cell

The developmental dismantling of pluripotency is reversed by ectopic Oct4 expression

(2012) R. Osorno et al.   DEVELOPMENT

Transcriptional Activation by Oct4 Is Sufficient for the Maintenance and Induction of Pluripotency

(2012) Fella Hammachi et al.   Cell Reports

Pluripotency Factors in Embryonic Stem Cells Regulate Differentiation into Germ Layers

(2011) Matt Thomson et al.   CELL

Clonal and molecular analysis of the prospective anterior neural boundary in the mouse embryo

(2011) M. Cajal et al.   DEVELOPMENT

WikiPathways: building research communities on biological pathways

(2011) T. Kelder et al.   NUCLEIC ACIDS RESEARCH

Intestinal Crypt Homeostasis Results from Neutral Competition between Symmetrically Dividing Lgr5 Stem Cells

(2010) Hugo J. Snippert et al.   CELL

Simultaneous overexpression of Oct4 and Nanog abrogates terminal myogenesis

(2009) Kuan Chih Lang et al.   AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY

GAGE: generally applicable gene set enrichment for pathway analysis

(2009) Weijun Luo et al.   BMC BIOINFORMATICS

Naive and Primed Pluripotent States

(2009) Jennifer Nichols et al.   Cell Stem Cell

Foxa2 regulates polarity and epithelialization in the endoderm germ layer of the mouse embryo

(2009) I. Burtscher et al.   DEVELOPMENT

Making a commitment: cell lineage allocation and axis patterning in the early mouse embryo

(2009) Sebastian J. Arnold et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells

(2009) Z. Ouyang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Presenting and exploring biological pathways with PathVisio

(2008) Martijn P van Iersel et al.   BMC BIOINFORMATICS

The T-box transcription factor Eomes/Tbr2 regulates neurogenesis in the cortical subventricular zone

(2008) S. J. Arnold et al.   GENES & DEVELOPMENT