Single cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development

Integrated analysis of single-cell embryo data yields a unified transcriptome signature for the human pre-implantation epiblast

(2018) Giuliano G. Stirparo et al.   DEVELOPMENT

ZSCAN10 expression corrects the genomic instability of iPSCs from aged donors

(2017) Maria Skamagki et al.   NATURE CELL BIOLOGY

The European Nucleotide Archive in 2017

(2017) Nicole Silvester et al.   NUCLEIC ACIDS RESEARCH

Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation

(2017) Hisham Mohammed et al.   Cell Reports

Zfp296 negatively regulates H3K9 methylation in embryonic development as a component of heterochromatin

(2017) Takumi Matsuura et al.   Scientific Reports

Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos

(2016) Sophie Petropoulos et al.   CELL

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

Tpbpa-Cre-mediated deletion of TFAP2C leads to deregulation ofCdkn1a,Akt1and the ERK pathway, causing placental growth arrest

(2016) Neha Sharma et al.   DEVELOPMENT

The Germ Cell Fate of Cynomolgus Monkeys Is Specified in the Nascent Amnion

(2016) Kotaro Sasaki et al.   DEVELOPMENTAL CELL

Self-organization of the in vitro attached human embryo

(2016) Alessia Deglincerti et al.   NATURE

A developmental coordinate of pluripotency among mice, monkeys and humans

(2016) Tomonori Nakamura et al.   NATURE

ZFP57 maintains the parent-of-origin-specific expression of the imprinted genes and differentially affects non-imprinted targets in mouse embryonic stem cells

(2016) Vincenzo Riso et al.   NUCLEIC ACIDS RESEARCH

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

(2016) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Twist1 is involved in trophoblast syncytialization by regulating GCM1

(2016) Xiaoyin Lu et al.   PLACENTA

Loss of the Otx2-Binding Site in the Nanog Promoter Affects the Integrity of Embryonic Stem Cell Subtypes and Specification of Inner Cell Mass-Derived Epiblast

(2016) Dario Acampora et al.   Cell Reports

The Developmental Control of Transposable Elements and the Evolution of Higher Species

(2015) Marc Friedli et al.   Annual Review of Cell and Developmental Biology

Sincell: an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq: Fig. 1.

(2015) Miguel Juliá et al.   BIOINFORMATICS

Reduced Gene Dosage of Tfap2c Impairs Trophoblast Lineage Differentiation and Alters Maternal Blood Spaces in the Mouse Placenta1

(2015) Stephanie Kaiser et al.   BIOLOGY OF REPRODUCTION

Sox7 is dispensable for primitive endoderm differentiation from mouse ES cells

(2015) Masaki Kinoshita et al.   BMC DEVELOPMENTAL BIOLOGY

Defining the three cell lineages of the human blastocyst by single-cell RNA-seq

(2015) P. Blakeley et al.   DEVELOPMENT

Epiblast morphogenesis before gastrulation

(2015) Guojun Sheng   DEVELOPMENTAL BIOLOGY

Lineage-Specific Profiling Delineates the Emergence and Progression of Naive Pluripotency in Mammalian Embryogenesis

(2015) Thorsten Boroviak et al.   DEVELOPMENTAL CELL

ETS-related Transcription Factors ETV4 and ETV5 Are Involved in Proliferation and Induction of Differentiation-associated Genes in Embryonic Stem (ES) Cells

(2015) Tadayuki Akagi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Pluripotency and Epigenetic Factors in Mouse Embryonic Stem Cell Fate Regulation

(2015) Lluis Morey et al.   MOLECULAR AND CELLULAR BIOLOGY

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation

(2015) Hannah Dueck et al.   GENOME BIOLOGY

FactoMineR: AnRPackage for Multivariate Analysis

(2015) Sébastien Lê et al.   Journal of Statistical Software

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

(2014) S. Anders et al.   BIOINFORMATICS

Self-Organizing Properties of Mouse Pluripotent Cells Initiate Morphogenesis upon Implantation

(2014) Ivan Bedzhov et al.   CELL

Reorganization of Enhancer Patterns in Transition from Naive to Primed Pluripotency

(2014) Christa Buecker et al.   Cell Stem Cell

Genetic Exploration of the Exit from Self-Renewal Using Haploid Embryonic Stem Cells

(2014) Martin Leeb et al.   Cell Stem Cell

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

(2014) Nadine Schrode et al.   DEVELOPMENTAL CELL

The R-spondin/Lgr5/Rnf43 module: regulator of Wnt signal strength

(2014) W. de Lau et al.   GENES & DEVELOPMENT

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

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

(2014) Simone Picelli et al.   Nature Protocols

AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors

(2014) Hong-Mei Zhang et al.   NUCLEIC ACIDS RESEARCH

Birth of Healthy Offspring following ICSI in In Vitro-Matured Common Marmoset (Callithrix jacchus) Oocytes

(2014) Tsukasa Takahashi et al.   PLoS One

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

(2014) Q. Deng et al.   SCIENCE

Otx2 and Oct4 Drive Early Enhancer Activation during Embryonic Stem Cell Transition from Naive Pluripotency

(2014) Shen-Hsi Yang et al.   Cell Reports

Sox17-Mediated XEN Cell Conversion Identifies Dynamic Networks Controlling Cell-Fate Decisions in Embryo-Derived Stem Cells

(2014) Angela C.H. McDonald et al.   Cell Reports

Zfp296 is a novel Klf4-interacting protein and functions as a negative regulator

(2013) Yuka Fujii et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Identification of the missing pluripotency mediator downstream of leukaemia inhibitory factor

(2013) Graziano Martello et al.   EMBO JOURNAL

Embryonic stem cell self-renewal pathways converge on the transcription factor Tfcp2l1

(2013) Shoudong Ye et al.   EMBO JOURNAL

Anatomy of a blastocyst: Cell behaviors driving cell fate choice and morphogenesis in the early mouse embryo

(2013) Nadine Schrode et al.   GENESIS

Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages

(2013) Yusuke Ohnishi et al.   NATURE CELL BIOLOGY

Systematic evaluation of spliced alignment programs for RNA-seq data

(2013) Pär G Engström et al.   NATURE METHODS

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Tcf15 Primes Pluripotent Cells for Differentiation

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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

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

Analysis of human embryos from zygote to blastocyst reveals distinct gene expression patterns relative to the mouse

(2012) Kathy K. Niakan et al.   DEVELOPMENTAL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Zfp296 Is a Novel, Pluripotent-Specific Reprogramming Factor

(2012) Gerrit Fischedick et al.   PLoS One

Early cell fate decisions in the mouse embryo

(2012) Néstor Saiz et al.   REPRODUCTION

Minimally invasive transabdominal collection of preimplantation embryos from the common marmoset monkey (Callithrix jacchus)

(2012) K. Hanazawa et al.   THERIOGENOLOGY

Troika of the Mouse Blastocyst: Lineage Segregation and Stem Cells

(2012) Jerome Artus et al.   Current Stem Cell Research & Therapy

Amnion formation in the mouse embryo: the single amniochorionic fold model

(2011) Paulo NG Pereira et al.   BMC DEVELOPMENTAL BIOLOGY

Differential plasticity of epiblast and primitive endoderm precursors within the ICM of the early mouse embryo

(2011) J. B. Grabarek et al.   DEVELOPMENT

p45NF-E2 represses Gcm1 in trophoblast cells to regulate syncytium formation, placental vascularization and embryonic growth

(2011) M. Kashif et al.   DEVELOPMENT

Human hypoblast formation is not dependent on FGF signalling

(2011) Mila Roode et al.   DEVELOPMENTAL BIOLOGY

Opposing effects of Tcf3 and Tcf1 control Wnt stimulation of embryonic stem cell self-renewal

(2011) Fei Yi et al.   NATURE CELL BIOLOGY

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

Silencing chromatin: comparing modes and mechanisms

(2011) Christian Beisel et al.   NATURE REVIEWS GENETICS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

A role for PDGF signaling in expansion of the extra-embryonic endoderm lineage of the mouse blastocyst

(2010) J. Artus et al.   DEVELOPMENT

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

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

(2009) J. Nichols et al.   DEVELOPMENT

Blastocyst lineage formation, early embryonic asymmetries and axis patterning in the mouse

(2009) J. Rossant et al.   DEVELOPMENT

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

(2009) Da Wei Huang et al.   Nature Protocols

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

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

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

(2008) B. Plusa et al.   DEVELOPMENT

A KRAB Domain Zinc Finger Protein in Imprinting and Disease

(2008) Ryutaro Hirasawa et al.   DEVELOPMENTAL CELL