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

Comprehensive characterization of distinct states of human naive pluripotency generated by reprogramming

(2017) Xiaodong Liu et al.   NATURE METHODS

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

(2017) Takumi Matsuura et al.   Scientific Reports

Evolutionary origin and functional divergence of totipotent cell homeobox genes in eutherian mammals

(2016) Ignacio Maeso et al.   BMC BIOLOGY

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

(2016) Sophie Petropoulos et al.   CELL

3D Chromosome Regulatory Landscape of Human Pluripotent Cells

(2016) Xiong Ji et al.   Cell Stem 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

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

European Nucleotide Archive in 2016

(2016) Ana Luisa Toribio et al.   NUCLEIC ACIDS RESEARCH

Asynchronous fate decisions by single cells collectively ensure consistent lineage composition in the mouse blastocyst

(2016) Néstor Saiz et al.   Nature Communications

Naive Pluripotent Stem Cells Derived Directly from Isolated Cells of the Human Inner Cell Mass

(2016) Ge Guo et al.   Stem Cell Reports

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

destiny: diffusion maps for large-scale single-cell data in R

(2015) Philipp Angerer et al.   BIOINFORMATICS

SOX17 Is a Critical Specifier of Human Primordial Germ Cell Fate

(2015) Naoko Irie et al.   CELL

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

(2015) P. Blakeley et al.   DEVELOPMENT

The pluripotent state in mouse and human

(2015) K. C. Davidson et al.   DEVELOPMENT

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

(2015) Thorsten Boroviak et al.   DEVELOPMENTAL CELL

The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition

(2015) Henrik Sperber et al.   NATURE CELL BIOLOGY

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

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

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

(2014) Yasuhiro Takashima et al.   CELL

The Naive State of Human Pluripotent Stem Cells: A Synthesis of Stem Cell and Preimplantation Embryo Transcriptome Analyses

(2014) Kevin Huang 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

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

(2014) Nadine Schrode et al.   DEVELOPMENTAL CELL

The DNA methylation landscape of human early embryos

(2014) Hongshan Guo et al.   NATURE

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

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

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

Derivation of naive human embryonic stem cells

(2014) C. B. Ware et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

DeconRNASeq: a statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-Seq data

(2013) Ting Gong et al.   BIOINFORMATICS

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

(2013) Zhigang Xue et al.   NATURE

Derivation of novel human ground state naive pluripotent stem cells

(2013) Ohad Gafni et al.   NATURE

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

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

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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The roles of FGF and MAP kinase signaling in the segregation of the epiblast and hypoblast cell lineages in bovine and human embryos

(2012) E. W. Kuijk 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

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Tracking the progression of the human inner cell mass during embryonic stem cell derivation

(2012) Thomas O'Leary et al.   NATURE BIOTECHNOLOGY

Zfp296 Is a Novel, Pluripotent-Specific Reprogramming Factor

(2012) Gerrit Fischedick et al.   PLoS One

Multiobjective evolutionary algorithms to identify highly autocorrelated areas: the case of spatial distribution in financially compromised farms

(2011) Carlos R. García-Alonso et al.   ANNALS OF OPERATIONS RESEARCH

Human hypoblast formation is not dependent on FGF signalling

(2011) Mila Roode 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

Optimal Timing of Inner Cell Mass Isolation Increases the Efficiency of Human Embryonic Stem Cell Derivation and Allows Generation of Sibling Cell Lines

(2009) Alice E. Chen et al.   Cell Stem Cell

Naive and Primed Pluripotent States

(2009) Jennifer Nichols et al.   Cell Stem Cell

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

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