Integrated pseudotime analysis of human pre-implantation embryo single-cell transcriptomes reveals the dynamics of lineage specification

Human naive epiblast cells possess unrestricted lineage potential

(2021) Ge Guo et al.   Cell Stem Cell

Derivation of trophoblast stem cells from naïve human pluripotent stem cells

(2020) Chen Dong et al.   eLife

Development of automated annotation software for human embryo morphokinetics

(2020) M Feyeux et al.   HUMAN REPRODUCTION

Naive Human Embryonic Stem Cells Can Give Rise to Cells with a Trophoblast-like Transcriptome and Methylome

(2020) Jessica K. Cinkornpumin et al.   Stem Cell Reports

Initiation of a conserved trophectoderm program in human, cow and mouse embryos

(2020) Claudia Gerri et al.   NATURE

Pluripotency and X chromosome dynamics revealed in pig pre-gastrulating embryos by single cell analysis

(2019) Priscila Ramos-Ibeas et al.   Nature Communications

Hydraulic control of mammalian embryo size and cell fate

(2019) Chii Jou Chan et al.   NATURE

Hydraulic fracturing and active coarsening position the lumen of the mouse blastocyst

(2019) Julien G. Dumortier et al.   SCIENCE

Worth the wait? Day 7 blastocysts have lower euploidy rates but similar sustained implantation rates as Day 5 and Day 6 blastocysts

(2019) A W Tiegs et al.   HUMAN REPRODUCTION

Reconstituting the transcriptome and DNA methylome landscapes of human implantation

(2019) Fan Zhou et al.   NATURE

The diverse roles of DNA methylation in mammalian development and disease

(2019) Maxim V. C. Greenberg et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

IFI16, a nuclear innate immune DNA sensor, mediates epigenetic silencing of herpesvirus genomes by its association with H3K9 methyltransferases SUV39H1 and GLP

(2019) Arunava Roy et al.   eLife

A developmental landscape of 3D-cultured human pre-gastrulation embryos

(2019) Lifeng Xiang et al.   NATURE

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

Instructions for Assembling the Early Mammalian Embryo

(2018) Melanie D. White et al.   DEVELOPMENTAL CELL

Blastocyst-like structures generated solely from stem cells

(2018) Nicolas C. Rivron et al.   NATURE

Parallel derivation of isogenic human primed and naive induced pluripotent stem cells

(2018) Stéphanie Kilens et al.   Nature Communications

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

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

(2018) Thorsten Boroviak et al.   DEVELOPMENT

BMP4 plays a role in apoptosis during human preimplantation development

(2018) C. De Paepe et al.   MOLECULAR REPRODUCTION AND DEVELOPMENT

HIPPO signaling resolves embryonic cell fate conflicts during establishment of pluripotency in vivo

(2018) Tristan Frum et al.   eLife

Embryo–epithelium interactions during implantation at a glance

(2017) John D. Aplin et al.   JOURNAL OF CELL SCIENCE

Pluripotent state transitions coordinate morphogenesis in mouse and human embryos

(2017) Marta N. Shahbazi et al.   NATURE

Genome editing reveals a role for OCT4 in human embryogenesis

(2017) Norah M. E. Fogarty et al.   NATURE

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

(2017) Xiaodong Liu et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Position- and Hippo signaling-dependent plasticity during lineage segregation in the early mouse embryo

(2017) Eszter Posfai et al.   eLife

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Cell Fate Specification Based on Tristability in the Inner Cell Mass of Mouse Blastocysts

(2016) Laurane De Mot et al.   BIOPHYSICAL JOURNAL

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

(2016) Sophie Petropoulos et al.   CELL

Molecular Criteria for Defining the Naive Human Pluripotent State

(2016) Thorold W. Theunissen et al.   Cell Stem Cell

Lineage specification in the mouse preimplantation embryo

(2016) Claire Chazaud et al.   DEVELOPMENT

New ISSCR guidelines: clinical translation of stem cell research

(2016) Jonathan Kimmelman et al.   LANCET

Self-organization of the in vitro attached human embryo

(2016) Alessia Deglincerti et al.   NATURE

Self-organization of the human embryo in the absence of maternal tissues

(2016) Marta N. Shahbazi et al.   NATURE CELL BIOLOGY

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

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

(2015) P. Blakeley et al.   DEVELOPMENT

Altered astrocyte morphology and vascular development in dystrophin-Dp71-null mice

(2015) Audrey Giocanti-Auregan et al.   GLIA

RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse

(2015) Zhi-Ping Liu et al.   Database-The Journal of Biological Databases and Curation

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

Reorganization of Enhancer Patterns in Transition from Naive to Primed Pluripotency

(2014) Christa Buecker 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

Proposed guidelines on the nomenclature and annotation of dynamic human embryo monitoring by a time-lapse user group

(2014) H. Nadir Ciray et al.   HUMAN REPRODUCTION

Trophectoderm morphology predicts outcomes of pregnancy in vitrified-warmed single-blastocyst transfer cycle in a Chinese population

(2014) Xiaojiao Chen et al.   JOURNAL OF ASSISTED REPRODUCTION AND GENETICS

Expression of Aquaporins in Human Embryos and Potential Role of AQP3 and AQP7 in Preimplantation Mouse Embryo Development

(2013) Yun Xiong et al.   CELLULAR PHYSIOLOGY AND BIOCHEMISTRY

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

(2013) Yoshikazu Hirate et al.   CURRENT BIOLOGY

A randomized clinical trial to evaluate the effect of granulocyte-macrophage colony-stimulating factor (GM-CSF) in embryo culture medium for in vitro fertilization

(2013) Søren Ziebe et al.   FERTILITY AND STERILITY

Trophectoderm grade predicts outcomes of single-blastocyst transfers

(2013) Micah J. Hill et al.   FERTILITY AND STERILITY

Blastocyst expansion score and trophectoderm morphology strongly predict successful clinical pregnancy and live birth following elective single embryo blastocyst transfer (eSET): a national study

(2013) Stephanie Marshall Thompson et al.   JOURNAL OF ASSISTED REPRODUCTION AND GENETICS

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

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

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

Human trophectoderm cells are not yet committed

(2012) C. De Paepe et al.   HUMAN REPRODUCTION

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

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

Human hypoblast formation is not dependent on FGF signalling

(2011) Mila Roode et al.   DEVELOPMENTAL BIOLOGY

Trophectoderm morphology: an important parameter for predicting live birth after single blastocyst transfer

(2011) A. Ahlstrom et al.   HUMAN REPRODUCTION

The Istanbul consensus workshop on embryo assessment: proceedings of an expert meeting

(2011) et al.   HUMAN REPRODUCTION

Models for Study of Human Embryo Implantation: Choice of Cell Lines?1

(2009) Natalie J. Hannan et al.   BIOLOGY OF REPRODUCTION

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Role of Cdx2 and cell polarity in cell allocation and specification of trophectoderm and inner cell mass in the mouse embryo

(2008) A. Jedrusik et al.   GENES & DEVELOPMENT

Implantation of the human embryo requires Rac1-dependent endometrial stromal cell migration

(2008) S. Grewal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA