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

Derivation of Human Trophoblast Stem Cells

(2018) Hiroaki Okae et al.   Cell Stem Cell

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

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Self-assembly of embryonic and two extra-embryonic stem cell types into gastrulating embryo-like structures

(2018) Berna Sozen et al.   NATURE CELL BIOLOGY

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

(2018) Sophie M Morgani et al.   eLife

Single-cell RNA-seq reveals the diversity of trophoblast subtypes and patterns of differentiation in the human placenta 

(2018) Yawei Liu et al.   CELL RESEARCH

Single-cell RNA-sequencing reveals the existence of naive and primed pluripotency in pre-implantation rhesus monkey embryos

(2018) Denghui Liu et al.   GENOME RESEARCH

Self-organization of a human organizer by combined Wnt and Nodal signalling

(2018) I. Martyn et al.   NATURE

Single-cell reconstruction of the early maternal–fetal interface in humans

(2018) Roser Vento-Tormo et al.   NATURE

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

Pluripotent state transitions coordinate morphogenesis in mouse and human embryos

(2017) Marta N. Shahbazi et al.   NATURE

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

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

(2016) Sophie Petropoulos et al.   CELL

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

(2016) Kotaro Sasaki et al.   DEVELOPMENTAL CELL

Implantation barrier overcome

(2016) Janet Rossant   NATURE

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

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

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

Self-organized amniogenesis by human pluripotent stem cells in a biomimetic implantation-like niche

(2016) Yue Shao et al.   NATURE MATERIALS

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

(2015) P. Blakeley et al.   DEVELOPMENT

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

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

(2014) Ivan Bedzhov et al.   CELL

Regulatory Principles of Pluripotency: From the Ground State Up

(2014) Jamie A. Hackett et al.   Cell Stem Cell

Distinct Wnt-driven primitive streak-like populations reflect in vivo lineage precursors

(2014) A. Tsakiridis et al.   DEVELOPMENT

Nanog co-regulated by Nodal/Smad2 and Oct4 is required for pluripotency in developing mouse epiblast

(2014) Liang Tso Sun et al.   DEVELOPMENTAL BIOLOGY

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

(2014) Simone Picelli et al.   Nature Protocols

The UCSC Genome Browser database: 2015 update

(2014) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases

(2011) Chen Xie et al.   NUCLEIC ACIDS RESEARCH

Cytoscape 2.8: new features for data integration and network visualization

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

On the origin of amniotic stem cells: of mice and men

(2010) Mariya P. Dobreva et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

The PluriNetWork: An Electronic Representation of the Network Underlying Pluripotency in Mouse, and Its Applications

(2010) Anup Som et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS