Rolling back human pluripotent stem cells to an eight-cell embryo-like stage

Evaluating totipotency using criteria of increasing stringency

(2021) Eszter Posfai et al.   NATURE CELL BIOLOGY

ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis

(2021) Jeffrey M. Granja et al.   NATURE GENETICS

Single-cell multiomics sequencing reveals the functional regulatory landscape of early embryos

(2021) Yang Wang et al.   Nature Communications

Mouse totipotent stem cells captured and maintained through spliceosomal repression

(2021) Hui Shen et al.   CELL

Human naive epiblast cells possess unrestricted lineage potential

(2021) Ge Guo et al.   Cell Stem Cell

Principles of signaling pathway modulation for enhancing human naive pluripotency induction

(2021) Jonathan Bayerl et al.   Cell Stem Cell

Naive stem cell blastocyst model captures human embryo lineage segregation

(2021) Ayaka Yanagida et al.   Cell Stem Cell

Blastocyst-like structures generated from human pluripotent stem cells

(2021) Leqian Yu et al.   NATURE

Single-Nucleus Chromatin Accessibility Landscape Reveals Diversity in Regulatory Regions Across Distinct Adult Rat Cortex

(2021) Yeya Yu et al.   Frontiers in Molecular Neuroscience

Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer’s disease

(2021) Samuel Morabito et al.   NATURE GENETICS

Single-cell chromatin state analysis with Signac

(2021) Tim Stuart et al.   NATURE METHODS

Derivation of trophoblast stem cells from naïve human pluripotent stem cells

(2020) Chen Dong et al.   eLife

β-Catenin safeguards the ground state of mousepluripotency by strengthening the robustness of the transcriptional apparatus

(2020) Meng Zhang et al.   Science Advances

Reprogramming roadmap reveals route to human induced trophoblast stem cells

(2020) Xiaodong Liu et al.   NATURE

Recent evolution of a TET-controlled and DPPA3/STELLA-driven pathway of passive DNA demethylation in mammals

(2020) Christopher B. Mulholland et al.   Nature Communications

An integrated chromatin accessibility and transcriptome landscape of human pre-implantation embryos

(2019) Longqi Liu et al.   Nature Communications

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Establishment of porcine and human expanded potential stem cells

(2019) Xuefei Gao et al.   NATURE CELL BIOLOGY

Resetting histone modifications during human parental-to-zygotic transition

(2019) Weikun Xia et al.   SCIENCE

Excluding Oct4 from Yamanaka Cocktail Unleashes the Developmental Potential of iPSCs

(2019) Sergiy Velychko et al.   Cell Stem Cell

A distinct metabolic state arises during the emergence of 2‐cell‐like cells

(2019) Diego Rodriguez‐Terrones et al.   EMBO REPORTS

Wnt Inhibition Facilitates RNA-Mediated Reprogramming of Human Somatic Cells to Naive Pluripotency

(2019) Nicholas Bredenkamp et al.   Stem Cell Reports

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

TFAP2C regulates transcription in human naive pluripotency by opening enhancers

(2018) William A. Pastor et al.   NATURE CELL BIOLOGY

Unique molecular events during reprogramming of human somatic cells to induced pluripotent stem cells (iPSCs) at naïve state

(2018) Yixuan Wang et al.   eLife

Chromatin analysis in human early development reveals epigenetic transition during ZGA

(2018) Jingyi Wu et al.   NATURE

Reduced MEK inhibition preserves genomic stability in naive human embryonic stem cells

(2018) Bruno Di Stefano et al.   NATURE METHODS

Stella safeguards the oocyte methylome by preventing de novo methylation mediated by DNMT1

(2018) Yingfeng Li et al.   NATURE

BMI1 enables interspecies chimerism with human pluripotent stem cells

(2018) Ke Huang et al.   Nature Communications

Overexpression of Stella improves the efficiency of nuclear transfer reprogramming

(2017) Leyun Wang et al.   Journal of Genetics and Genomics

Establishment of mouse expanded potential stem cells

(2017) Jian Yang et al.   NATURE

DUX-family transcription factors regulate zygotic genome activation in placental mammals

(2017) Alberto De Iaco et al.   NATURE GENETICS

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

Naive Human Pluripotent Cells Feature a Methylation Landscape Devoid of Blastocyst or Germline Memory

(2016) William A. Pastor et al.   Cell Stem Cell

MERVL/Zscan4 Network Activation Results in Transient Genome-wide DNA Demethylation of mESCs

(2016) Mélanie A. Eckersley-Maslin et al.   Cell Reports

What Is Trophoblast? A Combination of Criteria Define Human First-Trimester Trophoblast

(2016) Cheryl Q.E. Lee et al.   Stem Cell Reports

Dynamic Transcription of Distinct Classes of Endogenous Retroviral Elements Marks Specific Populations of Early Human Embryonic Cells

(2015) Jonathan Göke et al.   Cell Stem Cell

Establishing the human naïve pluripotent state

(2015) Yair S Manor et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

CD24 tracks divergent pluripotent states in mouse and human cells

(2015) Nika Shakiba et al.   Nature Communications

Dppa3 expression is critical for generation of fully reprogrammed iPS cells and maintenance of Dlk1-Dio3 imprinting

(2015) Xingbo Xu et al.   Nature Communications

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

(2014) Yasuhiro Takashima et al.   CELL

Systematic Identification of Culture Conditions for Induction and Maintenance of Naive Human Pluripotency

(2014) Thorold W. Theunissen et al.   Cell Stem Cell

DNA methylation dynamics of the human preimplantation embryo

(2014) Zachary D. Smith et al.   NATURE

The DNA methylation landscape of human early embryos

(2014) Hongshan Guo et al.   NATURE

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

(2014) Sébastien A Smallwood et al.   NATURE METHODS

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

(2014) Simone Picelli et al.   Nature Protocols

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Q. Deng et al.   SCIENCE

BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data

(2013) Weilong Guo et al.   BMC GENOMICS

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

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

Embryonic stem cell potency fluctuates with endogenous retrovirus activity

(2012) Todd S. Macfarlan et al.   NATURE

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Vitamin C Enhances the Generation of Mouse and Human Induced Pluripotent Stem Cells

(2010) Miguel Angel Esteban et al.   Cell Stem Cell

DZNep is a global histone methylation inhibitor that reactivates developmental genes not silenced by DNA methylation

(2009) T. B. Miranda et al.   MOLECULAR CANCER THERAPEUTICS

Dynamic Equilibrium and Heterogeneity of Mouse Pluripotent Stem Cells with Distinct Functional and Epigenetic States

(2008) Katsuhiko Hayashi et al.   Cell Stem Cell