8C-like cells capture the human zygotic genome activation program in vitro

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

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

Mouse totipotent stem cells captured and maintained through spliceosomal repression

(2021) Hui Shen et al.   CELL

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei

(2020) Shan Jiang et al.   PLoS Genetics

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

A Single-Cell Transcriptomics CRISPR-Activation Screen Identifies Epigenetic Regulators of the Zygotic Genome Activation Program

(2020) Celia Alda-Catalinas et al.   Cell Systems

ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation

(2020) Mette Bentsen et al.   Nature Communications

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

(2019) Longqi Liu et al.   Nature Communications

Transcriptional Heterogeneity in Naive and Primed Human Pluripotent Stem Cells at Single-Cell Resolution

(2019) Tobias Messmer et al.   Cell Reports

Hominoid-Specific Transposable Elements and KZFPs Facilitate Human Embryonic Genome Activation and Control Transcription in Naive Human ESCs

(2019) Julien Pontis et al.   Cell Stem Cell

Capacitation of human naïve pluripotent stem cells for multi-lineage differentiation

(2019) Maria Rostovskaya et al.   DEVELOPMENT

DUX4-Induced Histone Variants H3.X and H3.Y Mark DUX4 Target Genes for Expression

(2019) Rebecca Resnick et al.   Cell Reports

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

(2019) Nicholas Bredenkamp et al.   Stem Cell Reports

A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity

(2018) Michelle Percharde et al.   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

Chromatin analysis in human early development reveals epigenetic transition during ZGA

(2018) Jingyi Wu et al.   NATURE

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

A molecular roadmap for the emergence of early-embryonic-like cells in culture

(2017) Diego Rodriguez-Terrones et al.   NATURE GENETICS

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

(2017) Alberto De Iaco et al.   NATURE GENETICS

Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons

(2017) Peter G Hendrickson et al.   NATURE GENETICS

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition

(2017) Yun Huang et al.   eLife

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

Molecular Criteria for Defining the Naive Human Pluripotent State

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

A developmental coordinate of pluripotency among mice, monkeys and humans

(2016) Tomonori Nakamura et al.   NATURE

Characterization and target genes of nine human PRD-like homeobox domain genes expressed exclusively in early embryos

(2016) Elo Madissoon et al.   Scientific Reports

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

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

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

(2016) Ge Guo et al.   Stem Cell Reports

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

(2015) Paul Blakeley et al.   DEVELOPMENT

Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells

(2015) Edward J. Grow et al.   NATURE

Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly

(2015) Takashi Ishiuchi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly

(2015) Takashi Ishiuchi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Zygotic Genome Activation During the Maternal-to-Zygotic Transition

(2014) Miler T. Lee et al.   Annual Review of Cell and Developmental Biology

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

DUX4-induced gene expression is the major molecular signature in FSHD skeletal muscle

(2014) Zizhen Yao et al.   HUMAN MOLECULAR GENETICS

Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells

(2014) Jichang Wang et al.   NATURE

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

(2013) Zhigang Xue 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

Epiblast Ground State Is Controlled by Canonical Wnt/β-Catenin Signaling in the Postimplantation Mouse Embryo and Epiblast Stem Cells

(2013) Tomoyuki Sumi et al.   PLoS One

Human pre-implantation embryo development

(2012) K. K. Niakan et al.   DEVELOPMENT

Embryonic stem cell potency fluctuates with endogenous retrovirus activity

(2012) Todd S. Macfarlan et al.   NATURE

Waves of early transcriptional activation and pluripotency program initiation during human preimplantation development

(2011) R. Vassena et al.   DEVELOPMENT

Human hypoblast formation is not dependent on FGF signalling

(2011) Mila Roode et al.   DEVELOPMENTAL BIOLOGY

Zscan4 regulates telomere elongation and genomic stability in ES cells

(2010) Michal Zalzman et al.   NATURE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Klf4 reverts developmentally programmed restriction of ground state pluripotency

(2009) G. Guo et al.   DEVELOPMENT

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY