Recapitulating early human development with 8C-like cells

Chemical-induced chromatin remodeling reprograms mouse ESCs to totipotent-like stem cells

(2022) Mingzhu Yang et al.   Cell Stem Cell

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

(2022) Jasmin Taubenschmid-Stowers et al.   Cell Stem Cell

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

(2022) Md. Abdul Mazid et al.   NATURE

DNA replication fork speed underlies cell fate changes and promotes reprogramming

(2022) Tsunetoshi Nakatani et al.   NATURE GENETICS

Mouse totipotent stem cells captured and maintained through spliceosomal repression

(2021) Hui Shen et al.   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

Modelling human blastocysts by reprogramming fibroblasts into iBlastoids

(2021) Xiaodong Liu et al.   NATURE

Blastocyst-like structures generated from human pluripotent stem cells

(2021) Leqian Yu et al.   NATURE

Control of DUX4 Expression in Facioscapulohumeral Muscular Dystrophy and Cancer

(2021) Anna Karpukhina et al.   TRENDS IN MOLECULAR MEDICINE

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

p53 convergently activates Dux/DUX4 in embryonic stem cells and in facioscapulohumeral muscular dystrophy cell models

(2021) Edward J. Grow et al.   NATURE GENETICS

Chemically defined and xeno-free culture condition for human extended pluripotent stem cells

(2021) Bei Liu et al.   Nature Communications

Reconstructing aspects of human embryogenesis with pluripotent stem cells

(2021) Berna Sozen et al.   Nature Communications

Probing the signaling requirements for naive human pluripotency by high-throughput chemical screening

(2021) Shafqat A. Khan et al.   Cell Reports

Generation of human blastocyst-like structures from pluripotent stem cells

(2021) Yong Fan et al.   Cell Discovery

Capture of Mouse and Human Stem Cells with Features of Formative Pluripotency

(2021) Masaki Kinoshita et al.   Cell Stem Cell

Human blastoids model blastocyst development and implantation

(2021) Harunobu Kagawa et al.   NATURE

Aberrant DNA and histone methylation during zygotic genome activation in goat cloned embryos

(2020) Mingtian Deng et al.   THERIOGENOLOGY

Chromatin architecture reorganization in murine somatic cell nuclear transfer embryos

(2020) Mo Chen et al.   Nature Communications

ATR expands embryonic stem cell fate potential in response to replication stress

(2020) Sina Atashpaz et al.   eLife

Transient inhibition of mTOR in human pluripotent stem cells enables robust formation of mouse-human chimeric embryos

(2020) Zhixing Hu et al.   Science Advances

P38&#945 Regulates Expression of DUX4 in a Model of Facioscapulohumeral Muscular Dystrophy

(2020) Luis A Rojas et al.   JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS

A cell in hand is worth two in the embryo: recent advances in 2-cell like cell reprogramming

(2020) Ane Iturbide et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Reprogramming roadmap reveals route to human induced trophoblast stem cells

(2020) Xiaodong Liu et al.   NATURE

Derivation of Intermediate Pluripotent Stem Cells Amenable to Primordial Germ Cell Specification

(2020) Leqian Yu et al.   Cell Stem Cell

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

(2019) Tobias Messmer et al.   Cell Reports

Resetting histone modifications during human parental-to-zygotic transition

(2019) Weikun Xia et al.   SCIENCE

Reconstituting the transcriptome and DNA methylome landscapes of human implantation

(2019) Fan Zhou et al.   NATURE

Chromatin Accessibility Landscape in Human Early Embryos and Its Association with Evolution

(2018) Lei Gao et al.   CELL

Derivation of Human Trophoblast Stem Cells

(2018) Hiroaki Okae et al.   Cell Stem Cell

Functional genetics of early human development

(2018) Nicolás M Ortega et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

Mechanisms regulating zygotic genome activation

(2018) Katharine N. Schulz et al.   NATURE REVIEWS GENETICS

Genome editing reveals a role for OCT4 in human embryogenesis

(2017) Norah M. E. Fogarty 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

Conservation and innovation in the DUX4-family gene network

(2017) Jennifer L Whiddon et al.   NATURE GENETICS

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

(2016) Philip Ewels et al.   BIOINFORMATICS

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

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

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Ge Guo et al.   Stem Cell Reports

TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets

(2015) Ying Jin et al.   BIOINFORMATICS

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

Histone Demethylase Expression Enhances Human Somatic Cell Nuclear Transfer Efficiency and Promotes Derivation of Pluripotent Stem Cells

(2015) Young Gie Chung et al.   Cell Stem Cell

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

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

Embryonic Development following Somatic Cell Nuclear Transfer Impeded by Persisting Histone Methylation

(2014) Shogo Matoba 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

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

(2014) Jichang Wang et al.   NATURE

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

(2014) Simone Picelli et al.   Nature Protocols

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro 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

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

DUX4 Activates Germline Genes, Retroelements, and Immune Mediators: Implications for Facioscapulohumeral Dystrophy

(2011) Linda N. Geng et al.   DEVELOPMENTAL CELL

A Unifying Genetic Model for Facioscapulohumeral Muscular Dystrophy

(2010) R. J. L. F. Lemmers et al.   SCIENCE

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

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

Molecular evolution of a novel hyperactive Sleeping Beauty transposase enables robust stable gene transfer in vertebrates

(2009) Lajos Mátés et al.   NATURE GENETICS