Klf5 establishes bi-potential cell fate by dual regulation of ICM and TE specification genes

Maternal factor NELFA drives a 2C-like state in mouse embryonic stem cells

(2020) Zhenhua Hu et al.   NATURE CELL BIOLOGY

Trajectory-based differential expression analysis for single-cell sequencing data

(2020) Koen Van den Berge et al.   Nature Communications

Retinoic Acid Induces Embryonic Stem Cells (ESCs) Transition to 2 Cell-Like State Through a Coordinated Expression of Dux and Duxbl1

(2020) Daniela Tagliaferri et al.   Frontiers in Cell and Developmental Biology

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

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

Dppa2 and Dppa4 directly regulate the Dux-driven zygotic transcriptional program

(2019) Mélanie Eckersley-Maslin et al.   GENES & DEVELOPMENT

Loss of DUX causes minor defects in zygotic genome activation and is compatible with mouse development

(2019) Zhiyuan Chen et al.   NATURE GENETICS

DPPA2/4 and SUMO E3 ligase PIAS4 opposingly regulate zygotic transcriptional program

(2019) Yao-Long Yan et al.   PLOS BIOLOGY

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

Single-Cell RNA-Seq Reveals Dynamic Early Embryonic-like Programs during Chemical Reprogramming

(2018) Ting Zhao et al.   Cell Stem Cell

Overlapping functions of Krüppel-like factor family members: targeting multiple transcription factors to maintain the naïve pluripotency of mouse embryonic stem cells

(2018) Mariko Yamane et al.   DEVELOPMENT

Efficient mouse genome engineering by CRISPR-EZ technology

(2018) Andrew J Modzelewski et al.   Nature Protocols

Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes

(2017) Vedran Franke et al.   GENOME RESEARCH

Totipotency in the mouse

(2017) Guangming Wu et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

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

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

Striking a balance: regulation of transposable elements by Zfp281 and Mll2 in mouse embryonic stem cells

(2017) Qian Dai et al.   NUCLEIC ACIDS RESEARCH

Deficiency of microRNAmiR-34aexpands cell fate potential in pluripotent stem cells

(2017) Yong Jin Choi et al.   SCIENCE

Totipotency segregates between the sister blastomeres of two-cell stage mouse embryos

(2017) E. Casser et al.   Scientific Reports

Plasticity of the inner cell mass in mouse blastocyst is restricted by the activity of FGF/MAPK pathway

(2017) M. Wigger et al.   Scientific Reports

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse

(2016) Shenglin Mei et al.   NUCLEIC ACIDS RESEARCH

KLF/SP Transcription Factor Family Evolution: Expansion, Diversification, and Innovation in Eukaryotes

(2015) Jason S. Presnell et al.   Genome Biology and Evolution

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

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

The Dfam database of repetitive DNA families

(2015) Robert Hubley et al.   NUCLEIC ACIDS RESEARCH

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

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

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

The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity

(2014) Xinyi Lu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2014) Q. Deng et al.   SCIENCE

Regulation of Mouse Retroelement MuERV-L/MERVL Expression by REX1 and Epigenetic Control of Stem Cell Potency

(2014) Jon Schoorlemmer et al.   Frontiers in Oncology

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

(2013) Y. Liao et al.   BIOINFORMATICS

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

(2013) Yoshikazu Hirate et al.   CURRENT BIOLOGY

The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data

(2013) Gautier Koscielny et al.   NUCLEIC ACIDS RESEARCH

Roles for Tbx3 in regulation of two-cell state and telomere elongation in mouse ES cells

(2013) Jiameng Dan et al.   Scientific Reports

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Developmental Bias in Cleavage-Stage Mouse Blastomeres

(2012) Inna Tabansky et al.   CURRENT BIOLOGY

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Embryonic stem cell potency fluctuates with endogenous retrovirus activity

(2012) Todd S. Macfarlan et al.   NATURE

Endogenous retroviruses and neighboring genes are coordinately repressed by LSD1/KDM1A

(2011) Todd S. Macfarlan et al.   GENES & DEVELOPMENT

Essential Roles of ECAT15-2/Dppa2 in Functional Lung Development

(2011) T. Nakamura et al.   MOLECULAR AND CELLULAR BIOLOGY

miR-34 miRNAs provide a barrier for somatic cell reprogramming

(2011) Yong Jin Choi et al.   NATURE CELL BIOLOGY

Klf5 regulates lineage formation in the pre-implantation mouse embryo

(2010) S.-C. J. Lin et al.   DEVELOPMENT

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Krüppel-like factor 5 Is Essential for Blastocyst Development and the Normal Self-Renewal of Mouse ESCs

(2008) Masatsugu Ema et al.   Cell Stem Cell

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY