A transcriptional roadmap for 2C-like–to–pluripotent state transition

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

(2019) Zhiyuan Chen et al.   NATURE GENETICS

Myc and Dnmt1 impede the pluripotent to totipotent state transition in embryonic stem cells

(2019) Xudong Fu et al.   NATURE CELL BIOLOGY

Precise temporal regulation of Dux is important for embryo development

(2019) Mingyue Guo et al.   CELL RESEARCH

Cell type-specific transcriptional programs in mouse prefrontal cortex during adolescence and addiction

(2019) Aritra Bhattacherjee et al.   Nature Communications

DUX is a non-essential synchronizer of zygotic genome activation

(2019) Alberto De Iaco et al.   DEVELOPMENT

Mitigating the adverse impact of batch effects in sample pattern detection

(2018) Teng Fei et al.   BIOINFORMATICS

A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity

(2018) Michelle Percharde et al.   CELL

Capturing Totipotent Stem Cells

(2018) Christopher L. Baker et al.   Cell Stem Cell

Deconstructing the pluripotency gene regulatory network

(2018) Mo Li et al.   NATURE CELL BIOLOGY

Detection and removal of barcode swapping in single-cell RNA-seq data

(2018) Jonathan A. Griffiths et al.   Nature Communications

Establishment of mouse expanded potential stem cells

(2017) Jian Yang 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

Conservation and innovation in the DUX4-family gene network

(2017) Jennifer L Whiddon et al.   NATURE GENETICS

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

(2017) Yong Jin Choi et al.   SCIENCE

Massively parallel digital transcriptional profiling of single cells

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

Allelic reprogramming of the histone modification H3K4me3 in early mammalian development

(2016) Bingjie Zhang et al.   NATURE

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

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

A feedback loop between nonsense-mediated decay and the retrogene DUX4 in facioscapulohumeral muscular dystrophy

(2015) Qing Feng et al.   eLife

Cell totipotency: molecular features, induction, and maintenance

(2015) Falong Lu et al.   National Science Review

Zygotic Genome Activation During the Maternal-to-Zygotic Transition

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

Transcriptional landscape of repetitive elements in normal and cancer human cells

(2014) Steven W Criscione et al.   BMC GENOMICS

Higher chromatin mobility supports totipotency and precedes pluripotency in vivo

(2014) A. Bo kovi  et al.   GENES & DEVELOPMENT

Role of Tet proteins in enhancer activity and telomere elongation

(2014) Falong Lu et al.   GENES & DEVELOPMENT

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

(2013) Zhigang Xue et al.   NATURE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Upf1 Senses 3′UTR Length to Potentiate mRNA Decay

(2010) J. Robert Hogg et al.   CELL

Stepwise Histone Replacement by SWR1 Requires Dual Activation with Histone H2A.Z and Canonical Nucleosome

(2010) Ed Luk et al.   CELL

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

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

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

Long 3′-UTRs target wild-type mRNAs for nonsense-mediated mRNA decay in Saccharomyces cerevisiae

(2009) Bessie W. Kebaara et al.   NUCLEIC ACIDS RESEARCH