Krüppel-like factor 5 rewires NANOG regulatory network to activate human naive pluripotency specific LTR7Ys and promote naive pluripotency

Mosaic cis-regulatory evolution drives transcriptional partitioning of HERVH endogenous retrovirus in the human embryo

(2022) Thomas Carter et al.   eLife

RAD: a web application to identify region associated differentially expressed genes

(2021) Yixin Guo et al.   BIOINFORMATICS

Human naive epiblast cells possess unrestricted lineage potential

(2021) Ge Guo et al.   Cell Stem Cell

Capturing human trophoblast development with naive pluripotent stem cells in vitro

(2021) Shingo Io et al.   Cell Stem Cell

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Transposable elements shape the evolution of mammalian development

(2021) Anna D. Senft et al.   NATURE REVIEWS GENETICS

A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development

(2021) Andrew J. Modzelewski et al.   CELL

DUX-miR-344-ZMYM2-Mediated Activation of MERVL LTRs Induces a Totipotent 2C-like State

(2020) Fan Yang et al.   Cell Stem Cell

SETDB1-Mediated Cell Fate Transition between 2C-Like and Pluripotent States

(2020) Kaixin Wu et al.   Cell Reports

Derivation of trophoblast stem cells from naïve human pluripotent stem cells

(2020) Chen Dong et al.   eLife

GATA3 Mediates a Fast, Irreversible Commitment to BMP4-Driven Differentiation in Human Embryonic Stem Cells

(2020) Alexandra Gunne-Braden et al.   Cell Stem Cell

Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation

(2020) Ava C Carter et al.   eLife

Transposable Elements: A Common Feature of Neurodevelopmental and Neurodegenerative Disorders

(2020) Marie E. Jönsson et al.   TRENDS IN GENETICS

Silencing and Transcriptional Regulation of Endogenous Retroviruses: An Overview

(2020) Franziska K. Geis et al.   Viruses-Basel

Naive Human Embryonic Stem Cells Can Give Rise to Cells with a Trophoblast-like Transcriptome and Methylome

(2020) Jessica K. Cinkornpumin et al.   Stem Cell Reports

Endogenous Retroviruses Function as Gene Expression Regulatory Elements During Mammalian Pre-implantation Embryo Development

(2019) Bo Fu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

A Dissection of Oligomerization by the TRIM28 Tripartite Motif and the Interaction with Members of the Krab-ZFP Family

(2019) Yunyuan Sun et al.   JOURNAL OF MOLECULAR BIOLOGY

CUT&Tag for efficient epigenomic profiling of small samples and single cells

(2019) Hatice S. Kaya-Okur et al.   Nature Communications

Reconstituting the transcriptome and DNA methylome landscapes of human implantation

(2019) Fan Zhou et al.   NATURE

Precise temporal regulation of Dux is important for embryo development

(2019) Mingyue Guo et al.   CELL RESEARCH

A Chemically Defined Feeder-free System for the Establishment and Maintenance of the Human Naive Pluripotent State

(2019) Iwona Szczerbinska et al.   Stem Cell Reports

Transposable elements: genome innovation, chromosome diversity, and centromere conflict

(2018) Savannah J. Klein et al.   CHROMOSOME RESEARCH

TFAP2C regulates transcription in human naive pluripotency by opening enhancers

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

Comparative analysis of naive, primed and ground state pluripotency in mouse embryonic stem cells originating from the same genetic background

(2018) Sabitri Ghimire et al.   Scientific Reports

The TFAP2C-Regulated OCT4 Naive Enhancer Is Involved in Human Germline Formation

(2018) Di Chen et al.   Cell Reports

KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks

(2017) Michaël Imbeault et al.   NATURE

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

GATA2/3-TFAP2A/C transcription factor network couples human pluripotent stem cell differentiation to trophectoderm with repression of pluripotency

(2017) Christian Krendl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Massively parallel digital transcriptional profiling of single cells

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

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

CTRL+INSERT: retrotransposons and their contribution to regulation and innovation of the transcriptome

(2016) Jonathan Göke et al.   EMBO REPORTS

Regulatory evolution of innate immunity through co-option of endogenous retroviruses

(2016) E. B. Chuong et al.   SCIENCE

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

Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells

(2015) Edward J. Grow et al.   NATURE

Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements

(2015) Pratiksha I Thakore et al.   NATURE METHODS

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

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

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

(2014) Jichang Wang et al.   NATURE

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

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

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Y. Liao et al.   BIOINFORMATICS

Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system

(2013) Albert W Cheng et al.   CELL RESEARCH

Induction of a Human Pluripotent State with Distinct Regulatory Circuitry that Resembles Preimplantation Epiblast

(2013) Yun-Shen Chan et al.   Cell Stem Cell

Exaptation of Transposable Elements into Novel Cis-Regulatory Elements: Is the Evidence Always Strong?

(2013) F. S. J. de Souza et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Embryonic stem cell potency fluctuates with endogenous retrovirus activity

(2012) Todd S. Macfarlan et al.   NATURE

Endogenous viruses: insights into viral evolution and impact on host biology

(2012) Cédric Feschotte et al.   NATURE REVIEWS GENETICS

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

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

Transposable Elements, Epigenetics, and Genome Evolution

(2012) N. V. Fedoroff   SCIENCE

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

KAP1 controls endogenous retroviruses in embryonic stem cells

(2010) Helen M. Rowe et al.   NATURE

Transposable elements have rewired the core regulatory network of human embryonic stem cells

(2010) Galih Kunarso et al.   NATURE GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

A core Klf circuitry regulates self-renewal of embryonic stem cells

(2008) Jianming Jiang et al.   NATURE CELL BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY