A hominoid-specific endogenous retrovirus may have rewired the gene regulatory network shared between primordial germ cells and naïve pluripotent cells

Human reproduction is regulated by retrotransposons derived from ancient Hominidae-specific viral infections

(2022) Xinyu Xiang et al.   Nature Communications

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

(2022) Thomas Carter et al.   eLife

Principles of signaling pathway modulation for enhancing human naive pluripotency induction

(2021) Jonathan Bayerl et al.   Cell Stem Cell

Primed to Naive-Like Conversion of the Common Marmoset Embryonic Stem Cells

(2020) Seiji Shiozawa et al.   STEM CELLS AND DEVELOPMENT

Endogenous retroviruses drive species-specific germline transcriptomes in mammals

(2020) Akihiko Sakashita et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Unique and redundant roles of SOX2 and SOX17 in regulating the germ cell tumor fate

(2019) Sina V. Jostes et al.   INTERNATIONAL JOURNAL OF CANCER

Human Primordial Germ Cells Are Specified from Lineage-Primed Progenitors

(2019) Di Chen et al.   Cell Reports

A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity

(2018) Michelle Percharde et al.   CELL

TFAP2C regulates transcription in human naive pluripotency by opening enhancers

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

On the origin of the human germline

(2018) Toshihiro Kobayashi et al.   DEVELOPMENT

Metabolic regulation of pluripotency and germ cell fate through α‐ketoglutarate

(2018) Julia Tischler et al.   EMBO JOURNAL

Generation of human oogonia from induced pluripotent stem cells in vitro

(2018) Chika Yamashiro et al.   SCIENCE

GTRD: a database on gene transcription regulation—2019 update

(2018) Ivan Yevshin et al.   NUCLEIC ACIDS RESEARCH

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Di Chen et al.   Cell Reports

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

(2017) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Distinct requirements for energy metabolism in mouse primordial germ cells and their reprogramming to embryonic germ cells

(2017) Yohei Hayashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic identification and characterization of regulatory elements derived from human endogenous retroviruses

(2017) Jumpei Ito et al.   PLoS Genetics

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

Glycolytic Metabolism Plays a Functional Role in Regulating Human Pluripotent Stem Cell State

(2016) Wen Gu et al.   Cell Stem Cell

Molecular Criteria for Defining the Naive Human Pluripotent State

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

Comparative Principles of DNA Methylation Reprogramming during Human and Mouse In Vitro Primordial Germ Cell Specification

(2016) Ferdinand von Meyenn et al.   DEVELOPMENTAL CELL

The Germ Cell Fate of Cynomolgus Monkeys Is Specified in the Nascent Amnion

(2016) Kotaro Sasaki et al.   DEVELOPMENTAL CELL

Co-repressor CBFA2T2 regulates pluripotency and germline development

(2016) Shengjiang Tu et al.   NATURE

Regulatory activities of transposable elements: from conflicts to benefits

(2016) Edward B. Chuong et al.   NATURE REVIEWS GENETICS

Specification and epigenetic programming of the human germ line

(2016) Walfred W. C. Tang et al.   NATURE REVIEWS GENETICS

Dynamic stem cell states: naive to primed pluripotency in rodents and humans

(2016) Leehee Weinberger et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Discovery of unfixed endogenous retrovirus insertions in diverse human populations

(2016) Julia Halo Wildschutte et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

A Unique Gene Regulatory Network Resets the Human Germline Epigenome for Development

(2015) Walfred W.C. Tang et al.   CELL

SOX17 Is a Critical Specifier of Human Primordial Germ Cell Fate

(2015) Naoko Irie et al.   CELL

Robust In Vitro Induction of Human Germ Cell Fate from Pluripotent Stem Cells

(2015) Kotaro Sasaki et al.   Cell Stem Cell

Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells

(2015) Edward J. Grow et al.   NATURE

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(2015) Alejandro De Los Angeles et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Enhancer RNAs: A Class of Long Noncoding RNAs Synthesized at Enhancers: Figure 1.

(2015) Tae-Kyung Kim et al.   Cold Spring Harbor Perspectives in Biology

Ancient Transposable Elements Transformed the Uterine Regulatory Landscape and Transcriptome during the Evolution of Mammalian Pregnancy

(2015) Vincent J. Lynch et al.   Cell Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Resetting Transcription Factor Control Circuitry toward Ground-State Pluripotency in Human

(2014) Yasuhiro Takashima et al.   CELL

Widespread contribution of transposable elements to the innovation of gene regulatory networks

(2014) Vasavi Sundaram et al.   GENOME RESEARCH

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

(2013) Y. Liao et al.   BIOINFORMATICS

The mammalian germline as a pluripotency cycle

(2013) H. G. Leitch et al.   DEVELOPMENT

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh 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

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements

(2013) Pierre-Étienne Jacques et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

HIF1α induced switch from bivalent to exclusively glycolytic metabolism during ESC-to-EpiSC/hESC transition

(2012) Wenyu Zhou et al.   EMBO JOURNAL

Primordial Germ Cells in Mice

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Evolution of Gene Regulatory Networks Controlling Body Plan Development

(2011) Isabelle S. Peter et al.   CELL

BEDTools: a flexible suite of utilities for comparing genomic features

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GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

SVA retrotransposons: Evolution and genetic instability

(2010) Dustin C. Hancks et al.   SEMINARS IN CANCER BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Naive and Primed Pluripotent States

(2009) Jennifer Nichols et al.   Cell Stem Cell

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

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS