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

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

(2021) Yixin Guo et al.   BIOINFORMATICS

Mammalian primordial germ cell specification

(2021) Grace V. Hancock et al.   DEVELOPMENT

The chromatin accessibility landscape reveals distinct transcriptional regulation in the induction of human primordial germ cell-like cells from pluripotent stem cells

(2021) Xiaoman Wang et al.   Stem Cell Reports

Divergent roles for KLF4 and TFCP2L1 in naive ground state pluripotency and human primordial germ cell development

(2021) G.V. Hancock et al.   Stem Cell Research

Single-cell transcriptomic characterization of a gastrulating human embryo

(2021) Richard C. V. Tyser et al.   NATURE

An Extended Culture System that Supports Human Primordial Germ Cell-like Cell Survival and Initiation of DNA Methylation Erasure

(2020) Joanna J. Gell et al.   Stem Cell Reports

A critical role of PRDM14 in human primordial germ cell fate revealed by inducible degrons

(2020) Anastasiya Sybirna et al.   Nature Communications

Reprogramming roadmap reveals route to human induced trophoblast stem cells

(2020) Xiaodong Liu et al.   NATURE

SQuIRE reveals locus-specific regulation of interspersed repeat expression

(2019) Wan R Yang et al.   NUCLEIC ACIDS RESEARCH

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

Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells

(2019) Yanxiao Zhang et al.   NATURE GENETICS

Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression

(2019) Matthew L. Bendall et al.   PLoS Computational Biology

Human Primordial Germ Cells Are Specified from Lineage-Primed Progenitors

(2019) Di Chen et al.   Cell Reports

Tools and best practices for retrotransposon analysis using high-throughput sequencing data

(2019) Aurélie Teissandier et al.   Mobile DNA

TFAP2C regulates transcription in human naive pluripotency by opening enhancers

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

GWAS4D: multidimensional analysis of context-specific regulatory variant for human complex diseases and traits

(2018) Dandan Huang et al.   NUCLEIC ACIDS RESEARCH

Outstanding questions in the study of archaic hominin admixture

(2018) Aaron B. Wolf et al.   PLoS Genetics

TRIM28-Regulated Transposon Repression Is Required for Human Germline Competency and Not Primed or Naive Human Pluripotency

(2018) Yu Tao et al.   Stem Cell Reports

Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation

(2018) Daniel R Fuentes et al.   eLife

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

(2018) Di Chen et al.   Cell Reports

3D Chromosome Regulatory Landscape of Human Pluripotent Cells

(2016) Xiong Ji et al.   Cell Stem Cell

Molecular Criteria for Defining the Naive Human Pluripotent State

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

The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans

(2016) Sriram Sankararaman et al.   CURRENT BIOLOGY

Long Terminal Repeats: From Parasitic Elements to Building Blocks of the Transcriptional Regulatory Repertoire

(2016) Peter J. Thompson et al.   MOLECULAR CELL

Regulatory activities of transposable elements: from conflicts to benefits

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

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

(2016) E. B. Chuong et al.   SCIENCE

The Developmental Control of Transposable Elements and the Evolution of Higher Species

(2015) Marc Friedli et al.   Annual Review of Cell and Developmental Biology

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

(2015) Ying Jin et al.   BIOINFORMATICS

The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells

(2015) Fan Guo et al.   CELL

DNA Demethylation Dynamics in the Human Prenatal Germline

(2015) Sofia Gkountela 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

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

(2015) Pratiksha I Thakore et al.   NATURE METHODS

The Dfam database of repetitive DNA families

(2015) Robert Hubley et al.   NUCLEIC ACIDS RESEARCH

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

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

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

(2013) Wei Xie et al.   CELL

Human endogenous retrovirus K (HML-2) RNA and protein expression is a marker for human embryonic and induced pluripotent stem cells

(2013) Nina V Fuchs et al.   Retrovirology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Transposable elements reveal a stem cell-specific class of long noncoding RNAs

(2012) David Kelley et al.   GENOME BIOLOGY

Human Endogenous Retrovirus K106 (HERV-K106) Was Infectious after the Emergence of Anatomically Modern Humans

(2011) Aashish R. Jha et al.   PLoS One

Identification, characterization, and comparative genomic distribution of the HERV-K (HML-2) group of human endogenous retroviruses

(2011) Ravi P Subramanian et al.   Retrovirology

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

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

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

(2010) Galih Kunarso et al.   NATURE GENETICS

A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers

(2010) Francesca De Santa et al.   PLOS BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Critical Function of AP-2gamma/TCFAP2C in Mouse Embryonic Germ Cell Maintenance1

(2009) Susanne Weber et al.   BIOLOGY OF REPRODUCTION

Conditional knockdown of Nanog induces apoptotic cell death in mouse migrating primordial germ cells

(2009) S. Yamaguchi et al.   DEVELOPMENT

Evidence for crucial role of hindgut expansion in directing proper migration of primordial germ cells in mouse early embryogenesis

(2009) Kenshiro Hara et al.   DEVELOPMENTAL BIOLOGY

 2-6 Linked Sialic Acids on N-Glycans Modulate Carcinoma Differentiation In vivo

(2008) M. Hedlund et al.   CANCER RESEARCH

Critical function of Prdm14 for the establishment of the germ cell lineage in mice

(2008) Masashi Yamaji et al.   NATURE GENETICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY