Evolution and antiviral activity of a human protein of retroviral origin

Sequential enhancer state remodelling defines human germline competence and specification

(2022) Walfred W. C. Tang et al.   NATURE CELL BIOLOGY

Involvement of the HERV-derived cell-fusion inhibitor, suppressyn, in the fusion defects characteristic of the trisomy 21 placenta

(2022) Jun Sugimoto et al.   Scientific Reports

QSER1 protects DNA methylation valleys from de novo methylation

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Molecular Evolutionary Genetics Analysis (MEGA) for macOS

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Alterations of redox and iron metabolism accompany the development of HIV latency

(2020) Iart Luca Shytaj et al.   EMBO JOURNAL

Endogenous Retroviral Envelope Syncytin Induces HIV-1 Spreading and Establishes HIV Reservoirs in Placenta

(2020) Yuyang Tang et al.   Cell Reports

Co-option of the lineage-specificLAVAretrotransposon in the gibbon genome

(2020) Mariam Okhovat et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Origins and evolutionary consequences of ancient endogenous retroviruses

(2019) Welkin E. Johnson   NATURE REVIEWS MICROBIOLOGY

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

Landscape of stimulation-responsive chromatin across diverse human immune cells

(2019) Diego Calderon et al.   NATURE GENETICS

Suppressyn localization and dynamic expression patterns in primary human tissues support a physiologic role in human placentation

(2019) Jun Sugimoto et al.   Scientific Reports

Human ADAR1 Prevents Endogenous RNA from Triggering Translational Shutdown

(2018) Hachung Chung et al.   CELL

Chromatin Accessibility Landscape in Human Early Embryos and Its Association with Evolution

(2018) Lei Gao et al.   CELL

Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells

(2018) Tahsin Stefan Barakat et al.   Cell Stem Cell

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Single-cell RNA-seq reveals the diversity of trophoblast subtypes and patterns of differentiation in the human placenta 

(2018) Yawei Liu et al.   CELL RESEARCH

Chromatin analysis in human early development reveals epigenetic transition during ZGA

(2018) Jingyi Wu et al.   NATURE

Anthropoid primate–specific retroviral element THE1B controls expression of CRH in placenta and alters gestation length

(2018) Caitlin E. Dunn-Fletcher et al.   PLOS BIOLOGY

Single-cell reconstruction of the early maternal–fetal interface in humans

(2018) Roser Vento-Tormo et al.   NATURE

The UCSC Genome Browser database: 2019 update

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GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

Single-cell transcriptomics of the human placenta: inferring the cell communication network of the maternal-fetal interface

(2017) Mihaela Pavličev et al.   GENOME RESEARCH

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Human haematopoietic stem cell lineage commitment is a continuous process

(2017) Lars Velten et al.   NATURE CELL BIOLOGY

Single-cell mRNA quantification and differential analysis with Census

(2017) Xiaojie Qiu et al.   NATURE METHODS

Single-Cell Profiling of an In Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation

(2017) Jennie L. Close et al.   NEURON

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

Identifying DNase I hypersensitive sites as driver distal regulatory elements in breast cancer

(2017) Matteo D′Antonio et al.   Nature Communications

Co-option of endogenous viral sequences for host cell function

(2017) John A .Frank et al.   Current Opinion in Virology

Retroviruses of the RDR superinfection interference group: ancient origins and broad host distribution of a promiscuous Env gene

(2017) Anindita Sinha et al.   Current Opinion in Virology

Co-option of an endogenous retrovirus envelope for host defense in hominid ancestors

(2017) Daniel Blanco-Melo et al.   eLife

Analysis of VSV pseudotype virus infection mediated by rubella virus envelope proteins

(2017) Masafumi Sakata et al.   Scientific Reports

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

gEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes

(2016) So Nakagawa et al.   Database-The Journal of Biological Databases and Curation

The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells

(2015) Fan Guo et al.   CELL

Fighting Fire with Fire: Endogenous Retrovirus Envelopes as Restriction Factors

(2015) Ray Malfavon-Borja et al.   JOURNAL OF VIROLOGY

Transcription factor binding dynamics during human ES cell differentiation

(2015) Alexander M. Tsankov et al.   NATURE

A survey of human brain transcriptome diversity at the single cell level

(2015) Spyros Darmanis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Endogenous Retroviruses in the Genomics Era

(2015) Welkin E. Johnson   Annual Review of Virology

Application of Gaussia luciferase in bicistronic and non-conventional secretion reporter constructs

(2014) Christin Luft et al.   BMC BIOCHEMISTRY

The Virome in Mammalian Physiology and Disease

(2014) Herbert W. Virgin   CELL

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

(2013) Y. Liao et al.   BIOINFORMATICS

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

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

Paleovirology of 'syncytins', retroviral env genes exapted for a role in placentation

(2013) C. Lavialle et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

LDL receptor and its family members serve as the cellular receptors for vesicular stomatitis virus

(2013) D. Finkelshtein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A novel human endogenous retroviral protein inhibits cell-cell fusion

(2013) Jun Sugimoto et al.   Scientific Reports

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Silencing of endogenous envelope genes in human choriocarcinoma cells shows that envPb1 is involved in heterotypic cell fusions

(2012) L. Aagaard et al.   JOURNAL OF GENERAL VIROLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Env-less endogenous retroviruses are genomic superspreaders

(2012) G. Magiorkinis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HIV infection and HERV expression: a review

(2012) Antoinette C van der Kuyl   Retrovirology

Neural development in human embryonic stem cells-applications of lentiviral vectors

(2011) Mirella Dottori et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

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(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

A Molecular Phylogeny of Living Primates

(2011) Polina Perelman et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

PHAST and RPHAST: phylogenetic analysis with space/time models

(2010) M. J. Hubisz et al.   BRIEFINGS IN BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Analyzing real-time PCR data by the comparative CT method

(2008) Thomas D Schmittgen et al.   Nature Protocols