Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis (Q30000090)

1

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8 June 2020

Marzia A Cremona

2

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8 June 2020

Alessia Pini

3

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8 June 2020

Francesca Chiaromonte

4

object named as

Francesca Chiaromonte

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8 June 2020

author name string

Kateryna D Makova

5

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PLOS Computational Biology

8 June 2020

language of work or name

English

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publication date

June 2016

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published in

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8 June 2020

volume

12

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8 June 2020

issue

6

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8 June 2020

page(s)

e1004956

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Creative Commons Attribution 4.0 International

8 June 2020

copyright license

start time

16 June 2016

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements

21 May 2017

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Retroviral elements and their hosts: insertional mutagenesis in the mouse germ line

21 May 2017

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A fine-scale map of recombination rates and hotspots across the human genome

21 May 2017

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Genomewide screening reveals high levels of insertional polymorphism in the human endogenous retrovirus family HERV-K(HML2): implications for present-day activity

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21 May 2017

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21 May 2017

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3 June 2018

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3 June 2018

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3 June 2018

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3 June 2018

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3 June 2018

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The effects of chromatin organization on variation in mutation rates in the genome

3 June 2018

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Dynamic transcription of distinct classes of endogenous retroviral elements marks specific populations of early human embryonic cells

3 June 2018

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DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data

3 June 2018

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Functional analysis of variance for association studies

3 June 2018

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Setdb1 is required for germline development and silencing of H3K9me3-marked endogenous retroviruses in primordial germ cells

3 June 2018

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Molecular mechanisms of retroviral integration site selection

3 June 2018

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The dynamics of DNA methylation fidelity during mouse embryonic stem cell self-renewal and differentiation

3 June 2018

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Genomic landscape of human, bat, and ex vivo DNA transposon integrations

3 June 2018

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Epistasis analysis for quantitative traits by functional regression model

3 June 2018

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Chromatin landscapes of retroviral and transposon integration profiles

3 June 2018

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A high-resolution map of the three-dimensional chromatin interactome in human cells

3 June 2018

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An introduction with medical applications to functional data analysis.

3 June 2018

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Recruitment and biological consequences of histone modification of H3K27me3 and H3K9me3.

3 June 2018

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DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape

3 June 2018

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Human-specific HERV-K insertion causes genomic variations in the human genome

3 June 2018

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Genetic and epigenetic determinants of DNA replication origins, position and activation

3 June 2018

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Distinct mutational behaviors differentiate short tandem repeats from microsatellites in the human genome

3 June 2018

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Rescuing Alu: recovery of new inserts shows LINE-1 preserves Alu activity through A-tail expansion

3 June 2018

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Transposable elements: an abundant and natural source of regulatory sequences for host genes.

3 June 2018

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Unraveling cell type-specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs.

3 June 2018

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The genomic landscape shaped by selection on transposable elements across 18 mouse strains

3 June 2018

1 reference

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Fine-scale maps of recombination rates and hotspots in the mouse genome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4911145

Env-less endogenous retroviruses are genomic superspreaders

3 June 2018

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A genome-wide analysis of common fragile sites: what features determine chromosomal instability in the human genome?

3 June 2018

1 reference

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Polymorphic integrations of an endogenous gammaretrovirus in the mule deer genome

3 June 2018

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

3 June 2018

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Retrotransposon-induced heterochromatin spreading in the mouse revealed by insertional polymorphisms

3 June 2018

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Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates

3 June 2018

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3 June 2018

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Distributions of transposable elements reveal hazardous zones in mammalian introns

3 June 2018

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Association studies for next-generation sequencing

3 June 2018

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Estimating enrichment of repetitive elements from high-throughput sequence data

3 June 2018

1 reference

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Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types

3 June 2018

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The (r)evolution of SINE versus LINE distributions in primate genomes: sex chromosomes are important

3 June 2018

1 reference

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Non-B DNA structure-induced genetic instability and evolution

3 June 2018

1 reference

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Classification and nomenclature of endogenous retroviral sequences (ERVs): problems and recommendations

3 June 2018

1 reference

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A new standard genetic map for the laboratory mouse

3 June 2018

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Integration target site selection by a resurrected human endogenous retrovirus

3 June 2018

1 reference

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Global reorganization of replication domains during embryonic stem cell differentiation

3 June 2018

1 reference

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Evolution of human endogenous retroviral sequences: a conceptual account

3 June 2018

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Genome-wide assessments reveal extremely high levels of polymorphism of two active families of mouse endogenous retroviral elements

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4911145

Chromodomains direct integration of retrotransposons to heterochromatin.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4911145

Effects of recombination rate on human endogenous retrovirus fixation and persistence.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4911145

Insertional polymorphisms: a new lease of life for endogenous retroviruses in human disease.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4911145

The evolutionary dynamics of human endogenous retroviral families

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4911145

Transcriptional regulation of early transposon elements, an active family of mouse long terminal repeat retrotransposons

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4911145

An active murine transposon family pair: retrotransposition of "master" MusD copies and ETn trans-mobilization

3 June 2018

1 reference

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Factors regulating endogenous retroviral sequences in human and mouse

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4911145

Comparative recombination rates in the rat, mouse, and human genomes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4911145

Replication timing of the human genome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4911145

Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4911145

Effects of recombination rate and gene density on transposable element distributions in Arabidopsis thaliana

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4911145

Human L1 element target-primed reverse transcription in vitro

3 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4911145

Retroelement distributions in the human genome: variations associated with age and proximity to genes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4911145

Functional data analysis with application to periodically stimulated foetal heart rate data. II: functional logistic regression

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4911145

Transposons but not retrotransposons are located preferentially in regions of high recombination rate in Caenorhabditis elegans

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4911145

Somatic mutation rates and specificities at TC/AG and GT/CA microsatellite sequences in nontumorigenic human lymphoblastoid cells

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4911145

Human immunodeficiency virus integrase directs integration to sites of severe DNA distortion within the nucleosome core

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4911145

DNA bending creates favored sites for retroviral integration: an explanation for preferred insertion sites in nucleosomes.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4911145

In vitro integration of human immunodeficiency virus type 1 cDNA into targets containing protein-induced bends

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4911145

Nucleosomes, DNA-binding proteins, and DNA sequence modulate retroviral integration target site selection

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4911145

Perpetually mobile footprints of ancient infections in human genome

3 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004956

Rate of recombinational deletion among human endogenous retroviruses

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004956

Retroviral invasion of the koala genome.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004956

High copy number in human endogenous retrovirus families is associated with copying mechanisms in addition to reinfection

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004956

Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004956

Identification of autonomous IAP LTR retrotransposons mobile in mammalian cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004956

Common physical properties of DNA affecting target site selection of sleeping beauty and other Tc1/mariner transposable elements.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004956

The evolutionary dynamics of endogenous retroviruses

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004956

A common sequence motif associated with recombination hot spots and genome instability in humans

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004956

Fine-scale recombination rate differences between sexes, populations and individuals

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004956

Active Alu elements are passed primarily through paternal germlines

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004956

Key determinants of target DNA recognition by retroviral intasomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004956

A functional data analysis approach for genetic association studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004956

Risk prediction for myocardial infarction via generalized functional regression models

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4911145

A preferred target DNA structure for retroviral integrase in vitro

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27309962

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Association of a host DNA structure with retroviral integration sites in chromosomal DNA

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27309962

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1004956

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27309962%20AND%20SRC:MED&resulttype=core&format=json

journals/ploscb/Campos-SanchezC16

8 June 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27309962%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

PubMed publication ID

27309962

2 references