(Q41924621)

12 January 2018

title

Genome-scale detection of positive selection in nine primates predicts human-virus evolutionary conflicts (English)

1 reference

12 January 2018

author

Robin van der Lee

1

1 reference

12 January 2018

Laurens Wiel

object named as

Laurens Wiel

2

0 references

Martijn A Huynen

object named as

Martijn A Huynen

4

0 references

author name string

Teunis J P van Dam

3

1 reference

12 January 2018

publication date

11 August 2017

1 reference

12 January 2018

number of pages

15

1 reference

based on heuristic

inferred from page(s)

published in

Nucleic Acids Research

1 reference

12 January 2018

volume

45

1 reference

12 January 2018

issue

18

1 reference

12 January 2018

page(s)

10634-10648

1 reference

12 January 2018

Creative Commons Attribution 4.0 International

copyright license

start time

11 August 2017

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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Selectome update: quality control and computational improvements to a database of positive selection

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5 June 2018

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A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes

5 June 2018

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Selection and adaptation in the human genome

5 June 2018

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5 June 2018

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5 June 2018

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5 June 2018

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5 June 2018

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Rules of engagement: molecular insights from host-virus arms races

5 June 2018

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Evolution-guided identification of antiviral specificity determinants in the broadly acting interferon-induced innate immunity factor MxA.

5 June 2018

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5 June 2018

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GogB is an anti-inflammatory effector that limits tissue damage during Salmonella infection through interaction with human FBXO22 and Skp1

5 June 2018

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5 June 2018

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Convergent evolution of escape from hepaciviral antagonism in primates

5 June 2018

1 reference

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Evolutionary and functional analyses of the interaction between the myeloid restriction factor SAMHD1 and the lentiviral Vpx protein

5 June 2018

1 reference

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CENP-T-W-S-X forms a unique centromeric chromatin structure with a histone-like fold

5 June 2018

1 reference

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Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection

5 June 2018

1 reference

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Weighing the evidence for adaptation at the molecular level

5 June 2018

1 reference

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Structural principles within the human-virus protein-protein interaction network.

5 June 2018

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Centromeres: unique chromatin structures that drive chromosome segregation

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

A molecular phylogeny of living primates

5 June 2018

1 reference

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Interaction of Decay-Accelerating Factor with Echovirus 7

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Detecting positive selection within genomes: the problem of biased gene conversion

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Positive selection of HIV host factors and the evolution of lentivirus genes

5 June 2018

1 reference

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Adaptation and constraint at Toll-like receptors in primates

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Estimates of positive Darwinian selection are inflated by errors in sequencing, annotation, and alignment.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

An alignment confidence score capturing robustness to guide tree uncertainty

5 June 2018

1 reference

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Genome-wide identification of susceptibility alleles for viral infections through a population genetics approach

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Structure of Adenovirus Type 21 Knob in Complex with CD46 Reveals Key Differences in Receptor Contacts among Species B Adenoviruses

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Structure of the measles virus hemagglutinin bound to the CD46 receptor

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Mutation of a single residue renders human tetherin resistant to HIV-1 Vpu-mediated depletion

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

The apolipoprotein L family of programmed cell death and immunity genes rapidly evolved in primates at discrete sites of host-pathogen interactions

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Protein kinase R reveals an evolutionary model for defeating viral mimicry

5 June 2018

1 reference

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EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

5 June 2018

1 reference

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Widespread balancing selection and pathogen-driven selection at blood group antigen genes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Patterns of positive selection in six Mammalian genomes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Alignment uncertainty and genomic analysis

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

A second generation human haplotype map of over 3.1 million SNPs

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

PAML 4: phylogenetic analysis by maximum likelihood

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

More genes underwent positive selection in chimpanzee evolution than in human evolution

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Evolutionary and Biomedical Insights from the Rhesus Macaque Genome

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Structural definition of a conserved neutralization epitope on HIV-1 gp120

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Positive natural selection in the human lineage

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

A map of recent positive selection in the human genome

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Natural selection on protein-coding genes in the human genome

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Initial sequence of the chimpanzee genome and comparison with the human genome

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

A scan for positively selected genes in the genomes of humans and chimpanzees

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Bayes empirical bayes inference of amino acid sites under positive selection

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Positive selection of primate TRIM5alpha identifies a critical species-specific retroviral restriction domain

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

5 June 2018

Adaptation and immunity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Positive selection on the human genome.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

MUSCLE: multiple sequence alignment with high accuracy and high throughput

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

The structure of echovirus type 12 bound to a two-domain fragment of its cellular attachment protein decay-accelerating factor (CD 55)

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Common exon duplication in animals and its role in alternative splicing

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Statistical methods for detecting molecular adaptation

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Codon-substitution models for heterogeneous selection pressure at amino acid sites

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Studies of protein-protein interfaces: a statistical analysis of the hydrophobic effect

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

WHAT IF: a molecular modeling and drug design program

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

The effects of alignment error and alignment filtering on the sitewise detection of positive selection.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Mitochondrial-nuclear interactions and accelerated compensatory evolution: evidence from the primate cytochrome C oxidase complex

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Improving the performance of positive selection inference by filtering unreliable alignment regions.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

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

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Major evolutionary transitions in centromere complexity.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Evolutionary trajectories of primate genes involved in HIV pathogenesis.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Comparison of fine-scale recombination rates in humans and chimpanzees.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737536

Activities at the Universal Protein Resource (UniProt)

18 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKX704

The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28977405

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKX704

1 reference

12 January 2018

PMC publication ID

5737536

1 reference

12 January 2018

PubMed publication ID

28977405

1 reference

12 January 2018