Synonymous site conservation in the HIV-1 genome (Q34893298)

5 August 2017

title

Synonymous site conservation in the HIV-1 genome (English)

1 reference

5 August 2017

8

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5 August 2017

Itay Mayrose

1

0 references

Eran Bacharach

object named as

Eran Bacharach

7

0 references

Adi Stern Grundland

object named as

Adi Stern

2

1 reference

ORCID Public Data File 2021

author name string

Ela O Burdelova

3

1 reference

5 August 2017

Yosef Sabo

4

1 reference

5 August 2017

Nihay Laham-Karam

5

1 reference

5 August 2017

Rachel Zamostiano

6

1 reference

5 August 2017

language of work or name

1 reference

4 August 2013

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5 August 2017

published in

BMC Evolutionary Biology

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5 August 2017

volume

13

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5 August 2017

page(s)

164

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Reduced stability of mRNA secondary structure near the translation-initiation site in dsDNA viruses

5 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

Detecting positive and purifying selection at synonymous sites in yeast and worm

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

Translation efficiency is determined by both codon bias and folding energy

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

Evolutionary fingerprinting of genes.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

Architecture and secondary structure of an entire HIV-1 RNA genome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

Coding-sequence determinants of gene expression in Escherichia coli

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

The trouble with sliding windows and the selective pressure in BRCA1.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

Quantitative effect of suboptimal codon usage on translational efficiency of mRNA encoding HIV-1 gag in intact T cells

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

Tetherin inhibits retrovirus release and is antagonized by HIV-1 Vpu

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

Transduction of human immunodeficiency virus type 1 vectors lacking encapsidation and dimerization signals.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

A "silent" polymorphism in the MDR1 gene changes substrate specificity

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

Comparative analysis identifies exonic splicing regulatory sequences--The complex definition of enhancers and silencers

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

Hearing silence: non-neutral evolution at synonymous sites in mammals

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

The power of phylogenetic comparison in revealing protein function

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

Selecton: a server for detecting evolutionary forces at a single amino-acid site

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

The conserved carboxy terminus of the capsid domain of human immunodeficiency virus type 1 gag protein is important for virion assembly and release

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

MUSCLE: multiple sequence alignment with high accuracy and high throughput

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

Positive selection detection in 40,000 human immunodeficiency virus (HIV) type 1 sequences automatically identifies drug resistance and positive fitness mutations in HIV protease and reverse transcriptase

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

Selection on Human Genes as Revealed by Comparisons to Chimpanzee cDNA

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

Rev inhibition strongly affects intracellular distribution of human immunodeficiency virus type 1 RNAs.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

The Ka/Ks ratio: diagnosing the form of sequence evolution

8 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

8 July 2018

https://api.crossref.org/works/10.1186/1471-2148-13-164

Secondary structure prediction for aligned RNA sequences

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

Purifying and directional selection in overlapping prokaryotic genes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

Codon bias and mutability in HIV sequences.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

8 July 2018

THE HIV-1 REV PROTEIN

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

Codon usage limitation in the expression of HIV-1 envelope glycoprotein

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

The human immunodeficiency virus type 1 encapsidation site is a multipartite RNA element composed of functional hairpin structures

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

Assays for retroviral reverse transcriptase

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

RNA secondary structure and binding sites for gag gene products in the 5' packaging signal of human immunodeficiency virus type 1.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

Use of a novel human immunodeficiency virus type 1 reporter virus expressing human placental alkaline phosphatase to detect an alternative viral receptor.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

HIV-1 Reverse Transcription A Termination Step at the Center of the Genome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

Codon usage and tRNA content in unicellular and multicellular organisms

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

HIV-1 structural gene expression requires binding of the Rev trans-activator to its RNA target sequence

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

A single-stranded gap in human immunodeficiency virus unintegrated linear DNA defined by a central copy of the polypurine tract.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

Evolution of overlapping genes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

Widespread adaptive evolution in the human immunodeficiency virus type 1 genome

8 July 2018

1 reference

https://api.crossref.org/works/10.1186/1471-2148-13-164

Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186/1471-2148-13-164

Evolutionary models accounting for layers of selection in protein-coding genes and their impact on the inference of positive selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1186/1471-2148-13-164

Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates

21 January 2018

1 reference

https://api.crossref.org/works/10.1186/1471-2148-13-164

Evolutionary traces of functional surfaces along G protein signaling pathway.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3750384

26 October 2018

Identifiers

DOI

10.1186/1471-2148-13-164

1 reference

Dimensions Publication ID

5 August 2017

0 references

1 reference

5 August 2017

1 reference