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Different types of secondary information in the genetic code.
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Europe PubMed Central
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4114694
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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24935971%20AND%20SRC:MED&resulttype=core&format=json
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20 March 2020
title
Different types of secondary information in the genetic code
(English)
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stated in
Europe PubMed Central
PMC publication ID
4114694
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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24935971%20AND%20SRC:MED&resulttype=core&format=json
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20 March 2020
author
Richard J. Maraia
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1
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Europe PubMed Central
PMC publication ID
4114694
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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24935971%20AND%20SRC:MED&resulttype=core&format=json
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20 March 2020
author name string
James R Iben
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2
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Europe PubMed Central
PMC publication ID
4114694
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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24935971%20AND%20SRC:MED&resulttype=core&format=json
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20 March 2020
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English
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1 July 2014
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4114694
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20 March 2020
published in
RNA
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4114694
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20 March 2020
volume
20
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Europe PubMed Central
PMC publication ID
4114694
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20 March 2020
issue
7
1 reference
stated in
Europe PubMed Central
PMC publication ID
4114694
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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24935971%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 March 2020
page(s)
977-984
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Europe PubMed Central
PMC publication ID
4114694
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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24935971%20AND%20SRC:MED&resulttype=core&format=json
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20 March 2020
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A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress
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A comprehensive analysis of translational missense errors in the yeast Saccharomyces cerevisiae.
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How the sequence of a gene can tune its translation
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5 July 2018
Human AlkB homolog ABH8 Is a tRNA methyltransferase required for wobble uridine modification and DNA damage survival
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A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes
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5 July 2018
tRNA over-expression in breast cancer and functional consequences
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5 July 2018
Silent (synonymous) SNPs: should we care about them?
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5 July 2018
Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation
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5 July 2018
The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins
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5 July 2018
Can GC content at third-codon positions be used as a proxy for isochore composition?
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5 July 2018
Coding-sequence determinants of gene expression in Escherichia coli
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5 July 2018
GtRNAdb: a database of transfer RNA genes detected in genomic sequence
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5 July 2018
tRNAdb 2009: compilation of tRNA sequences and tRNA genes
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5 July 2018
Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima
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Bringing order to translation: the contributions of transfer RNA anticodon-domain modifications
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5 July 2018
Trm9-catalyzed tRNA modifications link translation to the DNA damage response
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5 July 2018
Differentiating between near- and non-cognate codons in Saccharomyces cerevisiae
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5 July 2018
Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels
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5 July 2018
Evolution and multilevel optimization of the genetic code
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5 July 2018
Splicing and the evolution of proteins in mammals
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5 July 2018
The genetic code is nearly optimal for allowing additional information within protein-coding sequences
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5 July 2018
Tissue-specific differences in human transfer RNA expression
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5 July 2018
tRNA's wobble decoding of the genome: 40 years of modification
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5 July 2018
A "silent" polymorphism in the MDR1 gene changes substrate specificity
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5 July 2018
The frequency of translational misreading errors in E. coli is largely determined by tRNA competition.
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5 July 2018
Hearing silence: non-neutral evolution at synonymous sites in mammals
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5 July 2018
Why highly expressed proteins evolve slowly
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5 July 2018
Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals
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5 July 2018
Variation in the strength of selected codon usage bias among bacteria
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5 July 2018
Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization
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5 July 2018
Solving the riddle of codon usage preferences: a test for translational selection
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5 July 2018
Selective and mutational patterns associated with gene expression in humans: influences on synonymous composition and intron presence
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5 July 2018
Decoding the genome: a modified view
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5 July 2018
Disruption of a receptor-mediated mechanism for intracellular sorting of proinsulin in familial hyperproinsulinemia
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5 July 2018
Evolution of synonymous codon usage in metazoans
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stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4114694
retrieved
5 July 2018
tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4114694
retrieved
5 July 2018
Silent mutations affect in vivo protein folding in Escherichia coli
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4114694
retrieved
5 July 2018
Codon-improved Cre recombinase (iCre) expression in the mouse
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4114694
retrieved
5 July 2018
Codon usage bias covaries with expression breadth and the rate of synonymous evolution in humans, but this is not evidence for selection
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4114694
retrieved
5 July 2018
Codon usage and tRNA genes in eukaryotes: correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4114694
retrieved
5 July 2018
tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4114694
retrieved
5 July 2018
Growth rate-optimised tRNA abundance and codon usage.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4114694
retrieved
5 July 2018
Recombination of protein domains facilitated by co-translational folding in eukaryotes.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4114694
retrieved
5 July 2018
A "humanized" green fluorescent protein cDNA adapted for high-level expression in mammalian cells
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4114694
retrieved
5 July 2018
Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4114694
retrieved
5 July 2018
Codon selection in yeast
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4114694
retrieved
5 July 2018
Codon catalog usage and the genome hypothesis
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4114694
retrieved
5 July 2018
Codon usage in bacteria: correlation with gene expressivity
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4114694
retrieved
5 July 2018
Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4114694
retrieved
5 July 2018
Codon usage and tRNA content in unicellular and multicellular organisms
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4114694
retrieved
5 July 2018
The efficiency of folding of some proteins is increased by controlled rates of translation in vivo. A hypothesis
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4114694
retrieved
5 July 2018
Coevolution of codon usage and transfer RNA abundance
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4114694
retrieved
5 July 2018
The selection-mutation-drift theory of synonymous codon usage
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4114694
retrieved
5 July 2018
Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4114694
retrieved
29 October 2018
Silent substitutions predictably alter translation elongation rates and protein folding efficiencies
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4114694
retrieved
29 October 2018
Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4114694
retrieved
29 October 2018
Tracing specific synonymous codon-secondary structure correlations through evolution.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4114694
retrieved
29 October 2018
Specific correlations between relative synonymous codon usage and protein secondary structure
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4114694
retrieved
29 October 2018
Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4114694
retrieved
29 October 2018
Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4114694
retrieved
29 October 2018
The sounds of silence: synonymous mutations affect function
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/24935971
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
What If There Are Only 30,000 Human Genes?
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/24935971
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Molecular biology and evolution. Can genes explain biological complexity?
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/24935971
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Translational efficiency of transfer RNA's: uses of an extended anticodon
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/24935971
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
It's a mod mod tRNA world
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/24935971
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
The sound of silence
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/24935971
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Codon usage table for Schizosaccharomyces pombe
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/24935971
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Identifiers
DOI
10.1261/RNA.044115.113
1 reference
stated in
Europe PubMed Central
PMC publication ID
4114694
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24935971%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 March 2020
PMC publication ID
4114694
1 reference
stated in
Europe PubMed Central
PMC publication ID
4114694
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24935971%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 March 2020
PubMed publication ID
24935971
1 reference
stated in
Europe PubMed Central
PMC publication ID
4114694
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24935971%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 March 2020
ResearchGate publication ID
263165792
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