Research graph
References from Bacterial gene 5′ ends have unusual mutation rates that can mislead tests of selection. Local targets link to admitted publications; unresolved targets remain external evidence.
Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution
10.1038/267275a0 · 1977 · External reference
Non-Darwinian evolution
10.1126/science.164.3881.788 · 1969 · External reference
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
10.1016/0022-2836(81)90003-6 · 1981 · External reference
Codon usage and tRNA content in unicellular and multicellular organisms
1985 · External reference
DNA sequence evolution: the sounds of silence
10.1098/rstb.1995.0108 · 1995 · External reference
The Codon Adaptation Index—a measure of directional synonymous codon usage bias, and its potential applications
10.1093/nar/15.3.1281 · 1987 · External reference
Synonymous codon usage in Escherichia coli: selection for translational accuracy
10.1093/molbev/msl166 · 2007 · External reference
Positively charged residues are the major determinants of ribosomal velocity
10.1371/journal.pbio.1001508 · 2013 · External reference
Codon catalog usage is a genome strategy modulated for gene expressivity
10.1093/nar/9.1.213-b · 1981 · External reference
Balanced codon usage optimizes eukaryotic translational efficiency
10.1371/journal.pgen.1002603 · 2012 · External reference
Codon usage determines translation rate in Escherichia coli
10.1016/0022-2836(89)90260-x · 1989 · External reference
Selection on synonymous sites: the unwanted transcript hypothesis
10.1038/s41576-023-00686-7 · 2024 · External reference
Hearing silence: non-neutral evolution at synonymous sites in mammals
10.1038/nrg1770 · 2006 · External reference
Exposing synonymous mutations
10.1016/j.tig.2014.04.006 · 2014 · External reference
Decoding mechanisms by which silent codon changes influence protein biogenesis and function
10.1016/j.biocel.2015.03.011 · 2015 · External reference
Functional synonymous mutations and their evolutionary consequences
10.1038/s41576-025-00850-1 · 2025 · External reference
Code inside the codon: the role of synonymous mutations in regulating splicing machinery and its impact on disease
10.1016/j.mrrev.2022.108444 · 2022 · External reference
Exonic splice regulation imposes strong selection at synonymous sites
10.1101/gr.233999.117 · 2018 · External reference
Codon usage and splicing jointly influence mRNA localization
2020 · External reference
Selection and mutation on microRNA target sequences during rice evolution
10.1186/1471-2164-9-454 · 2008 · External reference
A large-scale analysis of the relationship of synonymous SNPs changing MicroRNA regulation with functionality and disease
10.3390/ijms161023545 · 2015 · External reference
Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals
10.1186/gb-2005-6-9-r75 · 2005 · External reference
RNA structural determinants of optimal codons revealed by MAGE-Seq
2016 · External reference
Codon optimality is a major determinant of mRNA stability
10.1016/j.cell.2015.02.029 · 2015 · External reference
Crosstalk between codon optimality and cis-regulatory elements dictates mRNA stability
10.1186/s13059-020-02251-5 · 2021 · External reference
A code within the genetic code: codon usage regulates co-translational protein folding
10.1186/s12964-020-00642-6 · 2020 · External reference
Synonymous but not silent: the codon usage code for gene expression and protein folding
10.1146/annurev-biochem-071320-112701 · 2021 · External reference
Codon optimality, bias and usage in translation and mRNA decay
10.1038/nrm.2017.91 · 2018 · External reference
Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity
10.1093/nar/gks1205 · 2013 · External reference
Regions of extreme synonymous codon selection in mammalian genes
10.1093/nar/gkl095 · 2006 · External reference
How common are intragene windows with Ka > Ks owing to purifying selection on synonymous mutations?
10.1007/s00239-006-0207-7 · 2007 · External reference
Evolution of codon usage bias in Drosophila
10.1073/pnas.94.15.7784 · 1997 · External reference
Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers
10.1093/molbev/msj035 · 2006 · External reference
Preliminary assessment of the impact of microRNA-mediated regulation on coding sequence evolution in mammals
10.1007/s00239-005-0273-2 · 2006 · External reference
Identification of deleterious synonymous variants in human genomes
10.1093/bioinformatics/btt308 · 2013 · External reference
Investigating DNA-, RNA-, and protein-based features as a means to discriminate pathogenic synonymous variants
10.1002/humu.23283 · 2017 · External reference
Computational identification of deleterious synonymous variants in human genomes using a feature-based approach
10.1186/s12920-018-0455-6 · 2019 · External reference
Decoding the effects of synonymous variants
10.1093/nar/gkab1159 · 2021 · External reference
Reduced synonymous substitution rate at the start of enterobacterial genes
10.1093/nar/21.19.4599 · 1993 · External reference
A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes
2010 · External reference
Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in Escherichia coli
10.1038/nbt.4238 · 2018 · External reference
Causes and effects of N-terminal codon bias in bacterial genes
10.1126/science.1241934 · 2013 · External reference
Coding-sequence determinants of gene expression in Escherichia coli
10.1126/science.1170160 · 2009 · External reference
Analyzing and enhancing mRNA translational efficiency in an Escherichia coli in vitro expression system
10.1016/j.bbrc.2004.04.064 · 2004 · External reference
Multifactorial determinants of protein expression in prokaryotic open reading frames
10.1016/j.jmb.2010.08.010 · 2010 · External reference
Revealing determinants of translation efficiency via whole-gene codon randomization and machine learning
10.1093/nar/gkad035 · 2023 · External reference
Translation at first sight: the influence of leading codons
10.1093/nar/gkaa430 · 2020 · External reference
High-resolution modeling of the selection on local mRNA folding strength in coding sequences across the tree of life
10.1186/s13059-020-01971-y · 2020 · External reference
Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function
10.1371/journal.pgen.1005613 · 2015 · External reference
mRNA helicase activity of the ribosome
10.1016/j.cell.2004.11.042 · 2005 · External reference
Accessibility of the Shine-Dalgarno sequence dictates N-terminal codon bias in E. coli
10.1016/j.molcel.2018.05.008 · 2018 · External reference
Fast translation within the first 45 codons decreases mRNA stability and increases premature transcription termination in E. coli
10.1016/j.jmb.2019.01.026 · 2019 · External reference
Composite effects of gene determinants on the translation speed and density of ribosomes
10.1186/gb-2011-12-11-r110 · 2011 · External reference
Evolutionary determinants of genome-wide nucleotide composition
10.1038/s41559-017-0425-y · 2018 · External reference
ViennaRNA package 2.0
10.1186/1748-7188-6-26 · 2011 · External reference
Rapid evolution of mutation rate and spectrum in response to environmental and population-genetic challenges
10.1038/s41467-022-32353-6 · 2022 · External reference
Spatial vulnerabilities of the Escherichia coli genome to spontaneous mutations revealed with improved duplex sequencing
10.1534/genetics.118.301345 · 2018 · External reference
Determinants of spontaneous mutation in the bacterium Escherichia coli as revealed by whole-genome sequencing
10.1073/pnas.1512136112 · 2015 · External reference
Detection of DNA replication errors and 8-oxo-dGTP-mediated mutations in E. coli by Duplex DNA Sequencing
10.1016/j.dnarep.2023.103462 · 2023 · External reference
Specificity and mutagenesis bias of the mycobacterial alternative mismatch repair analyzed by mutation accumulation studies
10.1126/sciadv.aay4453 · 2020 · External reference
The rate and spectrum of spontaneous mutations in Mycobacterium smegmatis, a bacterium naturally devoid of the postreplicative mismatch repair pathway
10.1534/g3.116.030130 · 2016 · External reference
Asymmetric context-dependent mutation patterns revealed through mutation-accumulation experiments
10.1093/molbev/msv055 · 2015 · External reference
Patterns of change in nucleotide diversity over gene length
2024 · External reference
Unresolved reference
1908 · External reference
Properties of overlapping genes are conserved across microbial genomes
10.1101/gr.2433104 · 2004 · External reference
Overlapping genes: a window on gene evolvability
10.1186/1471-2164-15-721 · 2014 · External reference
An evolutionarily conserved mechanism for controlling the efficiency of protein translation
10.1016/j.cell.2010.03.031 · 2010 · External reference
Multiple roles of the coding sequence 5’ end in gene expression regulation
10.1093/nar/gku1313 · 2015 · External reference
Rate-limiting steps in yeast protein translation
10.1016/j.cell.2013.05.049 · 2013 · External reference
Improved ribosome-footprint and mRNA measurements provide insights into dynamics and regulation of yeast translation
10.1016/j.celrep.2016.01.043 · 2016 · External reference
Positive charge loading at protein termini is due to membrane protein topology, not a translational ramp
10.1093/molbev/mst169 · 2014 · External reference
Efficient translation initiation dictates codon usage at gene start
10.1038/msb.2013.32 · 2013 · External reference
Why AGG is associated with high transgene output: passenger effects and their implications for transgene design
2025 · External reference
An improved estimation of tRNA expression to better elucidate the coevolution between tRNA abundance and codon usage in bacteria
10.1038/s41598-019-39369-x · 2019 · External reference
Solving the riddle of codon usage preferences: a test for translational selection
10.1093/nar/gkh834 · 2004 · External reference
Quantitative elucidation of associations between nucleotide identity and physicochemical properties of amino acids and the functional insight
10.1016/j.csbj.2021.07.012 · 2021 · External reference
Translation in Bacillus subtilis: roles and trends of initiation and termination, insights from a genome analysis
10.1093/nar/27.17.3567 · 1999 · External reference
Relative importance for linear regression in R: the package relaimpo
10.18637/jss.v017.i01 · 2006 · External reference
A short translational ramp determines the efficiency of protein synthesis
10.1038/s41467-019-13810-1 · 2019 · External reference
Functionally uncoupled transcription-translation in Bacillus subtilis
10.1038/s41586-020-2638-5 · 2020 · External reference
Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases
10.1093/nar/15.19.8023 · 1987 · External reference
Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing
2012 · External reference
Products of DNA mismatch repair genes mutS and mutL are required for transcription-coupled nucleotide-excision repair of the lactose operon in Escherichia coli
10.1073/pnas.93.3.1292 · 1996 · External reference
Mechanistic insights into transcription coupled DNA repair
10.1016/j.dnarep.2017.06.006 · 2017 · External reference
Mutagenic deamination of cytosine residues in DNA
10.1038/287560a0 · 1980 · External reference
Context dependency of nucleotide probabilities and variants in human DNA
10.1186/s12864-021-08246-1 · 2022 · External reference
Evidence that mutation is universally biased towards AT in bacteria
10.1371/journal.pgen.1001115 · 2010 · External reference
Evidence of selection upon genomic GC-content in bacteria
10.1371/journal.pgen.1001107 · 2010 · External reference
Unusual mammalian usage of TGA stop codons reveals that sequence conservation need not imply purifying selection
2022 · External reference
Genes for highly abundant proteins in Escherichia coli avoid 5’ codons that promote ribosomal initiation
10.1371/journal.pcbi.1011581 · 2023 · External reference
Noise minimization in eukaryotic gene expression
10.1371/journal.pbio.0020137 · 2004 · External reference
Optimization of ribosome utilization in Saccharomyces cerevisiae
2023 · External reference
Gene architectures that minimize cost of gene expression
10.1016/j.molcel.2016.11.007 · 2017 · External reference
Optimizing the dynamics of protein expression
10.1038/s41598-019-43857-5 · 2019 · External reference
Gene optimization mechanisms: a multi-gene study reveals a high success rate of full-length human proteins expressed in Escherichia coli
10.1002/pro.408 · 2010 · External reference
Unresolved reference
2013 · External reference
The new mutation theory of phenotypic evolution
10.1073/pnas.0703349104 · 2007 · External reference
Comparisons of dN/dS are time dependent for closely related bacterial genomes
10.1016/j.jtbi.2005.08.037 · 2006 · External reference
Coexistence of different base periodicities in prokaryotic genomes as related to DNA curvature, supercoiling, and transcription
10.1016/j.ygeno.2011.06.006 · 2011 · External reference
A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes
1985 · External reference
Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions
1986 · External reference
Consecutive low-usage leucine codons block translation only when near the 5’ end of a message in Escherichia coli
10.1006/jmbi.1994.0038 · 1995 · External reference
Site-to-site variation of synonymous substitution rates
10.1093/molbev/msi232 · 2005 · External reference
Unraveling patterns of site-to-site synonymous rates variation and associated gene properties of protein domains and families
10.1371/journal.pone.0095034 · 2014 · External reference
Virus attenuation by genome-scale changes in codon pair bias
10.1126/science.1155761 · 2008 · External reference
Understanding the Genetic Code
2019 · External reference
The Ka/Ks ratio: diagnosing the form of sequence evolution
10.1016/s0168-9525(02)02722-1 · 2002 · External reference
Comparative analyses of selection operating on nontranslated intergenic regions of diverse bacterial species
10.1534/genetics.116.195784 · 2017 · External reference
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
2016 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
ppcor: an R package for a fast calculation to semi-partial correlation coefficients
2015 · External reference
PaxDb, a database of protein abundance averages across all three domains of life
10.1074/mcp.o111.014704 · 2012 · External reference
Translation efficiency is determined by both codon bias and folding energy
10.1073/pnas.0909910107 · 2010 · External reference
Differential translation efficiency of orthologous genes is involved in phenotypic divergence of yeast species
10.1038/ng1967 · 2007 · External reference
OrthoFinder: phylogenetic orthology inference for comparative genomics
10.1186/s13059-019-1832-y · 2019 · External reference
Unresolved reference
2018 · External reference
MAFFT multiple sequence alignment software version 7: improvements in performance and usability
10.1093/molbev/mst010 · 2013 · External reference
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
10.1093/nar/gkl315 · 2006 · External reference
IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era
10.1093/molbev/msaa015 · 2020 · External reference
PAML 4: phylogenetic analysis by maximum likelihood
10.1093/molbev/msm088 · 2007 · External reference
Revisiting operons: an analysis of the landscape of transcriptional units in E. coli
10.1186/s12859-015-0805-8 · 2015 · External reference
BSGatlas: a unified Bacillus subtilis genome and transcriptome annotation atlas with enhanced information access
2021 · External reference
GFF-Ex: a genome feature extraction package
10.1186/1756-0500-7-315 · 2014 · External reference
BEDTools: a flexible suite of utilities for comparing genomic features
10.1093/bioinformatics/btq033 · 2010 · External reference
Pybedtools: a flexible Python library for manipulating genomic datasets and annotations
10.1093/bioinformatics/btr539 · 2011 · External reference
A simple method for displaying the hydropathic character of a protein
10.1016/0022-2836(82)90515-0 · 1982 · External reference
Amino acid difference formula to help explain protein evolution
10.1126/science.185.4154.862 · 1974 · External reference
10.1201/b17118
10.1201/b17118 · 2014 · External reference
Refractive indices of amino acids, proteins, and related substances
10.1021/ba-1964-0044.ch004 · 1964 · External reference
Amino acid properties and side-chain orientation in proteins: a cross correlation appraoch
10.1016/0022-5193(75)90031-4 · 1975 · External reference
Evidence for strong mutation bias toward, and selection against, U content in SARS-CoV-2: implications for vaccine design
10.1093/molbev/msaa188 · 2021 · External reference
Atypical at skew in Firmicute genomes results from selection and not from mutation
10.1371/journal.pgen.1002283 · 2011 · External reference
Array programming with NumPy
10.1038/s41586-020-2649-2 · 2020 · External reference
