Research graph
References from Codon-based indices for modeling gene expression and transcript evolution. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1007/bf02099948
10.1007/bf02099948 · External reference
10.1073/pnas.1016719108
10.1073/pnas.1016719108 · External reference
10.1016/s0378-1119(97)00400-9
10.1016/s0378-1119(97)00400-9 · External reference
10.1007/s00239-003-2507-5
10.1007/s00239-003-2507-5 · External reference
Unresolved reference
2020 · External reference
10.1038/nrm1488
10.1038/nrm1488 · External reference
10.1016/s0092-8240(89)80087-4
10.1016/s0092-8240(89)80087-4 · External reference
10.1093/gbe/evv044
10.1093/gbe/evv044 · External reference
Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula
10.1093/molbev/msl212 · 2007 · External reference
Translation and Protein Quality Control: codon optimality, bias and usage in translation and mRNA decay
10.1038/nrm.2017.91 · 2018 · External reference
10.1016/j.tibtech.2004.04.006
10.1016/j.tibtech.2004.04.006 · External reference
10.1016/j.gene.2020.144554
10.1016/j.gene.2020.144554 · External reference
Codon usage and phenotypic divergences of SARS-CoV-2 genes
10.3390/v12050498 · 2020 · External reference
Cytochrome P450 genes in coronary artery diseases: codon usage analysis reveals genomic GC adaptation
10.1016/j.gene.2016.06.011 · 2016 · External reference
Codon bias among synonymous rare variants is associated with Alzheimer’s disease imaging biomarker
2018 · External reference
Differences in codon bias and GC content contribute to the balanced expression of TLR7 and TLR9
10.1073/pnas.1518976113 · 2016 · External reference
10.1007/s00239-019-09921-4
10.1007/s00239-019-09921-4 · External reference
Analysis of codon usage patterns of the chloroplast genomes in the Poaceae family
10.1071/bt12073 · 2012 · External reference
Codon bias signatures, organization of microorganisms in codon space, and lifestyle
10.1093/molbev/msi040 · 2005 · External reference
10.1038/nrg2899
10.1038/nrg2899 · External reference
10.1016/j.molcel.2015.05.035
10.1016/j.molcel.2015.05.035 · External reference
10.1101/gr.2896904
10.1101/gr.2896904 · External reference
Forces that influence the evolution of codon bias
10.1098/rstb.2009.0305 · 2010 · External reference
An evaluation of measures of synonymous codon usage bias
10.1007/pl00006384 · 1998 · External reference
Indices of codon usage bias
10.4172/jpb.1000e34 · 2017 · External reference
10.1111/j.1469-185x.2012.00242.x
10.1111/j.1469-185x.2012.00242.x · External reference
10.1016/0378-1119(90)90491-9
10.1016/0378-1119(90)90491-9 · External reference
Codon usage in Kluyveromyces lactis and in yeast cytochrome c-encoding genes
10.1016/0378-1119(94)90521-5 · 1994 · External reference
‘Silent’ sites in Drosophila genes are not neutral: evidence of selection among synonymous codons
1988 · External reference
10.1186/1471-2148-4-19
10.1186/1471-2148-4-19 · External reference
10.1080/03081070500502967
10.1080/03081070500502967 · External reference
A new informatics method for measuring synonymous codon usage bias
2003 · 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
10.1016/0022-2836(81)90003-6
10.1016/0022-2836(81)90003-6 · External reference
Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer R
10.1016/0022-2836(82)90250-9 · 1982 · External reference
10.1016/s0021-9258(19)81068-2
10.1016/s0021-9258(19)81068-2 · External reference
10.1038/nature02046
10.1038/nature02046 · External reference
A survey of codon and amino acid frequency bias in microbial genomes focusing on translational efficiency
10.1007/s00239-003-2499-1 · 2003 · External reference
10.1016/j.jmb.2020.01.011
10.1016/j.jmb.2020.01.011 · External reference
10.1016/j.cell.2012.01.050
10.1016/j.cell.2012.01.050 · External reference
Modelling the efficiency of codon-tRNA interactions based on codon usage bias
10.1093/dnares/dsu017 · 2014 · External reference
10.1261/rna.030775.111
10.1261/rna.030775.111 · External reference
10.1016/j.cell.2010.02.036
10.1016/j.cell.2010.02.036 · External reference
Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation
10.1371/journal.pgen.1000548 · 2009 · External reference
10.1126/science.1170160
10.1126/science.1170160 · External reference
10.1016/j.cell.2010.03.031
10.1016/j.cell.2010.03.031 · External reference
10.1038/nature10965
10.1038/nature10965 · External reference
10.1261/rna.02890211
10.1261/rna.02890211 · External reference
10.1016/j.tig.2012.07.006
10.1016/j.tig.2012.07.006 · External reference
10.1093/nar/gkh834
10.1093/nar/gkh834 · External reference
10.1038/nsmb.2466
10.1038/nsmb.2466 · External reference
Codon usage in bacteria: correlation with gene expressivity
10.1093/nar/10.22.7055 · 1982 · External reference
10.1006/jmbi.1997.0942
10.1006/jmbi.1997.0942 · External reference
10.1016/s0378-1119(99)00225-5
10.1016/s0378-1119(99)00225-5 · External reference
10.1016/s0168-9525(00)02041-2
10.1016/s0168-9525(00)02041-2 · External reference
10.1371/journal.pgen.0020221
10.1371/journal.pgen.0020221 · External reference
10.1093/bioinformatics/btu797
10.1093/bioinformatics/btu797 · External reference
10.1093/bioinformatics/btz080
10.1093/bioinformatics/btz080 · External reference
10.1016/j.jmb.2019.04.021
10.1016/j.jmb.2019.04.021 · External reference
10.1126/science.1155761
10.1126/science.1155761 · External reference
10.1016/j.celrep.2015.12.011
10.1016/j.celrep.2015.12.011 · External reference
SCUMBLE: a method for systematic and accurate detection of codon usage bias by maximum likelihood estimation
10.1093/nar/gkn288 · 2008 · External reference
10.1126/science.1168978
10.1126/science.1168978 · External reference
10.1534/g3.114.015099
10.1534/g3.114.015099 · External reference
Measurement of average decoding rates of the 61 sense codons in vivo
10.7554/elife.03735 · 2014 · External reference
10.1080/15476286.2017.1384118
10.1080/15476286.2017.1384118 · External reference
10.1002/0471142727.mb0414s98
10.1002/0471142727.mb0414s98 · External reference
10.1002/pmic.201400441
10.1002/pmic.201400441 · External reference
Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources
10.1371/journal.pcbi.1006055 · 2018 · External reference
10.1016/j.gene.2004.11.035
10.1016/j.gene.2004.11.035 · External reference
10.1073/pnas.0909910107
10.1073/pnas.0909910107 · External reference
Synonymous codon usage in Saccharomyces cerevisiae
10.1002/yea.320070702 · 1991 · External reference
Unresolved reference
External reference
10.1093/nar/12.24.9567
10.1093/nar/12.24.9567 · External reference
COUSIN (COdon Usage Similarity INdex): a normalized measure of codon usage preferences
10.1093/gbe/evz262 · 2019 · External reference
Unresolved reference
External reference
The codon preference plot: graphic analysis of protein coding sequences and prediction of gene expression
10.1093/nar/12.1part2.539 · 1984 · External reference
Predicting gene expression level from relative codon usage bias: an application to Escherichia coli genome
2009 · External reference
PICDI, a simple program for codon bias calculation
1996 · External reference
Measure of synonymous codon usage diversity among genes in bacteria
10.1186/1471-2105-10-167 · 2009 · External reference
The ‘weighted sum of relative entropy’: a new index for synonymous codon usage bias
10.1016/j.gene.2004.03.001 · 2004 · External reference
Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity
10.1186/1471-2105-6-182 · 2005 · External reference
10.1093/genetics/159.3.1191
10.1093/genetics/159.3.1191 · External reference
Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance
10.1186/1471-2105-13-43 · 2012 · External reference
10.1080/15216549700203871
10.1080/15216549700203871 · External reference
CodonExplorer: an online tool for analyzing codon usage and sequence composition, scaling from genes to genomes
10.1093/bioinformatics/btp141 · 2009 · External reference
CAIcal: a combined set of tools to assess codon usage adaptation
10.1186/1745-6150-3-38 · 2008 · External reference
Synonymous codon usage, accuracy of translation, and gene length in Caenorhabditis elegans
10.1007/s002390010155 · 2001 · External reference
What drives codon choices in human genes?
10.1006/jmbi.1996.0528 · 1996 · External reference
Codon usages in different gene classes of the Escherichia coli genome
10.1046/j.1365-2958.1998.01008.x · 1998 · External reference
The codon bias database
10.1186/1471-2105-13-62 · 2012 · External reference
Relative codon adaptation index, a sensitive measure of codon usage bias
2010 · External reference
A major controversy in codon-Anticodon adaptation resolved by a new codon usage index
10.1534/genetics.114.172106 · 2014 · External reference
10.1093/dnares/dsq012
10.1093/dnares/dsq012 · External reference
10.1007/s00239-005-0250-9
10.1007/s00239-005-0250-9 · External reference
Codon adaptation index as a measure of dominating codon bias
10.1093/bioinformatics/btg272 · 2003 · External reference
10.1093/bioinformatics/btw647
10.1093/bioinformatics/btw647 · External reference
Codon bias patterns of E. coli’s interacting proteins
10.1371/journal.pone.0142127 · 2015 · External reference
Measures of codon bias in yeast, the tRNA pairing index and possible DNA repair mechanisms
2006 · External reference
10.1093/nar/22.13.2437
10.1093/nar/22.13.2437 · External reference
Combining models of protein translation and population genetics to predict protein production rates from codon usage patterns
10.1093/molbev/msm169 · 2007 · External reference
10.1038/nature02458
10.1038/nature02458 · External reference
Unresolved reference
External reference
Computational identification of rare codons of Escherichia coli based on codon pairs preference
2010 · External reference
Factors influencing codon usage bias in genomes
2008 · External reference
Estimation of ribosome profiling performance and reproducibility at various levels of resolution
10.1186/s13062-016-0127-4 · 2016 · External reference
10.1093/nar/gkw822
10.1093/nar/gkw822 · External reference
A novel framework for evaluating the performance of codon usage bias metrics
2018 · External reference
10.1101/gr.164996.113
10.1101/gr.164996.113 · External reference
10.1093/nar/gku646
10.1093/nar/gku646 · External reference
