Willemsen A, Manzano-Marin A, Horn M
Genome Biol Evol. 2025; 17(1).
PMID: 39760805
PMC: 11702301.
DOI: 10.1093/gbe/evae271.
Zhang Z
Genomics Proteomics Bioinformatics. 2024; 22(4).
PMID: 39213341
PMC: 11514846.
DOI: 10.1093/gpbjnl/qzae061.
Anwer A, Shahzadi A, Nawaz H, Majeed M, Alshammari A, Albekairi N
RSC Adv. 2024; 14(28):20290-20299.
PMID: 38932985
PMC: 11200166.
DOI: 10.1039/d4ra01735h.
Farookhi H, Xia X
Microorganisms. 2024; 12(4).
PMID: 38674712
PMC: 11052298.
DOI: 10.3390/microorganisms12040768.
Wielgoss S, Van Dyken J, Velicer G
Genome Biol Evol. 2024; 16(5).
PMID: 38526062
PMC: 11069108.
DOI: 10.1093/gbe/evae066.
Omics data analysis reveals the system-level constraint on cellular amino acid composition.
Huang Y, Mao Z, Zhang Y, Zhao J, Luan X, Wu K
Synth Syst Biotechnol. 2024; 9(2):304-311.
PMID: 38510205
PMC: 10951587.
DOI: 10.1016/j.synbio.2024.03.001.
No Evidence that Selection on Synonymous Codon Usage Affects Patterns of Protein Evolution in Bacteria.
Moutinho A, Eyre-Walker A
Genome Biol Evol. 2023; 16(2).
PMID: 38149940
PMC: 10849182.
DOI: 10.1093/gbe/evad232.
Molecular bases for strong phenotypic effects of single synonymous codon substitutions in the E. coli ccdB toxin gene.
Bajaj P, Bhasin M, Varadarajan R
BMC Genomics. 2023; 24(1):732.
PMID: 38049728
PMC: 10694988.
DOI: 10.1186/s12864-023-09817-0.
Main Factors Shaping Amino Acid Usage Across Evolution.
Lamolle G, Simon D, Iriarte A, Musto H
J Mol Evol. 2023; 91(4):382-390.
PMID: 37264211
DOI: 10.1007/s00239-023-10120-5.
The effect of the genomic GC content bias of prokaryotic organisms on the secondary structures of their proteins.
Barcelo-Antemate D, Fontove-Herrera F, Santos W, Merino E
PLoS One. 2023; 18(5):e0285201.
PMID: 37141209
PMC: 10159118.
DOI: 10.1371/journal.pone.0285201.
Phylogenetic Analysis That Models Compositional Heterogeneity over the Tree.
Foster P
Methods Mol Biol. 2022; 2569:119-135.
PMID: 36083446
DOI: 10.1007/978-1-0716-2691-7_6.
Mechanisms governing codon usage bias and the implications for protein expression in the chloroplast of Chlamydomonas reinhardtii.
Fages-Lartaud M, Hundvin K, Hohmann-Marriott M
Plant J. 2022; 112(4):919-945.
PMID: 36071273
PMC: 9828097.
DOI: 10.1111/tpj.15970.
Stop Codon Usage as a Window into Genome Evolution: Mutation, Selection, Biased Gene Conversion and the TAG Paradox.
Ho A, Hurst L
Genome Biol Evol. 2022; 14(8).
PMID: 35867377
PMC: 9348620.
DOI: 10.1093/gbe/evac115.
Strong Selectional Forces Fine-Tune CpG Content in Genes Involved in Neurological Disorders as Revealed by Codon Usage Patterns.
Khandia R, Sharma A, Alqahtani T, Alqahtani A, Asiri Y, Alqahtani S
Front Neurosci. 2022; 16:887929.
PMID: 35757545
PMC: 9226491.
DOI: 10.3389/fnins.2022.887929.
Evolutionary jumps in bacterial GC content.
Mahajan S, Agashe D
G3 (Bethesda). 2022; 12(8).
PMID: 35579351
PMC: 9339322.
DOI: 10.1093/g3journal/jkac108.
An overview of dinucleotide and codon usage in all viruses.
Simon D, Cristina J, Musto H
Arch Virol. 2022; 167(6):1443-1448.
PMID: 35467158
DOI: 10.1007/s00705-022-05454-2.
Determination of the Amino Acid Recruitment Order in Early Life by Genome-Wide Analysis of Amino Acid Usage Bias.
Zhao M, Ding R, Liu Y, Ji Z, Zhao Y
Biomolecules. 2022; 12(2).
PMID: 35204672
PMC: 8961565.
DOI: 10.3390/biom12020171.
The microbial ecology of Escherichia coli in the vertebrate gut.
Foster-Nyarko E, Pallen M
FEMS Microbiol Rev. 2022; 46(3).
PMID: 35134909
PMC: 9075585.
DOI: 10.1093/femsre/fuac008.
Formation of the Codon Degeneracy during Interdependent Development between Metabolism and Replication.
Li D
Genes (Basel). 2021; 12(12).
PMID: 34946975
PMC: 8701183.
DOI: 10.3390/genes12122023.
A computational screen for alternative genetic codes in over 250,000 genomes.
Shulgina Y, Eddy S
Elife. 2021; 10.
PMID: 34751130
PMC: 8629427.
DOI: 10.7554/eLife.71402.