Cited by 3,992RNA and protein synthesis mechanismsGenomics and Phylogenetic StudiesEvolution and Genetic Dynamics

The DOI matches its Crossref record; 30 of the 30 references it cites were found in a registry or an index.

The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications

Open access

Sharp, Paul M., Li, Wen-Hsiung·1987·Nucleic Acids Research

Open this paper in CoChat — free account

Abstract

A simple, effective measure of synonymous codon usage bias, the Codon Adaptation Index, is detailed. The index uses a reference set of highly expressed genes from a species to assess the relative merits of each codon, and a score for a gene is calculated from the frequency of use of all codons in that gene. The index assesses the extent to which selection has been effective in moulding the pattern of codon usage. In that respect it is useful for predicting the level of expression of a gene, for assessing the adaptation of viral genes to their hosts, and for making comparisons of codon usage in different organisms. The index may also give an approximate indication of the likely success of heterologous gene expression.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1093/nar/15.3.1281

Cites

30 of 30 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

The Neutral Theory of Molecular Evolution
Kimura, M. (1979) · Scientific American · doi:10.1038/scientificamerican1179-98 · Cited by 7,687
Codon usage and tRNA content in unicellular and multicellular organisms.
Ikemura, T. (1985) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040335 · Cited by 1,710
Codon selection in yeast.
Bennetzen, J. L., & Hall, B. D. (1982) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)81068-2 · Cited by 1,584
The neutral theory of molecular evolution
Dover, G. A. (1984) · Endeavour · doi:10.1016/0160-9327(84)90064-4 · Cited by 1,394
Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes
Sharp, P. M., Tuohy, T. M. F., & Mosurski, K. (1986) · Nucleic Acids Research · doi:10.1093/nar/14.13.5125 · Cited by 1,206
Self-citation
Codon usage in bacteria: correlation with gene expressivity.
Gouy, M., & Gautier, C. (1982) · Nucleic Acids Research · doi:10.1093/nar/10.22.7055 · Cited by 1,182
Codon catalog usage is a genome strategy modulated for gene expressivity
Grantham, R. L., Gautier, C., Gouy, M., Jacobzone, M., & Mercier, R. (1981) · Nucleic Acids Research · doi:10.1093/nar/9.1.213-b · Cited by 939
Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes
Ikemura, T. (1981) · Journal of Molecular Biology · doi:10.1016/0022-2836(81)90363-6 · Cited by 875
The mosaic genome of warm-blooded vertebrates
Bernardi, G., Olofsson, B., Filipski, J., Zerial, M., Salinas, J., Cuny, G., Meunier-Rotival, M., & Rodier, F. (1985) · Science · doi:10.1126/science.4001930 · Cited by 875
Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes
Ikemura, T. (1982) · Journal of Molecular Biology · doi:10.1016/0022-2836(82)90250-9 · Cited by 605

Flagged first, then by citations

Show all 30 references

Research works printed but not linked: 5

Toh, H. (1986) FEBS Letters 194, 245-248.
Miyata, T. and Hayashida, H. (1981) Proc. Natl. Acad. Sci. USA 78, 5739- 5743.
Sharp, P.M. and Li, W-H. (1986) J. Mol. Evol. (in press)
Li, W-H. (1987) J. Mol. Evol. (in press)
Ochman, H. and Selander, R.K. (1984) Proc. Natl. Acad. Sci. USA 81, 198- 201.

Sorted by citations

Items 501–600 of 1,006

Codon Usage and Phenotypic Divergences of SARS-CoV-2 Genes
Dilucca, M., Forcelloni, S., Georgakilas, A. G., Giansanti, A., & Pavlopoulou, A. (2020) · Viruses · doi:10.3390/v12050498 · Cited by 91
Ohanin, a Novel Protein from King Cobra Venom, Induces Hypolocomotion and Hyperalgesia in Mice
Pung, Y. F., Wong, P. T. ‐., Kumar, P. P., Hodgson, W. C., & Kini, R. M. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m414137200 · Cited by 91
Genomic characterization of the conditionally dispensable chromosome in Alternaria arborescens provides evidence for horizontal gene transfer
Hu, J., Chen, C., Peever, T. L., Dang, H. X., Lawrence, C. B., & Mitchell, T. K. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-171 · Cited by 91
RCDI/eRCDI: a web-server to estimate codon usage deoptimization
Puigbò, P., Aragonès, L., & Garcı́a-Vallvé, S. (2010) · BMC Research Notes · doi:10.1186/1756-0500-3-87 · Cited by 90
Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States
Rudolph, K. L. M., Schmitt, B. M., Villar, D., White, R. J., Marioni, J. C., Kutter, C., & Odom, D. T. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006024 · Cited by 92
Predicting Functional Effects of Synonymous Variants: A Systematic Review and Perspectives
Zeng, Z., & Bromberg, Y. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00914 · Cited by 95
Exploring Lassa Virus Proteome to Design a Multi-epitope Vaccine Through Immunoinformatics and Immune Simulation Analyses
Sayed, S. B., Nain, Z., Khan, M. S. A., Abdulla, F., Tasmin, R., & Adhikari, U. K. (2020) · International Journal of Peptide Research and Therapeutics · doi:10.1007/s10989-019-10003-8 · Cited by 90
A Partial Least Squares based algorithm for parsimonious variable selection
Mehmood, T., Martens, H. A., Sæbø, S., Warringer, J., & Snipen, L. G. (2011) · Algorithms for Molecular Biology · doi:10.1186/1748-7188-6-27 · Cited by 92
Comparative context analysis of codon pairs on an ORFeome scale
Moura, G., Pinheiro, M., Silva, R., Miranda, I., Afreixo, V., Dias, G., Freitas, A., Oliveira, J. L., & Santos, M. A. (2005) · Genome Biology · doi:10.1186/gb-2005-6-3-r28 · Cited by 90
Transcriptional activators in yeast
Titz, B. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj493 · Cited by 90
The proteome of Mycoplasma genitalium
Wasinger, V. C., Pollack, J. D., & Humphery‐Smith, I. (2000) · European Journal of Biochemistry · doi:10.1046/j.1432-1327.2000.01183.x · Cited by 90
Codon usage and intragenic position
Bulmer, M. G. (1988) · Journal of Theoretical Biology · doi:10.1016/s0022-5193(88)80024-9 · Cited by 90
USING HITCHHIKING GENES TO STUDY ADAPTATION AND DIVERGENCE DURING SPECIATION WITHIN THE DROSOPHILA MELANOGASTER SPECIES COMPLEX
Hilton, H., Kliman, R. M., & Hey, J. (1994) · Evolution · doi:10.1111/j.1558-5646.1994.tb02222.x · Cited by 90
Translational Control by Ribosome Pausing in Bacteria: How a Non-uniform Pace of Translation Affects Protein Production and Folding
Samatova, E., Daberger, J., Liutkute, M., & Rodnina, M. V. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.619430 · Cited by 92
Environmental perturbations lift the degeneracy of the genetic code to regulate protein levels in bacteria
Subramaniam, A. R., Pan, T., & Cluzel, P. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1211077110 · Cited by 90
Codon optimizer: a freeware tool for codon optimization
Fuglsang, A. (2003) · Protein Expression and Purification · doi:10.1016/s1046-5928(03)00213-4 · Cited by 89
Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X.
Galibert, F., Alexandraki, D., Baur, A., Boles, E., Chalwatzis, N., Chuat, J., Coster, F., Cziepluch, C., HAAN, M. D., Domdey, H., et al. (1996) · The EMBO Journal · doi:10.1002/j.1460-2075.1996.tb00557.x · Cited by 89
Genome-wide analysis of codon usage bias in Ebolavirus
Cristina, J., Moreno, P., Moratorio, G., & Musto, H. (2014) · Virus Research · doi:10.1016/j.virusres.2014.11.005 · Cited by 86
Translational Selection Is Ubiquitous in Prokaryotes
Supek, F., Škunca, N., Repar, J., Vlahoviček, K., & Šmuc, T. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001004 · Cited by 89
Comparative Genomics and Phylogenomics of East Asian Tulips (Amana, Liliaceae)
Li, P., Lu, R., Xu, W., Ohi‐Toma, T., Cai, M., Qiu, Y., Cameron, K. M., & Fu, C. (2017) · Frontiers in Plant Science · doi:10.3389/fpls.2017.00451 · Cited by 89
Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses
Chan, C. S. C., Pham, P., Dedon, P. C., & Begley, T. J. (2018) · Genome biology · doi:10.1186/s13059-018-1611-1 · Cited by 86
Nucleotide sequence, function, activation, and evolution of the cryptic asc operon of Escherichia coli K12.
Hall, B. G., & Xu, L. (1992) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040753 · Cited by 88
Horizontal Gene Transfer Regulation in Bacteria as a “Spandrel” of DNA Repair Mechanisms
Fall, S., Mercier, A., Bertolla, F., Calteau, A., Guéguen, L., Perrière, G., Vogel, T. M., & Simonet, P. (2007) · PLoS ONE · doi:10.1371/journal.pone.0001055 · Cited by 94
A model of protein translation including codon bias, nonsense errors, and ribosome recycling
Gilchrist, M. A., & Wagner, A. (2005) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2005.08.007 · Cited by 88
The transmission sense of information
Bergstrom, C. T., & Rosvall, M. (2009) · Biology & Philosophy · doi:10.1007/s10539-009-9180-z · Cited by 90
Visual gene developer: a fully programmable bioinformatics software for synthetic gene optimization
Jung, S., & McDonald, K. A. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-340 · Cited by 90
Synonymous codon usage in Pseudomonas aeruginosa PA01
Grocock, R., & Sharp, P. M. (2002) · Gene · doi:10.1016/s0378-1119(02)00503-6 · Cited by 88
Self-citation
The Acid-Inducible asr Gene in Escherichia coli : Transcriptional Control by the phoBR Operon
Sužiedėlienė, E., Sužiedėlis, K., ̇, V. G., & Normark, S. J. (1999) · Journal of Bacteriology · doi:10.1128/jb.181.7.2084-2093.1999 · Cited by 88
Molecular characterization of the Escherichia coli K-12 zwf gene encoding glucose 6-phosphate dehydrogenase
Rowley, D. L., & Wolf, R. E. (1991) · Journal of Bacteriology · doi:10.1128/jb.173.3.968-977.1991 · Cited by 88
Codon usage and base composition inRickettsia prowazekii
Andersson, S. G. E., & Sharp, P. M. (1996) · Journal of Molecular Evolution · doi:10.1007/bf02352282 · Cited by 88
Self-citation
Similar compositional biases are caused by very different mutational effectsPreprint
Rocha, E. P. C., Touchon, M., & Feil, E. J. (2006) · Genome Research · doi:10.1101/gr.5525106 · Cited by 88
Structural basis and designing of peptide vaccine using PE-PGRS family protein of Mycobacterium ulcerans—An integrated vaccinomics approach
Nain, Z., Karim, M. M., Sen, M. K., & Adhikari, U. K. (2020) · Molecular Immunology · doi:10.1016/j.molimm.2020.02.009 · Cited by 85
Autoinduction of Protein Expression
Fox, B. G., & Blommel, P. G. (2009) · Current Protocols in Protein Science · doi:10.1002/0471140864.ps0523s56 · Cited by 87
Folding at the rhythm of the rare codon beat
Marı́n, M. (2008) · Biotechnology Journal · doi:10.1002/biot.200800089 · Cited by 92
Variation in G+C-content and codon choice: differences among synonymous codon groups in vertebrate genes
Martín, A., Bertranpetit, J., Oliver, J. L. T., & Medina, J. (1989) · Nucleic Acids Research · doi:10.1093/nar/17.15.6181 · Cited by 87
Mutational and selective pressures on codon and amino acid usage in Buchnera, endosymbiotic bacteria of aphids.Preprint
Rispe, C., Delmotte, F., van Ham, R. V., & Moya, A. (2003) · Genome Research · doi:10.1101/gr.1358104 · Cited by 96
Characteristics and clustering of human ribosomal protein genes
Ishii, K., Washio, T., Uechi, T., Yoshihama, M., Kenmochi, N., & Tomita, M. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-37 · Cited by 88
Single synonymous mutation in factor IX alters protein properties and underlies haemophilia B
Simhadri, V. L., Hamasaki‐Katagiri, N., Lin, B. C., Hunt, R., Jha, S. S., Tseng, S. C., Wu, A., Bentley, A. A., Zichel, R., Lü, Q., et al. (2016) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2016-104072 · Cited by 85
Codon Bias is a Major Factor Explaining Phage Evolution in Translationally Biased Hosts
Carbone, A. (2008) · Journal of Molecular Evolution · doi:10.1007/s00239-008-9068-6 · Cited by 85
Differential Translation Tunes Uneven Production of Operon-Encoded Proteins
Quax, T. E. F., Wolf, Y. I., Koehorst, J. J., Wurtzel, O., van der Oost, R., Ran, W., Blombach, F., Makarova, K. S., Brouns, S. J. J., Forster, A. C., et al. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.07.049 · Cited by 86
Compensatory gene amplification restores fitness after inter‐species gene replacements
Lind, P. A., Tobin, C., Berg, O. G., Kurland, C. G., & Andersson, D. I. (2010) · Molecular Microbiology · doi:10.1111/j.1365-2958.2009.07030.x · Cited by 87
Crystallin gene expression during rat lens development
Aarts, H. J. M., Lubsen, N. H., & Schoenmakers, J. G. G. (1989) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1989.tb14892.x · Cited by 85
Pyrococcus genome comparison evidences chromosome shuffling-driven evolution
Zivanovic, Y. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.9.1902 · Cited by 85
Ribosome profiling: a Hi‐Def monitor for protein synthesis at the genome‐wide scale
Michel, A. M., & Baranov, P. V. (2013) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1172 · Cited by 86
Gene losses and partial deletion of small single-copy regions of the chloroplast genomes of two hemiparasitic Taxillus species
Li, Y., Zhou, J., Chen, X., Cui, Y., Xu, Z., Li, Y.-H., Song, J., Duan, B., & Yao, H. (2017) · Scientific Reports · doi:10.1038/s41598-017-13401-4 · Cited by 84
Reconstitution of translesion synthesis reveals a mechanism of eukaryotic DNA replication restart
Guilliam, T. A., & Yeeles, J. T. P. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-0418-4 · Cited by 82
Rapid discovery of novel prophages using biological feature engineering and machine learning
Sirén, K., Millard, A. D., Petersen, B., Gilbert, M. T. P., Clokie, M. R. J., & Sicheritz‐Pontén, T. (2021) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqaa109 · Cited by 84
Geptop: A Gene Essentiality Prediction Tool for Sequenced Bacterial Genomes Based on Orthology and Phylogeny
Wei, W., Ning, L., Ye, Y., & Guo, F. (2013) · PLoS ONE · doi:10.1371/journal.pone.0072343 · Cited by 83
Successful Lateral Transfer Requires Codon Usage Compatibility Between Foreign Genes and Recipient Genomes
Medrano-Soto, A., Moreno‐Hagelsieb, G., Vinuesa, P., Christen, J. A., & Collado‐Vides, J. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh202 · Cited by 84
Sequence and expression of NUC1 , the gene encoding the mitochondrial nuclease in Saccharomyces cerevisiae
Vincent, R. D., Hofmann, T. J., & Zassenhaus, H. P. (1988) · Nucleic Acids Research · doi:10.1093/nar/16.8.3297 · Cited by 84
Evaluating Phylostratigraphic Evidence for Widespread De Novo Gene Birth in Genome Evolution
Moyers, B. A., & Zhang, J. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw008 · Cited by 86
Comparative Analysis of Codon Bias in the Chloroplast Genomes of Theaceae Species
Wang, Z., Cai, Q., Wang, Y., Li, M., Wang, C., Wang, Z., Jiao, C., Xu, C., Wang, H., & Zhang, Z. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.824610 · Cited by 83
Phylogenomic analysis of polyketide synthase-encoding genes in Trichoderma
Baker, S., Perrone, G., Richardson, N. M., Gallo, A., & Kubicek, C. P. (2011) · Microbiology · doi:10.1099/mic.0.053462-0 · Cited by 83
Detecting Alien Genes in Bacterial Genomesa
MRÁZEK, J., & Karlin, S. (1999) · Annals of the New York Academy of Sciences · doi:10.1111/j.1749-6632.1999.tb08893.x · Cited by 83
Sequence invariance of the antigen-coding central region of the phase 1 flagellar filament gene (fliC) among strains of Salmonella typhimurium
Smith, N. H., & Selander, R. K. (1990) · Journal of Bacteriology · doi:10.1128/jb.172.2.603-609.1990 · Cited by 82
Effects of codon optimization on coagulation factor IX translation and structure: Implications for protein and gene therapies
Alexaki, A., Hettiarachchi, G. K., Athey, J. C., Katneni, U. K., Simhadri, V., Hamasaki-Katagiri, N., Nanavaty, P., Lin, B., Takeda, K., Freedberg, D., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-51984-2 · Cited by 78
Correlation of codon bias measures with mRNA levels: analysis of transcriptome data from Escherichia coli
Goetz, R. M., & Fuglsang, A. (2004) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2004.11.134 · Cited by 82
Comparison of Correspondence Analysis Methods for Synonymous Codon Usage in Bacteria
Suzuki, H., Brown, C. J., Forney, L. J., & Top, E. M. (2008) · DNA Research · doi:10.1093/dnares/dsn028 · Cited by 82
Kluyveromyces lactis
Wésolowski‐Louvel, M., Breunig, K. D., & Fukuhara, H. (1996) · Springer eBooks · doi:10.1007/978-3-642-79856-6_5 · Cited by 82
Charging levels of four tRNA species in Escherichia coli Rel+ and Rel− strains during amino acid starvation: a simple model for the effect of ppGpp on translational accuracy11Edited by D. E. Draper
Sørensen, M. A. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4525 · Cited by 82
Analysis of Codon Usage Patterns in Herbaceous Peony (Paeonia lactiflora Pall.) Based on Transcriptome Data
Wu, Y., Zhao, D., & Tao, J. (2015) · Genes · doi:10.3390/genes6041125 · Cited by 81
Development of multi-epitope driven subunit vaccine against Fasciola gigantica using immunoinformatics approach
Kalita, P., Lyngdoh, D. L., Padhi, A. K., Shukla, H., & Tripathi, T. (2019) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2019.07.024 · Cited by 81
Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition
Tan, M. H., Gan, H. M., Lee, Y. P., Bracken‐Grissom, H. D., Chan, T., Miller, A. D., & Austin, C. M. (2019) · Scientific Reports · doi:10.1038/s41598-019-47145-0 · Cited by 80
The gene of the N‐acetylglucosaminidase, a Bacillus subtilis 168 cell wall hydrolase not involved in vegetative cell autolysis
Margot, P., Mauël, C., & Karamata, D. (1994) · Molecular Microbiology · doi:10.1111/j.1365-2958.1994.tb01040.x · Cited by 81
Exploring the Precursor Ion Exclusion Feature of Liquid Chromatography−Electrospray Ionization Quadrupole Time-of-Flight Mass Spectrometry for Improving Protein Identification in Shotgun Proteome Analysis
Wang, N., & Li, L. (2008) · Analytical Chemistry · doi:10.1021/ac800260w · Cited by 81
Quantitative Proteomics of the Archaeon Methanococcus maripaludis Validated by Microarray Analysis and Real Time PCR
Xia, Q., Hendrickson, E. L., Zhang, Y., Wang, T., Taub, F., Moore, B. C., Porat, I., Whitman, W. B., Hackett, M., & Leigh, J. A. (2006) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500369-mcp200 · Cited by 81
Codon pairs in the genome of Escherichia coli
Boycheva, S., Chkodrov, G., & Ivanov, I. G. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg082 · Cited by 81
Characterization of Coding Synonymous and Non-Synonymous Variants in ADAMTS13 Using Ex Vivo and In Silico Approaches
Edwards, N. C., Hing, Z. A., Perry, A., Blaisdell, A., Kopelman, D., Fathke, R. L., Plum, W. G., Newell, J. M., Allen, C. E., Geetha, S., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0038864 · Cited by 87
Exploiting the reverse vaccinology approach to design novel subunit vaccines against Ebola virus
Ullah, M. A., Sarkar, B., & Islam, S. S. (2020) · Immunobiology · doi:10.1016/j.imbio.2020.151949 · Cited by 80
Codon choice directs constitutive mRNA levels in trypanosomes
Nascimento, J. D. F., Kelly, S. L., Sunter, J. D., & Carrington, M. (2018) · eLife · doi:10.7554/elife.32467 · Cited by 77
Codon usage in Aspergillus nidulans
Lloyd, A. T., & Sharp, P. M. (1991) · Molecular and General Genetics MGG · doi:10.1007/bf00290679 · Cited by 80
Self-citation
Nuclear mRNA accumulation causes nucleolar fragmentation in yeast mtr2 mutant.
Kadowaki, T., Hitomi, M., Chen, S., & Tartakoff, A. M. (1994) · Molecular Biology of the Cell · doi:10.1091/mbc.5.11.1253 · Cited by 80
Young proteins experience more variable selection pressures than old proteinsPreprint
Vishnoi, A., Kryazhimskiy, S., Bazykin, G. A., Hannenhalli, S. S., & Plotkin, J. B. (2010) · Genome Research · doi:10.1101/gr.109595.110 · Cited by 76
Python Implementation of Codon Adaptation Index
Lee, B. D. (2018) · The Journal of Open Source Software · doi:10.21105/joss.00905 · Cited by 79
Complete Chloroplast Genome Sequences of Kaempferia Galanga and Kaempferia Elegans: Molecular Structures and Comparative Analysis
Li, D., Zhao, C., & Liu, X. (2019) · Molecules · doi:10.3390/molecules24030474 · Cited by 79
Codon usage bias and environmental adaptation in microbial organisms
Arella, D., Dilucca, M., & Giansanti, A. (2021) · Molecular Genetics and Genomics · doi:10.1007/s00438-021-01771-4 · Cited by 81
Ribosome dynamics and mRNA turnover, a complex relationship under constant cellular scrutiny
Morris, C., Cluet, D., & Ricci, E. P. (2021) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1658 · Cited by 82
Codon language embeddings provide strong signals for use in protein engineering
Outeiral, C., & Deane, C. M. (2024) · Nature Machine Intelligence · doi:10.1038/s42256-024-00791-0 · Cited by 90
Deep generative models design mRNA sequences with enhanced translational capacity and stability
Zhang, H., Liu, H., Xu, Y., Huang, H., Liu, Y., Wang, J., Qin, Y., Wang, H., Ma, L., Xun, Z., et al. (2025) · Science · doi:10.1126/science.adr8470 · Cited by 98
A detailed comparative analysis on the overall codon usage patterns in West Nile virus
Moratorio, G., Iriarte, A., Moreno, P., Musto, H., & Cristina, J. (2013) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2013.01.001 · Cited by 79
The impact of intragenic CpG content on gene expression
Bauer, A. P., Leikam, D., Krinner, S., Notka, F., Ludwig, C., Längst, G., & Wagner, R. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq115 · Cited by 82
The role of tRNA and ribosome competition in coupling the expression of different mRNAs in Saccharomyces cerevisiae
Chu, D., Barnes, D. J., & von der Haar, T. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr300 · Cited by 79
Trash DNA is what gets thrown away: high rate of DNA loss in Drosophila
Petrov, D. A., & Hartl, D. L. (1997) · Gene · doi:10.1016/s0378-1119(97)00516-7 · Cited by 79
Cloning of the Schizosaccharomyces pombe gene encoding diadenosine 5′,5′′′-P1,P4-tetraphosphate (Ap4A) asymmetrical hydrolase: sequence similarity with the histidine triad (HIT) protein family
Huang, Y., Garrison, P. N., & Barnes, L. D. (1995) · Biochemical Journal · doi:10.1042/bj3120925 · Cited by 79
Codon usage is associated with the evolutionary age of genes in metazoan genomes
Prat, Y., Fromer, M., Linial, N., & Michal Linial, B. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-285 · Cited by 78
De novo design of modular peptide-binding proteins by superhelical matching
Wu, K., Bai, H., Chang, Y., Redler, R. L., McNally, K. E., Sheffler, W., Brunette, T., Hicks, D. R., Morgan, T. E., Stevens, T. J., et al. (2023) · Nature · doi:10.1038/s41586-023-05909-9 · Cited by 74
mRNA vaccine sequence and structure design and optimization: Advances and challenges
Jin, L., Zhou, Y., Zhang, S., & Chen, S. (2024) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2024.108015 · Cited by 89
Production of anti‐cancer immunotoxins in algae: Ribosome inactivating proteins as fusion partners
Tran, M., Henry, R. E., Siefker, D. T., Van, C., Newkirk, G. M., Kim, J. J., Bui, J. D., & Mayfield, S. P. (2013) · Biotechnology and Bioengineering · doi:10.1002/bit.24966 · Cited by 79
Think big – giant genes in bacteria
Reva, O. N., & Tümmler, B. (2008) · Environmental Microbiology · doi:10.1111/j.1462-2920.2007.01500.x · Cited by 78
Response of Porphyromonas gingivalis to Heme Limitation in Continuous Culture
Dashper, S., Ang, C., Veith, P., Mitchell, H., Lo, A. W., Seers, C., Walsh, K., Slakeski, N., Chen, D.-N., Lissel, J. P., et al. (2008) · Journal of Bacteriology · doi:10.1128/jb.01270-08 · Cited by 80
Gene Synthesis
Hughes, R. A., Miklos, A. E., & Ellington, A. D. (2011) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-385120-8.00012-7 · Cited by 81
Synonymous substitution rates in enterobacteria.
Eyre‐Walker, A., & Bulmer, M. G. (1995) · Genetics · doi:10.1093/genetics/140.4.1407 · Cited by 78
The cold sensitivity of a mutant of Saccharomyces cerevisiae lacking a mitochondrial heat shock protein 70 is suppressed by loss of mitochondrial DNA.
Schilke, B. A., Forster, J., Davis, J., James, P., Walter, W. A., Laloraya, S., Johnson, J. L., Miao, B., & Craig, E. A. (1996) · The Journal of Cell Biology · doi:10.1083/jcb.134.3.603 · Cited by 78
Spread of the pandemic Zika virus lineage is associated with NS1 codon usage adaptation in humansPreprint
Freire, C. C. D. M., Iamarino, A., Neto, D. F. D. L., Sall, A. A., & Zanotto, P. M. D. A. (2015) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/032839 · Cited by 78
Rare codons capacitate Kras-driven de novo tumorigenesis
Pershing, N. L. K., Lampson, B. L., Belsky, J. A., Kaltenbrun, E., MacAlpine, D. M., & Counter, C. M. (2015) · Journal of Clinical Investigation · doi:10.1172/jci77627 · Cited by 77
A rare codon-based translational program of cell proliferation
Guimaraes, J. C., Mittal, N., Gnann, A., Jedlinski, D., Riba, A., Buczak, K., Schmidt, A., & Zavolan, M. (2020) · Genome biology · doi:10.1186/s13059-020-1943-5 · Cited by 73
The influence of translational selection on codon usage in fishes from the family Cyprinidae
Romero, H., Zavala, A., Musto, H., & Bernardi, G. (2003) · Gene · doi:10.1016/s0378-1119(03)00701-7 · Cited by 77
Codon usage suggests that translational selection has a major impact on protein expression in trypanosomatids
Horn, D. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-2 · Cited by 76
Integrative Analyses of Posttranscriptional Regulation in the Yeast Saccharomyces cerevisiae Using Transcriptomic and Proteomic Data
Wu, G., Nie, L., & Zhang, W. (2008) · Current Microbiology · doi:10.1007/s00284-008-9145-5 · Cited by 77
Evolutionary Consequences of DNA Methylation in a Basal Metazoan
Dixon, G., Bay, L. K., & Matz, M. V. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw100 · Cited by 74

Authors: Sharp, P. M., & Li, W.-H.
Affiliations: The University of Texas System (US)
Corresponding author: Sharp, Paul M.
ORCID: Sharp, Paul M.
Li, Wen-Hsiung
Venue: Nucleic Acids Research
Publisher: Oxford University Press (OUP)
Published: 1987
Volume: 15
Issue: 3
Pages: 1281-1295
ISSN: 0305-1048 (ISSN-L)
1362-4962
DOI: 10.1093/nar/15.3.1281
PMC: PMC340524
OpenAlex: W2018590530
Cited by: 3,992
References: 30
Citations by year: 2026: 223 · 2025: 203 · 2024: 205 · 2023: 177 · 2022: 198 · 2021: 239 · 2020: 212 · 2019: 147 · 2018: 155 · 2017: 120 · 2016: 133 · 2015: 112 · 2014: 147 · 2013: 145 · 2012: 137
FWCI: 7.58
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Locations: Nucleic Acids Research (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, other-oa)
Funders: National Institutes of Health
National Institute of General Medical Sciences (GM30998)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
Keywords: codon adaptation index, codon usage bias, codon usage, gene expression prediction, heterologous expression, highly expressed genes, natural selection
MeSH terms: Animals, Base Sequence, Cattle, Codon, Escherichia coli, Biological Evolution, Genes, Genes, Bacterial, Genes, Fungal, Humans, Mathematics, Models, Genetic, RNA, Messenger, Saccharomyces cerevisiae

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks