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The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications
Open accessAbstract
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.
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“The codon optimization applied to BNT-162b2 and mRNA-1273 leads to a much increased codon adaptation index (CAI) [21,22] and index of translation efficiency (ITE) [11,36] for the two vaccine mRNAs.”
From Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines (2021) · cites this paper as [21]
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In the citing paper
“Usually, the frequencies of the peptides displayed on phages are not even in the library. There were some reasons for the heterogenous phage amount, such as biases in library construction, variance in the use of cryptography,45,46 the different growth rates of phages and peptide degradation by protease.47”
From Identification of heptapeptides targeting a lethal bacterial strain in septic mice through an integrative approach (2022) · cites this paper as [45]
Experimental — accuracy not yet measuredIn the citing paper
“Codon preference varies extensively in different organisms,249 therefore adjusting the balance between codon usage frequency and host tRNA availability can significantly improve translation efficiency and in vivo expression of the target antigen.250,251”
From Advances in COVID-19 mRNA vaccine development (2022) · cites this paper as [249]
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Citations
Cites
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
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-citationCodon 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
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
Ikemura, T. (1982) · Journal of Molecular Biology · doi:10.1016/0022-2836(82)90250-9 · Cited by 605
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.
Cited by
Sorted by citations
Items 301–400 of 1,006
The ‘effective number of codons’ revisited
Fuglsang, A. (2004) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2004.03.138 · Cited by 138
Dynamic evolution of translation initiation mechanisms in prokaryotes
Nakagawa, S., Niimura, Y., Miura, K., & Gojobori, T. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1002036107 · Cited by 143
Impact of Nonsense-Mediated mRNA Decay on the Global Expression Profile of Budding Yeast
Guan, Q., Zheng, W., Tang, S., Liu, X., Zinkel, R. A., Tsui, K., Yandell, B. S., & Culbertson, M. R. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020203 · Cited by 138
Serero, A., Giglione, C., Sardini, A., Martinez‐Sanz, J., & Meinnel, T. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m309770200 · Cited by 138
Evolution of Viral Proteins Originated De Novo by Overprinting
Sabath, N., Wagner, A., & Karlin, D. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss179 · Cited by 148
Distribution, Expression, and Motif Variability of Ankyrin Domain Genes in Wolbachia pipientis
Iturbe‐Ormaetxe, I., Burke, G. R., Riegler, M., & O’Neill, S. L. (2005) · Journal of Bacteriology · doi:10.1128/jb.187.15.5136-5145.2005 · Cited by 137
Bloom, J. D., & Adami, C. (2003) · BMC Evolutionary Biology · doi:10.1186/1471-2148-3-21 · Cited by 134
Artieri, C. G., & Fraser, H. B. (2014) · Genome Research · doi:10.1101/gr.175893.114 · Cited by 136
DNA damage-induced cell death relies on SLFN11-dependent cleavage of distinct type II tRNAs
Li, M., Kao, E., Malone, D., Gao, X., Wang, J. Y. J., & David, M. (2018) · Nature Structural & Molecular Biology · doi:10.1038/s41594-018-0142-5 · Cited by 136
The distribution of fitness effects among synonymous mutations in a gene under directional selection
Lebeuf‐Taylor, E., McCloskey, N., Bailey, S. F., Hinz, A. J., & Kassen, R. (2019) · eLife · doi:10.7554/elife.45952 · Cited by 135
Lateral gene transfer in Salmonella
Porwollik, S., & McClelland, M. (2003) · Microbes and Infection · doi:10.1016/s1286-4579(03)00186-2 · Cited by 135
Species independence of mutual information in coding and noncoding DNA
Große, I., Herzel, H., Buldyrev, S. V., & Stanley, E. (2000) · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics · doi:10.1103/physreve.61.5624 · Cited by 135
Echols, N. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.11.2515 · Cited by 135
Man, O., & Pilpel, Y. (2007) · Nature Genetics · doi:10.1038/ng1967 · Cited by 134
Horizontal gene transfer and bacterial diversity
Dutta, C., & Pan, A. (2002) · Journal of Biosciences · doi:10.1007/bf02703681 · Cited by 134
Synonymous Codon Usage inLactococcus lactis: Mutational Bias Versus Translational Selection
GUPTA, S. K., Bhattacharyya, T., & Ghosh, T. C. (2004) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2004.10506946 · Cited by 133
Modelling the Efficiency of Codon–tRNA Interactions Based on Codon Usage Bias
Sabi, R., & Tuller, T. (2014) · DNA Research · doi:10.1093/dnares/dsu017 · Cited by 135
Uchijima, M., Yoshida, A., Nagata, T., & Koide, Y. (1998) · The Journal of Immunology · doi:10.4049/jimmunol.161.10.5594 · Cited by 132
McGrath, C., Goût, J.-F., Johri, P., Doak, T. G., & Lynch, M. (2014) · Genome Research · doi:10.1101/gr.173740.114 · Cited by 138
Pharming and transgenic plants
Liénard, D., Sourrouille, C., Gomord, V., & Faye, L. J.-Y. (2007) · Biotechnology annual review · doi:10.1016/s1387-2656(07)13006-4 · Cited by 132
Alga-Produced Cholera Toxin-Pfs25 Fusion Proteins as Oral Vaccines
Gregory, J. A., Topol, A. B., Doerner, D. Z., & Mayfield, S. P. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.00714-13 · Cited by 132
Analysis of codon usage pattern in Taenia saginata based on a transcriptome dataset
Yang, X., Luo, X., & Cai, X. (2014) · Parasites & Vectors · doi:10.1186/preaccept-2085838153126611 · Cited by 132
Identification of Ligularia Herbs Using the Complete Chloroplast Genome as a Super-Barcode
Chen, X., Zhou, J., Cui, Y., Wang, Y., Duan, B., & Yao, H. (2018) · Frontiers in Pharmacology · doi:10.3389/fphar.2018.00695 · Cited by 132
Unraveling the hidden universe of small proteins in bacterial genomes
Miravet‐Verde, S., Ferrar, T. S., Espadas, G., Mazzolini, R., Gharrab, A., Sabidó, E., Serrano, L. G., & Lluch‐Senar, M. (2019) · Molecular Systems Biology · doi:10.15252/msb.20188290 · Cited by 129
CodonO: codon usage bias analysis within and across genomes
Angellotti, M. C., Bhuiyan, S., Chen, G., & Wan, X. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm392 · Cited by 132
Molecular and evolutionary relationships among enteric bacteria
Lawrence, J. G., Ochman, H., & Hartl, D. L. (1991) · Journal of General Microbiology · doi:10.1099/00221287-137-8-1911 · Cited by 135
Connections Underlying Translation and mRNA Stability
Radhakrishnan, A., & Green, R. (2016) · Journal of Molecular Biology · doi:10.1016/j.jmb.2016.05.025 · Cited by 132
Local Absence of Secondary Structure Permits Translation of mRNAs that Lack Ribosome-Binding Sites
Scharff, L. B., Childs, L. H., Walther, D., & Bock, R. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002155 · Cited by 137
Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles
Botzman, M., & Margalit, H. (2011) · Genome biology · doi:10.1186/gb-2011-12-10-r109 · Cited by 128
Deng, J., Deng, L., Su, S., Zhang, M., Lin, X. S., Lan, W., Minai, A. A., Hassett, D. J., & Lu, L. J. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq784 · Cited by 129
HIV-1 modulates the tRNA pool to improve translation efficiency
van Weringh, A., Ragonnet-Cronin, M., Pranckeviciene, E., Pavon-Eternod, M., Kleiman, L., & Xia, X. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr005 · Cited by 130
Dekker, P., Keil, P., Rassow, J., Maarse, A. C., Pfanner, N., & Meijer, M. (1993) · FEBS Letters · doi:10.1016/0014-5793(93)80921-g · Cited by 130
Association between translation efficiency and horizontal gene transfer within microbial communities
Tuller, T., Girshovich, Y., Sella, Y., Kreimer, A., Freilich, S., Kupiec, M., Gophna, U., & Ruppin, E. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr054 · Cited by 130
Hönlinger, A., Kübrich, M., Moczko, M., Gärtner, F., Mallet, L., Bussereau, F., Eckerskorn, C., Lottspeich, F., Dietmeier, K., Jacquet, M., et al. (1995) · Molecular and Cellular Biology · doi:10.1128/mcb.15.6.3382 · Cited by 129
Evolutionary rate covariation reveals shared functionality and coexpression of genesPreprint
Clark, N. L., Alani, E., & Aquadro, C. F. (2012) · Genome Research · doi:10.1101/gr.132647.111 · Cited by 121
Optimization of Protein Expression in Mammalian Cells
Hunter, M., Yuan, P., Vavilala, D. T., & Fox, M. (2018) · Current Protocols in Protein Science · doi:10.1002/cpps.77 · Cited by 138
Adams, M. D., Wagner, L. M., Graddis, T. J., Landick, R. C., Antonucci, T. K., Gibson, A. L., & Oxender, D. L. (1990) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)38417-0 · Cited by 128
Gangloff, S., Marguet, D., & Lauquin, G. J. ‐. (1990) · Molecular and Cellular Biology · doi:10.1128/mcb.10.7.3551 · Cited by 128
Genomic organization and expression of Campylobacter flagellin genes
Guerry, P., Logan, S. M., Thornton, S. A., & Trevor J. TRUST (1990) · Journal of Bacteriology · doi:10.1128/jb.172.4.1853-1860.1990 · Cited by 128
Sonntag, F., Kroner, C., Lubuta, P., Peyraud, R., Horst, A., Buchhaupt, M., & Schrader, J. (2015) · Metabolic Engineering · doi:10.1016/j.ymben.2015.09.004 · Cited by 124
Real, F., Vidal, R. O., Carazzolle, M. F., Mondego, J. M. C., Costa, G. G. L., Herai, R. H., Wurtele, M., de Carvalho, L. M., Ferreira, R. C., Mortara, R. A., et al. (2013) · DNA Research · doi:10.1093/dnares/dst031 · Cited by 123
Gorochowski, T. E., Ignatova, Z., Bovenberg, R. A. L., & Roubos, J. A. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv199 · Cited by 123
Lloyd, A. T., & Sharp, P. M. (1992) · Nucleic Acids Research · doi:10.1093/nar/20.20.5289 · Cited by 124
Self-citationEvolution of the Caenorhabditis elegans Genome
Cutter, A. D., Dey, A., & Murray, R. L. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp048 · Cited by 122
Jones, C. J., Homma, M., & Macnab, R. M. (1989) · Journal of Bacteriology · doi:10.1128/jb.171.7.3890-3900.1989 · Cited by 125
Genome Sequence of a Nephritogenic and Highly Transformable M49 Strain ofStreptococcus pyogenes
McShan, W. M., Ferretti, J. J., Karasawa, T., Suvorov, A. N., Lin, S., Qin, B., Jia, H., Kenton, S., Najar, F. Z., Wu, H., et al. (2008) · Journal of Bacteriology · doi:10.1128/jb.00672-08 · Cited by 124
Zhang, C. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.14.2804 · Cited by 124
Ciandrini, L., Stansfield, I., & Romano, M. C. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002866 · Cited by 121
Jans, C., Meile, L., Lacroix, C., & Stevens, M. J. A. (2014) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2014.09.017 · Cited by 126
Mawuenyega, K. G., Kaji, H., Yamauchi, Y., Shinkawa, T., Saito, H., Taoka, M., Takahashi, N., & Isobe, T. (2002) · Journal of Proteome Research · doi:10.1021/pr025551y · Cited by 123
Grant, C. M., & Hinnebusch, A. G. (1994) · Molecular and Cellular Biology · doi:10.1128/mcb.14.1.606-618.1994 · Cited by 123
The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeastPreprint
Musso, G. A., Costanzo, M., Huangfu, M., Smith, A. M., Paw, J., Luis, B.-J. S., Boone, C. M., Giaever, G. N., Nislow, C., Emili, A., et al. (2008) · Genome Research · doi:10.1101/gr.076174.108 · Cited by 122
Adaptive Molecular Evolution for 13,000 Phage Generations
Wichman, H. A., Millstein, J., & Bull, J. J. (2005) · Genetics · doi:10.1534/genetics.104.034488 · Cited by 122
Flórez, L. V., Scherlach, K., Miller, I. J., Rodrigues, A. L., Kwan, J. C., Hertweck, C., & Kaltenpoth, M. (2018) · Nature Communications · doi:10.1038/s41467-018-04955-6 · Cited by 126
Disome-seq reveals widespread ribosome collisions that promote cotranslational protein folding
Zhao, T., Chen, Y., Li, Y., Wang, J., Chen, S., Gao, N., & Qian, W. (2021) · Genome biology · doi:10.1186/s13059-020-02256-0 · Cited by 125
Localization and characterization of the gene encoding release factor RF3 in Escherichia coli.
Grentzmann, G., Bréchemier‐Baey, D., Heurgué‐Hamard, V., Mora, L., & Buckingham, R. H. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.13.5848 · Cited by 122
Nasrullah, I., Butt, A. M., Tahir, S., Idrees, M., & Tong, Y. (2015) · BMC Evolutionary Biology · doi:10.1186/s12862-015-0456-4 · Cited by 121
Differences in codon bias and GC content contribute to the balanced expression of TLR7 and TLR9
Newman, Z. R., Young, J. M., Ingolia, N. T., & Barton, G. M. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1518976113 · Cited by 118
Comparative analysis of codon usage patterns in chloroplast genomes of six Euphorbiaceae species
Wang, Z., Xu, B., Li, B., Zhou, Q., Wang, G., Jiang, X., Wang, C., & Xu, Z. (2020) · PeerJ · doi:10.7717/peerj.8251 · Cited by 121
Crouzet, M., Urdaci, M. C., Dulau, L., & Aigle, M. (1991) · Yeast · doi:10.1002/yea.320070708 · Cited by 121
You're one in a googol: optimizing genes for protein expression
Welch, M., Villalobos, A., Gustafsson, C., & Minshull, J. (2009) · Journal of The Royal Society Interface · doi:10.1098/rsif.2008.0520.focus · Cited by 120
Gomes, A. C., Miranda, I. M., Silva, R. M., Moura, G. R., Thomas, B., Akoulitchev, A. V., & Santos, M. A. S. (2007) · Genome biology · doi:10.1186/gb-2007-8-10-r206 · Cited by 126
Structure of the tetragonal surface virulence array protein and gene of Aeromonas salmonicida
Chu, S., Cavaignac, S. M., Feutrier, J., Phipps, B. M., Kostrzyńska, M., Kay, W. W., & Trevor J. TRUST (1991) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)98611-4 · Cited by 120
The signal for the termination of protein synthesis in procaryotes
Brown, C. M., Stockwell, P. A., Trotman, C. N. A., & Tate, W. P. (1990) · Nucleic Acids Research · doi:10.1093/nar/18.8.2079 · Cited by 120
Relative Amino Acid Composition Signatures of Organisms and Environments
Moura, A., Savageau, M. A., & Alves, R. (2013) · PLoS ONE · doi:10.1371/journal.pone.0077319 · Cited by 119
A selective force favoring increased G+C content in bacterial genes
Raghavan, R., Kelkar, Y., & Ochman, H. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1205683109 · Cited by 123
Global translational impacts of the loss of the tRNA modification t6A in yeast
Thiaville, P. C., Legendre, R., Rojas‐Benítez, D., Baudin‐Baillieu, A., Hatin, I., Chalancon, G., Glavic, Á., Namy, O., & de Crécy‐Lagard, V. (2015) · Microbial Cell · doi:10.15698/mic2016.01.473 · Cited by 121
Lu, M., & Kleckner, N. E. (1994) · Journal of Bacteriology · doi:10.1128/jb.176.18.5847-5851.1994 · Cited by 119
Proteomic analysis of Lactococcus lactis, a lactic acid bacterium
Guillot, A., Gitton, C., Anglade, P., & Mistou, M. (2003) · PROTEOMICS · doi:10.1002/pmic.200390047 · Cited by 122
Temporal Fragmentation of Speciation in Bacteria
Retchless, A. C., & Lawrence, J. G. (2007) · Science · doi:10.1126/science.1144876 · Cited by 119
Wu, G., Culley, D. E., & Zhang, W. (2005) · Microbiology · doi:10.1099/mic.0.27833-0 · Cited by 119
Gao, X. (2003) · Nucleic Acids Research · doi:10.1093/nar/gng143 · Cited by 118
Translation initiation region sequence preferences in Escherichia coli
Vimberg, V., Brauer, A., Remm, M., & Tenson, T. (2007) · BMC Molecular Biology · doi:10.1186/1471-2199-8-100 · Cited by 118
Nain, Z., Abdulla, F., Rahman, M., Karim, M. M., Khan, M. S. A., Sayed, S. B., Mahmud, S., Rahman, S. M. R., Sheam, M. M., Haque, Z., et al. (2019) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2019.1692072 · Cited by 117
Narum, D. L., Kumar, S., Rogers, W. O., Fuhrmann, S. R., Liang, H., Oakley, M. S., Taye, A., Sim, B. K. L., & Hoffman, S. L. (2001) · Infection and Immunity · doi:10.1128/iai.69.12.7250-7253.2001 · Cited by 117
Souza, C. M., Schwabe, T. M. E., Pichler, H., Ploier, B., Leitner, E., Guan, X. L., Wenk, M. R., Riezman, I., & Riezman, H. (2011) · Metabolic Engineering · doi:10.1016/j.ymben.2011.06.006 · Cited by 117
An integrated approach for finding overlooked genes in yeast
Kumar, A., Harrison, P. M., Cheung, K.-H., Lan, N., Echols, N., Bertone, P., Miller, P. L., Gerstein, M., & Snyder, M. P. (2002) · Nature Biotechnology · doi:10.1038/nbt0102-58 · Cited by 117
Widespread position-specific conservation of synonymous rare codons within coding sequences
Chaney, J. L., Steele, A., Carmichael, R., Rodríguez, A., Specht, A. T., Ngo, K., Li, J., Emrich, S., & Clark, P. L. (2017) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005531 · Cited by 120
Nguyen, A. D., Hwang, I. Y., Lee, O. K., Kim, D., Kalyuzhnaya, M., Mariyana, R., Hadiyati, S., Kim, M., & Lee, E. Y. (2018) · Metabolic Engineering · doi:10.1016/j.ymben.2018.04.010 · Cited by 116
Decoding with the A:I wobble pair is inefficient
Curran, J. F. (1995) · Nucleic Acids Research · doi:10.1093/nar/23.4.683 · Cited by 116
Dana, A., & Tuller, T. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002755 · Cited by 112
Chen, F., Wu, P., Deng, S., Zhang, H., Hou, Y., Hu, Z., Zhang, J., Chen, X., & Yang, J. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-020-1124-7 · Cited by 112
Translation and mRNA Stability Control
Wu, Q., & Bazzini, A. (2023) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-052621-091808 · Cited by 120
Chromosomal Location and Evolutionary Rate Variation in Enterobacterial Genes
Sharp, P. M., Shields, D. C., Wolfe, K. H., & Li, W. (1989) · Science · doi:10.1126/science.2683084 · Cited by 115
Self-citationZuo, L., Shang, A.-Q., Zhang, S., Yu, X.-Y., Ren, Y.-C., Yang, M., & Wang, J. (2017) · PLoS ONE · doi:10.1371/journal.pone.0171264 · Cited by 114
Lanza, A. M., Curran, K. A., Rey, L. G., & Alper, H. S. (2014) · BMC Systems Biology · doi:10.1186/1752-0509-8-33 · Cited by 114
Camirand, A., Heysen, A., Grondin, B., & Herscovics, A. A. (1991) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)98594-7 · Cited by 114
Sharp, P. M., & Lloyd, A. T. (1993) · Nucleic Acids Research · doi:10.1093/nar/21.2.179 · Cited by 114
Self-citationPredicting essential genes in fungal genomesPreprint
Seringhaus, M. R., Paccanaro, A., Borneman, A. R., Snyder, M. P., & Gerstein, M. (2006) · Genome Research · doi:10.1101/gr.5144106 · Cited by 114
Carretero‐Paulet, L., & Fares, M. A. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss162 · Cited by 111
An Improved Implementation of Effective Number of Codons (Nc)
Sun, X., Yang, Q., & Xia, X. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss201 · Cited by 110
He, B., Dong, H., Jiang, C., Cao, F., Tao, S., & Xu, L. (2016) · Scientific Reports · doi:10.1038/srep35927 · Cited by 113
Wiedemann, B., & Boles, E. (2008) · Applied and Environmental Microbiology · doi:10.1128/aem.02395-07 · Cited by 113
The complete coenzyme B12 biosynthesis gene cluster of Lactobacillus reuteri CRL1098
dos Santos, F. B., Vera, J. L., van der Heijden, R. T. J. M., de Valdez, G. F., de Vos, W. M., Sesma, F. J. M., & Hugenholtz, J. (2008) · Microbiology · doi:10.1099/mic.0.2007/011569-0 · Cited by 113
Correlations in DNA sequences: The role of protein coding segments
Herzel, H., & Große, I. (1997) · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics · doi:10.1103/physreve.55.800 · Cited by 113
Preferred and avoided codon pairs in three domains of life
Tats, A., Tenson, T., & Remm, M. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-463 · Cited by 112
“RSCU values are the number of times a particular codon is observed, relative to the number of times that the codon would be observed in the absence of any codon usage bias [37].”
BackgroundEstimating Translational Selection in Eukaryotic Genomes
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Metadata
- Authors
- Sharp, P. M., & Li, W.-H.
- Affiliations
- The University of Texas System (US)
- Corresponding author
- Sharp, Paul M.
- 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
- 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
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