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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
Flagged first, then by citations
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 101–200 of 1,006
mRNA vaccines for COVID-19: what, why and how
Park, J. W., Lagniton, P. N. P., Liu, Y., & Xu, R.-H. (2021) · International Journal of Biological Sciences · doi:10.7150/ijbs.59233 · Cited by 321
Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency
Qian, W., Yang, J.-R., Pearson, N. M., Maclean, C. J., & Zhang, J. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002603 · Cited by 308
Lobry, J. R., & Gautier, C. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.15.3174 · Cited by 310
Defensive Bacteriome Symbiont with a Drastically Reduced Genome
Nakabachi, A., Ueoka, R., Oshima, K., Teta, R., Mangoni, A., Gurgui, M., Oldham, N. J., van Echten‐Deckert, G., Okamura, K., Yamamoto, K., et al. (2013) · Current Biology · doi:10.1016/j.cub.2013.06.027 · Cited by 304
Efficient translation initiation dictates codon usage at gene start
Bentele, K., Saffert, P., Rauscher, R., Ignatova, Z., & Blüthgen, N. (2013) · Molecular Systems Biology · doi:10.1038/msb.2013.32 · Cited by 306
Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus
Andersen, K. G., Shapiro, B. J., Matranga, C. B., Sealfon, R. S. G., Lin, A. E., Moses, L., Folarin, O. A., Goba, A., Odia, I., Ehiane, P. E., et al. (2015) · Cell · doi:10.1016/j.cell.2015.07.020 · Cited by 302
Bazzini, A., Viso, F. D., Moreno-Mateos, M. A., Johnstone, T. G., Vejnar, C. E., Qin, Y., Yao, J., Khokha, M. K., & Giráldez, A. J. (2016) · The EMBO Journal · doi:10.15252/embj.201694699 · Cited by 309
Morita, H., Toh, H., Fukuda, S., Horikawa, H., Oshima, K., Suzuki, T., Murakami, M., Hisamatsu, S., Kato, Y., Takizawa, T., et al. (2008) · DNA Research · doi:10.1093/dnares/dsn009 · Cited by 310
Seo, S. W., Yang, J.-S., Kim, I., Yang, J., Min, B. E., Kim, S., & Jung, G. Y. (2013) · Metabolic Engineering · doi:10.1016/j.ymben.2012.10.006 · Cited by 300
Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae
Percudani, R., Pavesi, A., & Ottonello, S. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.0942 · Cited by 302
Gerashchenko, M. V., Lobanov, A. V., & Gladyshev, V. N. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1120799109 · Cited by 302
Synonymous mutations in representative yeast genes are mostly strongly non-neutral
Shen, X., Song, S., Li, C., & Zhang, J. (2022) · Nature · doi:10.1038/s41586-022-04823-w · Cited by 298
Codon Usage and 3′ UTR Length Determine Maternal mRNA Stability in Zebrafish
Mishima, Y., & Tomari, Y. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.02.027 · Cited by 288
Shields, D. C., & Sharp, P. M. (1987) · Nucleic Acids Research · doi:10.1093/nar/15.19.8023 · Cited by 293
Self-citationLarge-Scale Phosphorylation Analysis of α-Factor-Arrested Saccharomyces cerevisiae
Li, X., Gerber, S. A., Rudner, A. D., Beausoleil, S. A., Haas, W., Villén, J., Elias, J. E., & Gygi, S. P. (2007) · Journal of Proteome Research · doi:10.1021/pr060559j · Cited by 294
The DEAD-Box Protein Dhh1p Couples mRNA Decay and Translation by Monitoring Codon Optimality
Radhakrishnan, A., Chen, Y.-H., Martin, S., Alhusaini, N., Green, R., & Coller, J. (2016) · Cell · doi:10.1016/j.cell.2016.08.053 · Cited by 297
Translational termination efficiency in mammals is influenced by the base following the stop codon
McCaughan, K. K., Brown, C. M., Dalphin, M. E., Berry, M. J., & Tate, W. P. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.12.5431 · Cited by 284
UBA 1: an essential yeast gene encoding ubiquitin‐activating enzyme.
McGrath, J. P., Jentsch, S., & Varshavsky, A. J. (1991) · The EMBO Journal · doi:10.1002/j.1460-2075.1991.tb07940.x · Cited by 288
Life at Depth: Photobacterium profundum Genome Sequence and Expression Analysis
Vezzi, A., Campanaro, S., D’Angelo, M., Simonato, F., Vitulo, N., Lauro, F. M., Cestaro, A., Malacrida, G., Simionati, B., Cannata, N., et al. (2005) · Science · doi:10.1126/science.1103341 · Cited by 282
A new and updated resource for codon usage tables
Athey, J. C., Alexaki, A., Osipova, E., Rostovtsev, A., Santana-Quintero, L. V., Katneni, U., Simonyan, V. V., & Kimchi‐Sarfaty, C. (2017) · BMC Bioinformatics · doi:10.1186/s12859-017-1793-7 · Cited by 281
Evolutionary and Physiological Importance of Hub Proteins
Batada, N. N., Hurst, L. D., & Tyers, M. (2005) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020088 · Cited by 284
Kanaya, S., Yamada, Y., Kinouchi, M., Kudo, Y., & Ikemura, T. (2001) · Journal of Molecular Evolution · doi:10.1007/s002390010219 · Cited by 279
The replication-related organization of bacterial genomes
Rocha, E. P. C. (2004) · Microbiology · doi:10.1099/mic.0.26974-0 · Cited by 279
Synonymous codon usage in Saccharomyces cerevisiae
Sharp, P. M., & Cowe, E. (1991) · Yeast · doi:10.1002/yea.320070702 · Cited by 278
Self-citationStrategies to Optimize Protein Expression in E. coli
Francis, D. M., & Page, R. (2010) · Current Protocols in Protein Science · doi:10.1002/0471140864.ps0524s61 · Cited by 276
Evaluation of the CaMAL2 promoter for regulated expression of genes in Candida albicans
Backen, A. C., Broadbent, I. D., Fetherston, R., Rosamond, J., Schnell, N. F., & Stark, M. J. R. (2000) · Yeast · doi:10.1002/1097-0061(20000915)16:12 · Cited by 64
Absolute in vivo translation rates of individual codons in Escherichia coli
Sørensen, M. A., & Pedersen, S. B. (1991) · Journal of Molecular Biology · doi:10.1016/0022-2836(91)90211-n · Cited by 270
Kofoid, E., Rappleye, C. A., Stojiljković, I., & Roth, J. R. (1999) · Journal of Bacteriology · doi:10.1128/jb.181.17.5317-5329.1999 · Cited by 267
Selection intensity for codon bias.
Hartl, D. L., Moriyama, E. N., & Sawyer, S. A. (1994) · Genetics · doi:10.1093/genetics/138.1.227 · Cited by 266
The Genome Sequence ofMycoplasma hyopneumoniaeStrain 232, the Agent of Swine Mycoplasmosis
Minion, F. C., Lefkowitz, E. J., Madsen, M. L., Cleary, B. J., Swartzell, S., & Mahairas, G. G. (2004) · Journal of Bacteriology · doi:10.1128/jb.186.21.7123-7133.2004 · Cited by 265
The effect of tRNA levels on decoding times of mRNA codons
Dana, A., & Tuller, T. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku646 · Cited by 258
Optimization and Use of Peptide Mass Measurement Accuracy in Shotgun Proteomics
Haas, W., Faherty, B. K., Gerber, S. A., Elias, J. E., Beausoleil, S. A., Bakalarski, C. E., Li, X., Villén, J., & Gygi, S. P. (2006) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500339-mcp200 · Cited by 262
General Rules for Optimal Codon Choice
Hershberg, R., & Petrov, D. A. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000556 · Cited by 244
ExploringLactobacillus plantarumGenome Diversity by Using Microarrays
Molenaar, D., Bringel, F., Schuren, F. H. J., de Vos, W. M., Siezen, R. J., & Kleerebezem, M. (2005) · Journal of Bacteriology · doi:10.1128/jb.187.17.6119-6127.2005 · Cited by 252
Codon usage of highly expressed genes affects proteome-wide translation efficiency
Frumkin, I., Lajoie, M. J., Gregg, C. J., Hornung, G., Church, G. M., & Pilpel, Y. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1719375115 · Cited by 247
Complete DNA sequence of yeast chromosome II.
Feldmann, H., Aigle, M., Aljinovic, G., André, B., Baclet, M. C., Barthe, C., Baur, A., Bécam, A. ‐., Biteau, N., & Boles, E. (1994) · The EMBO Journal · doi:10.1002/j.1460-2075.1994.tb06923.x · Cited by 251
Umezu, K., Chi, N. W., & Kolodner, R. D. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.9.3875 · Cited by 250
Coevolution of gene expression among interacting proteins
Fraser, H. B., Hirsh, A. E., Wall, D. P., & Eisen, M. B. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0402591101 · Cited by 244
Roadblocks and resolutions in eukaryotic translation
Schuller, A. P., & Green, R. (2018) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-018-0011-4 · Cited by 245
The hexose transporter family of Saccharomyces cerevisiae
Kruckeberg, A. L. (1996) · Archives of Microbiology · doi:10.1007/s002030050385 · Cited by 255
Codon usage: Nature's roadmap to expression and folding of proteins
Angov, E. (2011) · Biotechnology Journal · doi:10.1002/biot.201000332 · Cited by 255
Black, W. C., & Roehrdanz, R. L. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025903 · Cited by 247
The Complete Genome and Proteome of Mycoplasma mobilePreprint
Jaffe, J. D., Stange-Thomann, N., Smith, C., DeCaprio, D., Fisher, S., Butler, J., Calvo, S. E., Elkins, T., FitzGerald, M. G., Hafez, N., et al. (2004) · Genome Research · doi:10.1101/gr.2674004 · Cited by 245
dos Reis, M. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg897 · Cited by 245
Nogueira, T., Rankin, D. J., Touchon, M., Taddéi, F., Brown, S. P., & Rocha, E. P. C. (2009) · Current Biology · doi:10.1016/j.cub.2009.08.056 · Cited by 242
Baker, R. T., Tobias, J. W., & Varshavsky, A. J. (1992) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)50100-9 · Cited by 245
Tian, C. F., Zhou, Y., Zhang, Y., Li, Q. Q., Zhang, Y., Li, D. F., Wang, S., Wang, J., Gilbert, L. B., Li, Y. R., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1120436109 · Cited by 246
Mohammad, F., Green, R., & Buskirk, A. R. (2019) · eLife · doi:10.7554/elife.42591 · Cited by 242
Strand compositional asymmetry in bacterial and large viral genomes
Mrázek, J., & Karlin, S. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.7.3720 · Cited by 239
Diversity of tRNA genes in eukaryotes
Goodenbour, J. M., & Pan, T. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl725 · Cited by 240
Ivanov, E. L., Sugawara, N., White, C. I., Fabre, F., & Haber, J. E. (1994) · Molecular and Cellular Biology · doi:10.1128/mcb.14.5.3414-3425.1994 · Cited by 243
Small Open Reading Frames: Beautiful Needles in the HaystackPreprint
Basrai, M. A., Hieter, P., & Boeke, J. D. (1997) · Genome Research · doi:10.1101/gr.7.8.768 · Cited by 240
Selective Charging of tRNA Isoacceptors Explains Patterns of Codon Usage
Elf, J., Nilsson, D., Tenson, T., & Ehrenberg, M. (2003) · Science · doi:10.1126/science.1083811 · Cited by 260
Ribosome‐mediated translational pause and protein domain organization
Thanaraj, T. A., & Argos, P. (1996) · Protein Science · doi:10.1002/pro.5560050814 · Cited by 239
Codon usage in twelve species of Drosophila
Vicario, S., Moriyama, E. N., & Powell, J. R. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-226 · Cited by 235
The impact of genomics on mammalian neurobiology
Hochgeschwender, U., & Brennan, M. B. (1999) · BioEssays · doi:10.1002/(sici)1521-1878(199902)21:2 · Cited by 6
Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates
Riba, A., Di Nanni, N., Mittal, N., Arhné, E., Schmidt, A., & Zavolan, M. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1817299116 · Cited by 209
Tissue-specific codon usage and the expression of human genes
Plotkin, J. B., Robins, H. S., & Levine, A. J. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0404957101 · Cited by 235
Cambray, G., Guimaraes, J. C., & Arkin, A. P. (2018) · Nature Biotechnology · doi:10.1038/nbt.4238 · Cited by 233
Codon optimization with deep learning to enhance protein expression
Fu, H., Liang, Y., Zhong, X., Pan, Z., Huang, L., Zhang, H., Xu, Y., Zhou, W., & Liu, Z. (2020) · Scientific Reports · doi:10.1038/s41598-020-74091-z · Cited by 232
Codon usages in different gene classes of the Escherichia coli genome
Karlin, S., Mrázek, J., & Campbell, A. (1998) · Molecular Microbiology · doi:10.1046/j.1365-2958.1998.01008.x · Cited by 232
Lazarevic, V., Margot, P., Soldo, B., & Karamata, D. (1992) · Journal of General Microbiology · doi:10.1099/00221287-138-9-1949 · Cited by 227
Synonymous Codons: Choose Wisely for Expression
Brule, C. E., & Grayhack, E. J. (2017) · Trends in Genetics · doi:10.1016/j.tig.2017.02.001 · Cited by 241
Kapur, V., Topouzis, S., Majesky, M. W., Li, L.-L., Hamrick, M. R., Hamill, R. J., Patti, J. M., & Musser, J. M. (1993) · Microbial Pathogenesis · doi:10.1006/mpat.1993.1083 · Cited by 226
Eyre‐Walker, A. (1996) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025646 · Cited by 224
Behura, S. K., & Severson, D. W. (2012) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/j.1469-185x.2012.00242.x · Cited by 227
Adjacent Codons Act in Concert to Modulate Translation Efficiency in Yeast
Gamble, C. E., Brule, C. E., Dean, K., Fields, S., & Grayhack, E. J. (2016) · Cell · doi:10.1016/j.cell.2016.05.070 · Cited by 229
A question of size: the eukaryotic proteome and the problems in defining it
Harrison, P. M. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.5.1083 · Cited by 224
Sharp, P. M. (1991) · Journal of Molecular Evolution · doi:10.1007/bf02100192 · Cited by 222
Self-citationWait, R., Gianazza, E., Eberini, I., Sironi, L., Dunn, M. J., Gemeiner, M., & Miller, I. (2001) · Electrophoresis · doi:10.1002/1522-2683(200108)22:14 · Cited by 91
Translational selection and molecular evolution
Akashi, H. D., & Eyre‐Walker, A. (1998) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(98)80038-5 · Cited by 220
Pérès, S. Y., Marchès, O., Daigle, F., Nougayrède, J., Herault, F., Tasca, C., de Rycke, J., & Oswald, É. (1997) · Molecular Microbiology · doi:10.1046/j.1365-2958.1997.4181785.x · Cited by 220
The interface of protein structure, protein biophysics, and molecular evolution
Liberles, D. A., Teichmann, S. A., Bahar, İ., Bastolla, U., Bloom, J. D., Bornberg‐Bauer, E., Colwell, L. J., de Koning, A. P. J., Dokholyan, N. V., Echave, J., et al. (2012) · Protein Science · doi:10.1002/pro.2071 · Cited by 224
Predicted Highly Expressed Genes of Diverse Prokaryotic Genomes
Karlin, S., & Mrázek, J. (2000) · Journal of Bacteriology · doi:10.1128/jb.182.18.5238-5250.2000 · Cited by 217
Delaveau, T., Delahodde, A., Carvajal, E., Šubík, J., & Jacq, C. (1994) · Molecular and General Genetics MGG · doi:10.1007/bf00583901 · Cited by 217
Muhua, L., Karpova, T., & Cooper, J. A. (1994) · Cell · doi:10.1016/0092-8674(94)90531-2 · Cited by 217
Leavis, H. L., Willems, R. J. L., van Wamel, W. J. B., Schuren, F. H. J., Caspers, M. P. M., & Bonten, M. J. M. (2007) · PLoS Pathogens · doi:10.1371/journal.ppat.0030007 · Cited by 220
Raab, D., Graf, M., Notka, F., Schödl, T., & Wagner, R. (2010) · Systems and Synthetic Biology · doi:10.1007/s11693-010-9062-3 · Cited by 209
Essentiality, not expressiveness, drives gene-strand bias in bacteria
Rocha, E. P. C., & Danchin, A. (2003) · Nature Genetics · doi:10.1038/ng1209 · Cited by 211
Couturier, E., & Rocha, E. (2006) · Molecular Microbiology · doi:10.1111/j.1365-2958.2006.05046.x · Cited by 220
Hey, J., & Kliman, R. M. (1993) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040044 · Cited by 209
Synthetic spider dragline silk proteins and their production in Escherichia coli
Fahnestock, S. R., & Irwin, S. (1997) · Applied Microbiology and Biotechnology · doi:10.1007/s002530050883 · Cited by 208
Genome-Wide Analysis of Codon Usage and Influencing Factors in Chikungunya Viruses
Butt, A. M., Nasrullah, I., & Tong, Y. (2014) · PLoS ONE · doi:10.1371/journal.pone.0090905 · Cited by 208
Organization and regulation of genes for amino acid biosynthesis in lactic acid bacteria
Chopin, A. (1993) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.1993.tb00011.x · Cited by 210
Boyd, E. F., & Hartl, D. L. (1998) · Journal of Bacteriology · doi:10.1128/jb.180.5.1159-1165.1998 · Cited by 206
An Essential Yeast Gene Encoding a Homolog of Ubiquitin-activating Enzyme
Dohmen, R. J., Stappen, R., McGrath, J. P., Forrová, H., Kolarov, J., Goffeau, A., & Varshavsky, A. J. (1995) · Journal of Biological Chemistry · doi:10.1074/jbc.270.30.18099 · Cited by 205
Dauga, C. (2002) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/00207713-52-2-531 · Cited by 204
Servos, J., Haase, E., & Brendel, M. (1993) · Molecular and General Genetics MGG · doi:10.1007/bf00277115 · Cited by 203
Widespread Selection for Local RNA Secondary Structure in Coding Regions of Bacterial GenesPreprint
Katz, L., & Burge, C. B. (2003) · Genome Research · doi:10.1101/gr.1257503 · Cited by 204
Sequence evolution in bacterial endosymbionts having extreme base compositions
Clark, M. A., Moran, N. A., & Baumann, P. (1999) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026071 · Cited by 202
Posttranscriptional expression regulation: what determines translation rates?
Brockmann, R., Beyer, A., Heinisch, J. J., & Wilhelm, T. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030057 · Cited by 201
Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines
Xia, X. (2021) · Vaccines · doi:10.3390/vaccines9070734 · Cited by 201
Selective and Mutational Patterns Associated With Gene Expression in Humans
Comeron, J. M. (2004) · Genetics · doi:10.1534/genetics.104.026351 · Cited by 197
Role of two flagellin genes in Campylobacter motility
Guerry, P., Alm, R. A., Power, M. E., Logan, S. M., & Trevor J. TRUST (1991) · Journal of Bacteriology · doi:10.1128/jb.173.15.4757-4764.1991 · Cited by 200
Clarke, T. F. E., & Clark, P. L. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003412 · Cited by 199
Theoretical basis for stabilizing messenger RNA through secondary structure design
Wayment-Steele, H. K., Kim, D. S., Choe, C. A., Nicol, J. J., Wellington-Oguri, R., Watkins, A. M., Parra Sperberg, R. A., Huang, P.-S., Participants, E., & Das, R. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab764 · Cited by 197
Vogler, A. P., Homma, M., Irikura, V. M., & Macnab, R. M. (1991) · Journal of Bacteriology · doi:10.1128/jb.173.11.3564-3572.1991 · Cited by 195
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Franzosa, E. A., & Xia, Y. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp146 · Cited by 206
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Nelson, D. R., Felix, C. M., & Swanson, J. M. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1594 · Cited by 194
Novel Proteins of the Phosphotransferase System Encoded within the rpoN Operon of Escherichia coli
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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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