Codon usage bias (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Codon usage bias" in English language version.

refsWebsite

Global rank English rank

46nih.gov

4^th place

30doi.org

2^nd place

6worldcat.org

5^th place

5semanticscholar.org

11^th place

8^th place

4harvard.edu

18^th place

17^th place

2handle.net

102^nd place

76^th place

1sourceforge.net

1,669^th place

1,290^th place

doi.org

Athey, John; Alexaki, Aikaterini; Osipova, Ekaterina; Rostovtsev, Alexandre; Santana-Quintero, Luis V.; Katneni, Upendra; Simonyan, Vahan; Kimchi-Sarfaty, Chava (2017-09-02). "A new and updated resource for codon usage tables". BMC Bioinformatics. 18 (391): 391. doi:10.1186/s12859-017-1793-7. PMC 5581930. PMID 28865429.
Alexaki, Aikaterini; Kames, Jacob; Holcomb, David D.; Athey, John; Santana-Quintero, Luis V.; Lam, Phuc Vihn Nguyen; Hamasaki-Katagiri, Nobuko; Osipova, Ekaterina; Simonyan, Vahan; Bar, Haim; Komar, Anton A.; Kimchi-Sarfaty, Chava (June 2019). "Codon and Codon-Pair Usage Tables (CoCoPUTs): Facilitating Genetic Variation Analyses and Recombinant Gene Design". Journal of Molecular Biology. 431 (13): 2434–2441. doi:10.1016/j.jmb.2019.04.021. PMID 31029701. S2CID 139104807.
Kames, Jacob; Alexaki, Aikaterini; Holcomb, David D.; Santana-Quintero, Luis V.; Athey, John C.; Hamasaki-Katagiri, Nobuko; Katneni, Upendra; Golikov, Anton; Ibla, Juan C.; Bar, Haim; Kimchi-Sarfaty, Chava (January 2020). "TissueCoCoPUTs: Novel Human Tissue-Specific Codon and Codon-Pair Usage Tables Based on Differential Tissue Gene Expression". Journal of Molecular Biology. 432 (11): 3369–3378. doi:10.1016/j.jmb.2020.01.011. PMID 31982380.
P. Shah and M. A. Gilchrist (2011). "Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift". Proceedings of the National Academy of Sciences of the United States of America. 108 (25): 10231–6. Bibcode:2011PNAS..10810231S. doi:10.1073/pnas.1016719108. PMC 3121864. PMID 21646514.
L. Duret and N. Galtier (2009). "Biased gene conversion and the evolution of mammalian genomic landscapes". Annu Rev Genomics Hum Genet. 10: 285–311. doi:10.1146/annurev-genom-082908-150001. PMID 19630562.
N. Galtier, C. Roux, M. Rousselle, J. Romiguier, E. Figuet, S. Glemin, N. Bierne and L. Duret (2018). "Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion". Mol Biol Evol. 35 (5): 1092–1103. doi:10.1093/molbev/msy015. hdl:20.500.12210/34500. PMID 29390090.{{cite journal}}: CS1 maint: multiple names: authors list (link)
Dong, Hengjiang; Nilsson, Lars; Kurland, Charles G. (1996). "Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates". Journal of Molecular Biology. 260 (5): 649–663. doi:10.1006/jmbi.1996.0428. ISSN 0022-2836. PMID 8709146.
Sharp, Paul M.; Stenico, Michele; Peden, John F.; Lloyd, Andrew T. (1993). "Codon usage: mutational bias, translational selection, or both?". Biochem. Soc. Trans. 21 (4): 835–841. doi:10.1042/bst0210835. PMID 8132077. S2CID 8582630.
Kanaya, Shigehiko; Yamada, Yuko; Kudo, Yoshihiro; Ikemura, Toshimichi (1999). "Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis". Gene. 238 (1): 143–155. doi:10.1016/s0378-1119(99)00225-5. ISSN 0378-1119. PMID 10570992.
Atherton, John C.; Sharp, Paul M.; Lafay, Bénédicte (2000-04-01). "Absence of translationally selected synonymous codon usage bias in Helicobacter pylori". Microbiology. 146 (4): 851–860. doi:10.1099/00221287-146-4-851. ISSN 1350-0872. PMID 10784043.
Bornelöv, Susanne; Selmi, Tommaso; Flad, Sophia; Dietmann, Sabine; Frye, Michaela (2019-06-07). "Codon usage optimization in pluripotent embryonic stem cells". Genome Biology. 20 (1): 119. doi:10.1186/s13059-019-1726-z. ISSN 1474-760X. PMC 6555954. PMID 31174582.
Duret, Laurent (2000). "tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes". Trends in Genetics. 16 (7): 287–289. doi:10.1016/s0168-9525(00)02041-2. ISSN 0168-9525. PMID 10858656.
Shin, Young C.; Bischof, Georg F.; Lauer, William A.; Desrosiers, Ronald C. (2015-09-10). "Importance of codon usage for the temporal regulation of viral gene expression". Proceedings of the National Academy of Sciences. 112 (45): 14030–14035. Bibcode:2015PNAS..11214030S. doi:10.1073/pnas.1515387112. PMC 4653223. PMID 26504241.
Lynn DJ, Singer GA, Hickey DA (October 2002). "Synonymous codon usage is subject to selection in thermophilic bacteria". Nucleic Acids Res. 30 (19): 4272–7. doi:10.1093/nar/gkf546. PMC 140546. PMID 12364606.
Paul S, Bag SK, Das S, Harvill ET, Dutta C (2008). "Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes". Genome Biol. 9 (4): R70. doi:10.1186/gb-2008-9-4-r70. PMC 2643941. PMID 18397532.
Kober, K. M.; Pogson, G. H. (2013). "Genome-Wide Patterns of Codon Bias Are Shaped by Natural Selection in the Purple Sea Urchin, Strongylocentrotus purpuratus". G3. 3 (7): 1069–1083. doi:10.1534/g3.113.005769. PMC 3704236. PMID 23637123.
McInerney, James O. (1998-09-01). "Replicational and transcriptional selection on codon usage in Borrelia burgdorferi". Proceedings of the National Academy of Sciences. 95 (18): 10698–10703. Bibcode:1998PNAS...9510698M. doi:10.1073/pnas.95.18.10698. ISSN 0027-8424. PMC 27958. PMID 9724767.
Seward, Emily; Kelly, Steve (2016). "Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms". Genome Biology. 17 (226): 3–15. doi:10.1186/s13059-016-1087-9. PMC 5109750. PMID 27842572.
Hershberg, R; Petrov, D. A. (2008). "Selection on codon bias". Annual Review of Genetics. 42: 287–99. doi:10.1146/annurev.genet.42.110807.091442. PMID 18983258. S2CID 7085012.
Novoa, E. M.; Ribas De Pouplana, L (2012). "Speeding with control: Codon usage, tRNAs, and ribosomes". Trends in Genetics. 28 (11): 574–81. doi:10.1016/j.tig.2012.07.006. PMID 22921354.
Shu, P.; Dai, H.; Gao, W.; Goldman, E. (2006). "Inhibition of translation by consecutive rare leucine codons in E. coli: absence of effect of varying mRNA stability". Gene Expr. 13 (2): 97–106. doi:10.3727/000000006783991881. PMC 6032470. PMID 17017124.
Correddu, D.; Montaño López, J. d. J.; Angermayr, S. A.; Middleditch, M. J.; Payne, L. S.; Leung, I. K. H. (2019). "Effect of Consecutive Rare Codons on the Recombinant Production of Human Proteins in Escherichia coli". IUBMB Life. 72 (2): 266–274. doi:10.1002/iub.2162. hdl:11343/286411. PMID 31509345. S2CID 202555575.
Mignon, C.; Mariano, N.; Stadthagen, G.; Lugari, A.; Lagoutte, P.; Donnat, S.; Chenavas, S.; Perot, C.; Sodoyer, R.; Werle, B. (2018). "Codon harmonization - going beyond the speed limit for protein expression". FEBS Letters. 592 (9): 1554–1564. doi:10.1002/1873-3468.13046. PMID 29624661.
Plotkin, J. B.; Kudla, G (2011). "Synonymous but not the same: The causes and consequences of codon bias". Nature Reviews Genetics. 12 (1): 32–42. doi:10.1038/nrg2899. PMC 3074964. PMID 21102527.
Spencer, P. S.; Barral, J. M. (2012). "Genetic Code Redundancy and Its Influence on the Encoded Polypeptides". Computational and Structural Biotechnology Journal. 1: 1–8. doi:10.5936/csbj.201204006. PMC 3962081. PMID 24688635.
Comeron JM, Aguadé M (September 1998). "An evaluation of measures of synonymous codon usage bias". J. Mol. Evol. 47 (3): 268–74. Bibcode:1998JMolE..47..268C. doi:10.1007/PL00006384. PMID 9732453. S2CID 21862217.
Ikemura T (September 1981). "Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system". J. Mol. Biol. 151 (3): 389–409. doi:10.1016/0022-2836(81)90003-6. PMID 6175758.
Fox JM, Erill I (June 2010). "Relative codon adaptation: a generic codon bias index for prediction of gene expression". DNA Res. 17 (3): 185–96. doi:10.1093/dnares/dsq012. PMC 2885275. PMID 20453079.
Sharp, Paul M.; Li, Wen-Hsiung (1987). "The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications". Nucleic Acids Research. 15 (3): 1281–1295. doi:10.1093/nar/15.3.1281. PMC 340524. PMID 3547335.
Suzuki H, Brown CJ, Forney LJ, Top EM (December 2008). "Comparison of correspondence analysis methods for synonymous codon usage in bacteria". DNA Res. 15 (6): 357–65. doi:10.1093/dnares/dsn028. PMC 2608848. PMID 18940873.

handle.net

hdl.handle.net

N. Galtier, C. Roux, M. Rousselle, J. Romiguier, E. Figuet, S. Glemin, N. Bierne and L. Duret (2018). "Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion". Mol Biol Evol. 35 (5): 1092–1103. doi:10.1093/molbev/msy015. hdl:20.500.12210/34500. PMID 29390090.{{cite journal}}: CS1 maint: multiple names: authors list (link)
Correddu, D.; Montaño López, J. d. J.; Angermayr, S. A.; Middleditch, M. J.; Payne, L. S.; Leung, I. K. H. (2019). "Effect of Consecutive Rare Codons on the Recombinant Production of Human Proteins in Escherichia coli". IUBMB Life. 72 (2): 266–274. doi:10.1002/iub.2162. hdl:11343/286411. PMID 31509345. S2CID 202555575.

harvard.edu

ui.adsabs.harvard.edu

P. Shah and M. A. Gilchrist (2011). "Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift". Proceedings of the National Academy of Sciences of the United States of America. 108 (25): 10231–6. Bibcode:2011PNAS..10810231S. doi:10.1073/pnas.1016719108. PMC 3121864. PMID 21646514.
Shin, Young C.; Bischof, Georg F.; Lauer, William A.; Desrosiers, Ronald C. (2015-09-10). "Importance of codon usage for the temporal regulation of viral gene expression". Proceedings of the National Academy of Sciences. 112 (45): 14030–14035. Bibcode:2015PNAS..11214030S. doi:10.1073/pnas.1515387112. PMC 4653223. PMID 26504241.
McInerney, James O. (1998-09-01). "Replicational and transcriptional selection on codon usage in Borrelia burgdorferi". Proceedings of the National Academy of Sciences. 95 (18): 10698–10703. Bibcode:1998PNAS...9510698M. doi:10.1073/pnas.95.18.10698. ISSN 0027-8424. PMC 27958. PMID 9724767.
Comeron JM, Aguadé M (September 1998). "An evaluation of measures of synonymous codon usage bias". J. Mol. Evol. 47 (3): 268–74. Bibcode:1998JMolE..47..268C. doi:10.1007/PL00006384. PMID 9732453. S2CID 21862217.

nih.gov

pubmed.ncbi.nlm.nih.gov

Athey, John; Alexaki, Aikaterini; Osipova, Ekaterina; Rostovtsev, Alexandre; Santana-Quintero, Luis V.; Katneni, Upendra; Simonyan, Vahan; Kimchi-Sarfaty, Chava (2017-09-02). "A new and updated resource for codon usage tables". BMC Bioinformatics. 18 (391): 391. doi:10.1186/s12859-017-1793-7. PMC 5581930. PMID 28865429.
Alexaki, Aikaterini; Kames, Jacob; Holcomb, David D.; Athey, John; Santana-Quintero, Luis V.; Lam, Phuc Vihn Nguyen; Hamasaki-Katagiri, Nobuko; Osipova, Ekaterina; Simonyan, Vahan; Bar, Haim; Komar, Anton A.; Kimchi-Sarfaty, Chava (June 2019). "Codon and Codon-Pair Usage Tables (CoCoPUTs): Facilitating Genetic Variation Analyses and Recombinant Gene Design". Journal of Molecular Biology. 431 (13): 2434–2441. doi:10.1016/j.jmb.2019.04.021. PMID 31029701. S2CID 139104807.
Kames, Jacob; Alexaki, Aikaterini; Holcomb, David D.; Santana-Quintero, Luis V.; Athey, John C.; Hamasaki-Katagiri, Nobuko; Katneni, Upendra; Golikov, Anton; Ibla, Juan C.; Bar, Haim; Kimchi-Sarfaty, Chava (January 2020). "TissueCoCoPUTs: Novel Human Tissue-Specific Codon and Codon-Pair Usage Tables Based on Differential Tissue Gene Expression". Journal of Molecular Biology. 432 (11): 3369–3378. doi:10.1016/j.jmb.2020.01.011. PMID 31982380.
P. Shah and M. A. Gilchrist (2011). "Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift". Proceedings of the National Academy of Sciences of the United States of America. 108 (25): 10231–6. Bibcode:2011PNAS..10810231S. doi:10.1073/pnas.1016719108. PMC 3121864. PMID 21646514.
L. Duret and N. Galtier (2009). "Biased gene conversion and the evolution of mammalian genomic landscapes". Annu Rev Genomics Hum Genet. 10: 285–311. doi:10.1146/annurev-genom-082908-150001. PMID 19630562.
N. Galtier, C. Roux, M. Rousselle, J. Romiguier, E. Figuet, S. Glemin, N. Bierne and L. Duret (2018). "Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion". Mol Biol Evol. 35 (5): 1092–1103. doi:10.1093/molbev/msy015. hdl:20.500.12210/34500. PMID 29390090.{{cite journal}}: CS1 maint: multiple names: authors list (link)
Dong, Hengjiang; Nilsson, Lars; Kurland, Charles G. (1996). "Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates". Journal of Molecular Biology. 260 (5): 649–663. doi:10.1006/jmbi.1996.0428. ISSN 0022-2836. PMID 8709146.
Sharp, Paul M.; Stenico, Michele; Peden, John F.; Lloyd, Andrew T. (1993). "Codon usage: mutational bias, translational selection, or both?". Biochem. Soc. Trans. 21 (4): 835–841. doi:10.1042/bst0210835. PMID 8132077. S2CID 8582630.
Kanaya, Shigehiko; Yamada, Yuko; Kudo, Yoshihiro; Ikemura, Toshimichi (1999). "Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis". Gene. 238 (1): 143–155. doi:10.1016/s0378-1119(99)00225-5. ISSN 0378-1119. PMID 10570992.
Atherton, John C.; Sharp, Paul M.; Lafay, Bénédicte (2000-04-01). "Absence of translationally selected synonymous codon usage bias in Helicobacter pylori". Microbiology. 146 (4): 851–860. doi:10.1099/00221287-146-4-851. ISSN 1350-0872. PMID 10784043.
Bornelöv, Susanne; Selmi, Tommaso; Flad, Sophia; Dietmann, Sabine; Frye, Michaela (2019-06-07). "Codon usage optimization in pluripotent embryonic stem cells". Genome Biology. 20 (1): 119. doi:10.1186/s13059-019-1726-z. ISSN 1474-760X. PMC 6555954. PMID 31174582.
Duret, Laurent (2000). "tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes". Trends in Genetics. 16 (7): 287–289. doi:10.1016/s0168-9525(00)02041-2. ISSN 0168-9525. PMID 10858656.
Shin, Young C.; Bischof, Georg F.; Lauer, William A.; Desrosiers, Ronald C. (2015-09-10). "Importance of codon usage for the temporal regulation of viral gene expression". Proceedings of the National Academy of Sciences. 112 (45): 14030–14035. Bibcode:2015PNAS..11214030S. doi:10.1073/pnas.1515387112. PMC 4653223. PMID 26504241.
Ermolaeva MD (October 2001). "Synonymous codon usage in bacteria". Curr Issues Mol Biol. 3 (4): 91–7. PMID 11719972.
Lynn DJ, Singer GA, Hickey DA (October 2002). "Synonymous codon usage is subject to selection in thermophilic bacteria". Nucleic Acids Res. 30 (19): 4272–7. doi:10.1093/nar/gkf546. PMC 140546. PMID 12364606.
Paul S, Bag SK, Das S, Harvill ET, Dutta C (2008). "Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes". Genome Biol. 9 (4): R70. doi:10.1186/gb-2008-9-4-r70. PMC 2643941. PMID 18397532.
Kober, K. M.; Pogson, G. H. (2013). "Genome-Wide Patterns of Codon Bias Are Shaped by Natural Selection in the Purple Sea Urchin, Strongylocentrotus purpuratus". G3. 3 (7): 1069–1083. doi:10.1534/g3.113.005769. PMC 3704236. PMID 23637123.
McInerney, James O. (1998-09-01). "Replicational and transcriptional selection on codon usage in Borrelia burgdorferi". Proceedings of the National Academy of Sciences. 95 (18): 10698–10703. Bibcode:1998PNAS...9510698M. doi:10.1073/pnas.95.18.10698. ISSN 0027-8424. PMC 27958. PMID 9724767.
Seward, Emily; Kelly, Steve (2016). "Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms". Genome Biology. 17 (226): 3–15. doi:10.1186/s13059-016-1087-9. PMC 5109750. PMID 27842572.
Hershberg, R; Petrov, D. A. (2008). "Selection on codon bias". Annual Review of Genetics. 42: 287–99. doi:10.1146/annurev.genet.42.110807.091442. PMID 18983258. S2CID 7085012.
Novoa, E. M.; Ribas De Pouplana, L (2012). "Speeding with control: Codon usage, tRNAs, and ribosomes". Trends in Genetics. 28 (11): 574–81. doi:10.1016/j.tig.2012.07.006. PMID 22921354.
Shu, P.; Dai, H.; Gao, W.; Goldman, E. (2006). "Inhibition of translation by consecutive rare leucine codons in E. coli: absence of effect of varying mRNA stability". Gene Expr. 13 (2): 97–106. doi:10.3727/000000006783991881. PMC 6032470. PMID 17017124.
Correddu, D.; Montaño López, J. d. J.; Angermayr, S. A.; Middleditch, M. J.; Payne, L. S.; Leung, I. K. H. (2019). "Effect of Consecutive Rare Codons on the Recombinant Production of Human Proteins in Escherichia coli". IUBMB Life. 72 (2): 266–274. doi:10.1002/iub.2162. hdl:11343/286411. PMID 31509345. S2CID 202555575.
Mignon, C.; Mariano, N.; Stadthagen, G.; Lugari, A.; Lagoutte, P.; Donnat, S.; Chenavas, S.; Perot, C.; Sodoyer, R.; Werle, B. (2018). "Codon harmonization - going beyond the speed limit for protein expression". FEBS Letters. 592 (9): 1554–1564. doi:10.1002/1873-3468.13046. PMID 29624661.
Plotkin, J. B.; Kudla, G (2011). "Synonymous but not the same: The causes and consequences of codon bias". Nature Reviews Genetics. 12 (1): 32–42. doi:10.1038/nrg2899. PMC 3074964. PMID 21102527.
Spencer, P. S.; Barral, J. M. (2012). "Genetic Code Redundancy and Its Influence on the Encoded Polypeptides". Computational and Structural Biotechnology Journal. 1: 1–8. doi:10.5936/csbj.201204006. PMC 3962081. PMID 24688635.
Comeron JM, Aguadé M (September 1998). "An evaluation of measures of synonymous codon usage bias". J. Mol. Evol. 47 (3): 268–74. Bibcode:1998JMolE..47..268C. doi:10.1007/PL00006384. PMID 9732453. S2CID 21862217.
Ikemura T (September 1981). "Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system". J. Mol. Biol. 151 (3): 389–409. doi:10.1016/0022-2836(81)90003-6. PMID 6175758.
Fox JM, Erill I (June 2010). "Relative codon adaptation: a generic codon bias index for prediction of gene expression". DNA Res. 17 (3): 185–96. doi:10.1093/dnares/dsq012. PMC 2885275. PMID 20453079.
Sharp, Paul M.; Li, Wen-Hsiung (1987). "The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications". Nucleic Acids Research. 15 (3): 1281–1295. doi:10.1093/nar/15.3.1281. PMC 340524. PMID 3547335.
Suzuki H, Brown CJ, Forney LJ, Top EM (December 2008). "Comparison of correspondence analysis methods for synonymous codon usage in bacteria". DNA Res. 15 (6): 357–65. doi:10.1093/dnares/dsn028. PMC 2608848. PMID 18940873.

ncbi.nlm.nih.gov

Athey, John; Alexaki, Aikaterini; Osipova, Ekaterina; Rostovtsev, Alexandre; Santana-Quintero, Luis V.; Katneni, Upendra; Simonyan, Vahan; Kimchi-Sarfaty, Chava (2017-09-02). "A new and updated resource for codon usage tables". BMC Bioinformatics. 18 (391): 391. doi:10.1186/s12859-017-1793-7. PMC 5581930. PMID 28865429.
P. Shah and M. A. Gilchrist (2011). "Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift". Proceedings of the National Academy of Sciences of the United States of America. 108 (25): 10231–6. Bibcode:2011PNAS..10810231S. doi:10.1073/pnas.1016719108. PMC 3121864. PMID 21646514.
Bornelöv, Susanne; Selmi, Tommaso; Flad, Sophia; Dietmann, Sabine; Frye, Michaela (2019-06-07). "Codon usage optimization in pluripotent embryonic stem cells". Genome Biology. 20 (1): 119. doi:10.1186/s13059-019-1726-z. ISSN 1474-760X. PMC 6555954. PMID 31174582.
Shin, Young C.; Bischof, Georg F.; Lauer, William A.; Desrosiers, Ronald C. (2015-09-10). "Importance of codon usage for the temporal regulation of viral gene expression". Proceedings of the National Academy of Sciences. 112 (45): 14030–14035. Bibcode:2015PNAS..11214030S. doi:10.1073/pnas.1515387112. PMC 4653223. PMID 26504241.
Lynn DJ, Singer GA, Hickey DA (October 2002). "Synonymous codon usage is subject to selection in thermophilic bacteria". Nucleic Acids Res. 30 (19): 4272–7. doi:10.1093/nar/gkf546. PMC 140546. PMID 12364606.
Paul S, Bag SK, Das S, Harvill ET, Dutta C (2008). "Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes". Genome Biol. 9 (4): R70. doi:10.1186/gb-2008-9-4-r70. PMC 2643941. PMID 18397532.
Kober, K. M.; Pogson, G. H. (2013). "Genome-Wide Patterns of Codon Bias Are Shaped by Natural Selection in the Purple Sea Urchin, Strongylocentrotus purpuratus". G3. 3 (7): 1069–1083. doi:10.1534/g3.113.005769. PMC 3704236. PMID 23637123.
McInerney, James O. (1998-09-01). "Replicational and transcriptional selection on codon usage in Borrelia burgdorferi". Proceedings of the National Academy of Sciences. 95 (18): 10698–10703. Bibcode:1998PNAS...9510698M. doi:10.1073/pnas.95.18.10698. ISSN 0027-8424. PMC 27958. PMID 9724767.
Seward, Emily; Kelly, Steve (2016). "Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms". Genome Biology. 17 (226): 3–15. doi:10.1186/s13059-016-1087-9. PMC 5109750. PMID 27842572.
Shu, P.; Dai, H.; Gao, W.; Goldman, E. (2006). "Inhibition of translation by consecutive rare leucine codons in E. coli: absence of effect of varying mRNA stability". Gene Expr. 13 (2): 97–106. doi:10.3727/000000006783991881. PMC 6032470. PMID 17017124.
Plotkin, J. B.; Kudla, G (2011). "Synonymous but not the same: The causes and consequences of codon bias". Nature Reviews Genetics. 12 (1): 32–42. doi:10.1038/nrg2899. PMC 3074964. PMID 21102527.
Spencer, P. S.; Barral, J. M. (2012). "Genetic Code Redundancy and Its Influence on the Encoded Polypeptides". Computational and Structural Biotechnology Journal. 1: 1–8. doi:10.5936/csbj.201204006. PMC 3962081. PMID 24688635.
Fox JM, Erill I (June 2010). "Relative codon adaptation: a generic codon bias index for prediction of gene expression". DNA Res. 17 (3): 185–96. doi:10.1093/dnares/dsq012. PMC 2885275. PMID 20453079.
Sharp, Paul M.; Li, Wen-Hsiung (1987). "The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications". Nucleic Acids Research. 15 (3): 1281–1295. doi:10.1093/nar/15.3.1281. PMC 340524. PMID 3547335.
Suzuki H, Brown CJ, Forney LJ, Top EM (December 2008). "Comparison of correspondence analysis methods for synonymous codon usage in bacteria". DNA Res. 15 (6): 357–65. doi:10.1093/dnares/dsn028. PMC 2608848. PMID 18940873.

semanticscholar.org

api.semanticscholar.org

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sourceforge.net

codonw.sourceforge.net

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worldcat.org

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