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For: Powell JR, Dion K. Effects of codon usage on gene expression: empirical studies on Drosophila. J Mol Evol 2015;80:219-26. [PMID: 25838108 DOI: 10.1007/s00239-015-9675-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 03/29/2015] [Indexed: 10/28/2022]
Number Cited by Other Article(s)
1
Fang J, Qin L, Liu H, Hu Z. Analysis of Codon Usage Bias of 30 Chloroplast Genomes in Ulva (Ulvophyceae, Chlorophyta). Genes (Basel) 2025;16:608. [PMID: 40428430 PMCID: PMC12111487 DOI: 10.3390/genes16050608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2025] [Revised: 05/15/2025] [Accepted: 05/19/2025] [Indexed: 05/29/2025]  Open
2
Pistek M, Andorfer P, Grabherr R, Kraus B, Hernandez Bort JA. Factors affecting rAAV titers during triple-plasmid transient transfection in HEK-293 cells. Biotechnol Lett 2024;46:945-959. [PMID: 39259435 PMCID: PMC11550245 DOI: 10.1007/s10529-024-03520-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 06/24/2024] [Accepted: 08/06/2024] [Indexed: 09/13/2024]
3
Shen L, Chen S, Liang M, Qu S, Feng S, Wang D, Wang G. Comparative analysis of codon usage bias in chloroplast genomes of ten medicinal species of Rutaceae. BMC PLANT BIOLOGY 2024;24:424. [PMID: 38764045 PMCID: PMC11103831 DOI: 10.1186/s12870-024-04999-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 04/08/2024] [Indexed: 05/21/2024]
4
Wang P, Mao Y, Su Y, Wang J. Comparative analysis of transcriptomic data shows the effects of multiple evolutionary selection processes on codon usage in Marsupenaeus japonicus and Marsupenaeus pulchricaudatus. BMC Genomics 2021;22:781. [PMID: 34717552 PMCID: PMC8557549 DOI: 10.1186/s12864-021-08106-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 10/19/2021] [Indexed: 11/10/2022]  Open
5
Huo X, Liu S, Li Y, Wei H, Gao J, Yan Y, Zhang G, Liu M. Analysis of synonymous codon usage of transcriptome database in Rheum palmatum. PeerJ 2021;9:e10450. [PMID: 33505783 PMCID: PMC7789865 DOI: 10.7717/peerj.10450] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/09/2020] [Indexed: 12/21/2022]  Open
6
Jitobaom K, Phakaratsakul S, Sirihongthong T, Chotewutmontri S, Suriyaphol P, Suptawiwat O, Auewarakul P. Codon usage similarity between viral and some host genes suggests a codon-specific translational regulation. Heliyon 2020;6:e03915. [PMID: 32395662 PMCID: PMC7205639 DOI: 10.1016/j.heliyon.2020.e03915] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/02/2020] [Accepted: 04/30/2020] [Indexed: 02/03/2023]  Open
7
Pal A, Saha BK, Saha J. Comparative in silico analysis of ftsZ gene from different bacteria reveals the preference for core set of codons in coding sequence structuring and secondary structural elements determination. PLoS One 2019;14:e0219231. [PMID: 31841523 PMCID: PMC6913975 DOI: 10.1371/journal.pone.0219231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/28/2019] [Indexed: 11/19/2022]  Open
8
Payne BL, Alvarez-Ponce D. Codon Usage Differences among Genes Expressed in Different Tissues of Drosophila melanogaster. Genome Biol Evol 2019;11:1054-1065. [PMID: 30859203 PMCID: PMC6456009 DOI: 10.1093/gbe/evz051] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2019] [Indexed: 12/22/2022]  Open
9
Liu SS, Hockenberry AJ, Jewett MC, Amaral LAN. A novel framework for evaluating the performance of codon usage bias metrics. J R Soc Interface 2019;15:rsif.2017.0667. [PMID: 29386398 DOI: 10.1098/rsif.2017.0667] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 01/04/2018] [Indexed: 11/12/2022]  Open
10
Khan MS, Guan DL, Ma LB, Xie JY, Xu SQ. Analysis of synonymous codon usage pattern of genes in unique non-blood-sucking leech Whitmania pigra. J Cell Biochem 2019;120:9850-9858. [PMID: 30681200 DOI: 10.1002/jcb.28267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 11/19/2018] [Indexed: 12/17/2022]
11
Ou X, Wang M, Mao S, Cao J, Cheng A, Zhu D, Chen S, Jia R, Liu M, Yang Q, Wu Y, Zhao X, Zhang S, Liu Y, Yu Y, Zhang L, Chen X, Peppelenbosch MP, Pan Q. Incompatible Translation Drives a Convergent Evolution and Viral Attenuation During the Development of Live Attenuated Vaccine. Front Cell Infect Microbiol 2018;8:249. [PMID: 30073153 PMCID: PMC6058041 DOI: 10.3389/fcimb.2018.00249] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 07/02/2018] [Indexed: 11/13/2022]  Open
12
Guan DL, Ma LB, Khan MS, Zhang XX, Xu SQ, Xie JY. Analysis of codon usage patterns in Hirudinaria manillensis reveals a preference for GC-ending codons caused by dominant selection constraints. BMC Genomics 2018;19:542. [PMID: 30016953 PMCID: PMC6050667 DOI: 10.1186/s12864-018-4937-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 07/10/2018] [Indexed: 02/07/2023]  Open
13
An AlgU-Regulated Antisense Transcript Encoded within the Pseudomonas syringae fleQ Gene Has a Positive Effect on Motility. J Bacteriol 2018;200:JB.00576-17. [PMID: 29311280 DOI: 10.1128/jb.00576-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/04/2018] [Indexed: 12/29/2022]  Open
14
Supek F. The Code of Silence: Widespread Associations Between Synonymous Codon Biases and Gene Function. J Mol Evol 2015;82:65-73. [PMID: 26538122 DOI: 10.1007/s00239-015-9714-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 10/30/2015] [Indexed: 02/07/2023]
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