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For: Doherty A, McInerney JO. Translational selection frequently overcomes genetic drift in shaping synonymous codon usage patterns in vertebrates. Mol Biol Evol 2013;30:2263-7. [PMID: 23883522 DOI: 10.1093/molbev/mst128] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]  Open
Number Cited by Other Article(s)
1
Weibel CA, Wheeler AL, James JE, Willis SM, McShea H, Masel J. The protein domains of vertebrate species in which selection is more effective have greater intrinsic structural disorder. eLife 2024;12:RP87335. [PMID: 39239703 PMCID: PMC11379457 DOI: 10.7554/elife.87335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2024]  Open
2
Kotari I, Kosiol C, Borges R. The Patterns of Codon Usage between Chordates and Arthropods are Different but Co-evolving with Mutational Biases. Mol Biol Evol 2024;41:msae080. [PMID: 38667829 PMCID: PMC11108087 DOI: 10.1093/molbev/msae080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 03/22/2024] [Accepted: 04/15/2024] [Indexed: 05/22/2024]  Open
3
Weibel CA, Wheeler AL, James JE, Willis SM, McShea H, Masel J. The protein domains of vertebrate species in which selection is more effective have greater intrinsic structural disorder. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.02.530449. [PMID: 38712167 PMCID: PMC11071303 DOI: 10.1101/2023.03.02.530449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
4
McInerney JO. Prokaryotic Pangenomes Act as Evolving Ecosystems. Mol Biol Evol 2022;40:6775222. [PMID: 36288801 PMCID: PMC9851318 DOI: 10.1093/molbev/msac232] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/11/2022] [Accepted: 10/20/2022] [Indexed: 01/24/2023]  Open
5
Miller JB, Meurs TE, Hodgman MW, Song B, Miller KN, Ebbert MTW, Kauwe JSK, Ridge PG. The Ramp Atlas: facilitating tissue and cell-specific ramp sequence analyses through an intuitive web interface. NAR Genom Bioinform 2022;4:lqac039. [PMID: 35664804 PMCID: PMC9155233 DOI: 10.1093/nargab/lqac039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 03/01/2022] [Accepted: 05/24/2022] [Indexed: 11/14/2022]  Open
6
A Genome-Wide Profiling of Glioma Patients with an IDH1 Mutation Using the Catalogue of Somatic Mutations in Cancer Database. Cancers (Basel) 2021;13:cancers13174299. [PMID: 34503108 PMCID: PMC8428353 DOI: 10.3390/cancers13174299] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/20/2021] [Accepted: 08/21/2021] [Indexed: 02/08/2023]  Open
7
Seoighe C, Kiniry SJ, Peters A, Baranov PV, Yang H. Selection Shapes Synonymous Stop Codon Use in Mammals. J Mol Evol 2020;88:549-561. [PMID: 32617614 DOI: 10.1007/s00239-020-09957-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/19/2020] [Indexed: 12/15/2022]
8
Laurin-Lemay S, Philippe H, Rodrigue N. Multiple Factors Confounding Phylogenetic Detection of Selection on Codon Usage. Mol Biol Evol 2019;35:1463-1472. [PMID: 29596640 DOI: 10.1093/molbev/msy047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
9
Galtier N, Roux C, Rousselle M, Romiguier J, Figuet E, Glémin S, Bierne N, Duret L. Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion. Mol Biol Evol 2019;35:1092-1103. [PMID: 29390090 DOI: 10.1093/molbev/msy015] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
10
Abrahams L, Hurst LD. Adenine Enrichment at the Fourth CDS Residue in Bacterial Genes Is Consistent with Error Proofing for +1 Frameshifts. Mol Biol Evol 2018;34:3064-3080. [PMID: 28961919 PMCID: PMC5850271 DOI: 10.1093/molbev/msx223] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
11
Paul P, Malakar AK, Chakraborty S. Codon usage vis-a-vis start and stop codon context analysis of three dicot species. J Genet 2018. [DOI: 10.1007/s12041-018-0892-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
12
Im EH, Choi SS. Synonymous Codon Usage Controls Various Molecular Aspects. Genomics Inform 2017;15:123-127. [PMID: 29307137 PMCID: PMC5769864 DOI: 10.5808/gi.2017.15.4.123] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 09/25/2017] [Indexed: 12/19/2022]  Open
13
Why prokaryotes have pangenomes. Nat Microbiol 2017;2:17040. [PMID: 28350002 DOI: 10.1038/nmicrobiol.2017.40] [Citation(s) in RCA: 243] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 02/22/2017] [Indexed: 01/07/2023]
14
Wen Y, Zou Z, Li H, Xiang Z, He N. Analysis of codon usage patterns in Morus notabilis based on genome and transcriptome data. Genome 2017;60:473-484. [PMID: 28177830 DOI: 10.1139/gen-2016-0129] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
15
Yang L, Zhang Z, He S. Both Male-Biased and Female-Biased Genes Evolve Faster in Fish Genomes. Genome Biol Evol 2016;8:3433-3445. [PMID: 27742722 PMCID: PMC5203780 DOI: 10.1093/gbe/evw239] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
16
Genome-wide comparative analysis of codon usage bias and codon context patterns among cyanobacterial genomes. Mar Genomics 2016;32:31-39. [PMID: 27733306 DOI: 10.1016/j.margen.2016.10.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 09/11/2016] [Accepted: 10/03/2016] [Indexed: 11/20/2022]
17
Chen CYA, Shyu AB. Emerging Themes in Regulation of Global mRNA Turnover in cis. Trends Biochem Sci 2016;42:16-27. [PMID: 27647213 DOI: 10.1016/j.tibs.2016.08.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/24/2016] [Accepted: 08/25/2016] [Indexed: 11/25/2022]
18
Velazquez-Salinas L, Zarate S, Eschbaumer M, Pereira Lobo F, Gladue DP, Arzt J, Novella IS, Rodriguez LL. Selective Factors Associated with the Evolution of Codon Usage in Natural Populations of Arboviruses. PLoS One 2016;11:e0159943. [PMID: 27455096 PMCID: PMC4959722 DOI: 10.1371/journal.pone.0159943] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 07/11/2016] [Indexed: 11/18/2022]  Open
19
Yin H, Ma L, Wang G, Li M, Zhang Z. Old genes experience stronger translational selection than young genes. Gene 2016;590:29-34. [PMID: 27259662 DOI: 10.1016/j.gene.2016.05.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/27/2016] [Accepted: 05/29/2016] [Indexed: 12/12/2022]
20
He J, Liu H, Yang J, Dong X, Wu C. Abundant members of Scavenger receptors family and their identification, characterization and expression against Vibrio alginolyticus infection in juvenile Larimichthys crocea. FISH & SHELLFISH IMMUNOLOGY 2016;50:297-309. [PMID: 26876357 DOI: 10.1016/j.fsi.2016.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 01/31/2016] [Accepted: 02/05/2016] [Indexed: 06/05/2023]
21
Kim JJ, Yu J, Bag J, Bakovic M, Cant JP. Translation attenuation via 3' terminal codon usage in bovine csn1s2 is responsible for the difference in αs2- and β-casein profile in milk. RNA Biol 2015;12:354-67. [PMID: 25826667 DOI: 10.1080/15476286.2015.1017231] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]  Open
22
Price N, Graur D. Are Synonymous Sites in Primates and Rodents Functionally Constrained? J Mol Evol 2015;82:51-64. [PMID: 26563252 DOI: 10.1007/s00239-015-9719-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 11/04/2015] [Indexed: 11/28/2022]
23
A Comprehensive Analysis of Codon Usage Patterns in Blunt Snout Bream (Megalobrama amblycephala) Based on RNA-Seq Data. Int J Mol Sci 2015;16:11996-2013. [PMID: 26016504 PMCID: PMC4490425 DOI: 10.3390/ijms160611996] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/19/2015] [Indexed: 11/21/2022]  Open
24
Kessler MD, Dean MD. Effective population size does not predict codon usage bias in mammals. Ecol Evol 2014;4:3887-900. [PMID: 25505518 PMCID: PMC4242573 DOI: 10.1002/ece3.1249] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 08/04/2014] [Accepted: 08/07/2014] [Indexed: 12/20/2022]  Open
25
Gingold H, Tehler D, Christoffersen N, Nielsen M, Asmar F, Kooistra S, Christophersen N, Christensen LL, Borre M, Sørensen K, Andersen L, Andersen C, Hulleman E, Wurdinger T, Ralfkiær E, Helin K, Grønbæk K, Ørntoft T, Waszak S, Dahan O, Pedersen J, Lund A, Pilpel Y. A Dual Program for Translation Regulation in Cellular Proliferation and Differentiation. Cell 2014;158:1281-1292. [DOI: 10.1016/j.cell.2014.08.011] [Citation(s) in RCA: 353] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Revised: 05/13/2014] [Accepted: 08/08/2014] [Indexed: 11/16/2022]
26
Sensory rewiring in an echolocator: genome-wide modification of retinogenic and auditory genes in the bat Myotis davidii. G3-GENES GENOMES GENETICS 2014;4:1825-35. [PMID: 25096539 PMCID: PMC4199690 DOI: 10.1534/g3.114.011262] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
27
Ma L, Cui P, Zhu J, Zhang Z, Zhang Z. Translational selection in human: more pronounced in housekeeping genes. Biol Direct 2014;9:17. [PMID: 25011537 PMCID: PMC4100034 DOI: 10.1186/1745-6150-9-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 07/02/2014] [Indexed: 02/17/2023]  Open
28
Evidence that natural selection on codon usage in Drosophila pseudoobscura varies across codons. G3-GENES GENOMES GENETICS 2014;4:681-92. [PMID: 24531731 PMCID: PMC4059240 DOI: 10.1534/g3.114.010488] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
29
Weber CC, Boussau B, Romiguier J, Jarvis ED, Ellegren H. Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition. Genome Biol 2014;15:549. [PMID: 25496599 PMCID: PMC4290106 DOI: 10.1186/s13059-014-0549-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 11/19/2014] [Indexed: 11/23/2022]  Open
30
Yona AH, Bloom-Ackermann Z, Frumkin I, Hanson-Smith V, Charpak-Amikam Y, Feng Q, Boeke JD, Dahan O, Pilpel Y. tRNA genes rapidly change in evolution to meet novel translational demands. eLife 2013;2:e01339. [PMID: 24363105 PMCID: PMC3868979 DOI: 10.7554/elife.01339] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]  Open
31
Halligan DL, Kousathanas A, Ness RW, Harr B, Eöry L, Keane TM, Adams DJ, Keightley PD. Contributions of protein-coding and regulatory change to adaptive molecular evolution in murid rodents. PLoS Genet 2013;9:e1003995. [PMID: 24339797 PMCID: PMC3854965 DOI: 10.1371/journal.pgen.1003995] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 10/16/2013] [Indexed: 12/22/2022]  Open
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