78 related articles for article (PubMed ID: 29596640)
1. Multiple Factors Confounding Phylogenetic Detection of Selection on Codon Usage.
Laurin-Lemay S; Philippe H; Rodrigue N
Mol Biol Evol; 2018 Jun; 35(6):1463-1472. PubMed ID: 29596640
[TBL] [Abstract][Full Text] [Related]
2. Conditional Approximate Bayesian Computation: A New Approach for Across-Site Dependency in High-Dimensional Mutation-Selection Models.
Laurin-Lemay S; Rodrigue N; Lartillot N; Philippe H
Mol Biol Evol; 2018 Nov; 35(11):2819-2834. PubMed ID: 30203003
[TBL] [Abstract][Full Text] [Related]
3. Detecting Adaptation in Protein-Coding Genes Using a Bayesian Site-Heterogeneous Mutation-Selection Codon Substitution Model.
Rodrigue N; Lartillot N
Mol Biol Evol; 2017 Jan; 34(1):204-214. PubMed ID: 27744408
[TBL] [Abstract][Full Text] [Related]
4. Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage.
Yang Z; Nielsen R
Mol Biol Evol; 2008 Mar; 25(3):568-79. PubMed ID: 18178545
[TBL] [Abstract][Full Text] [Related]
5. Large-Scale Comparative Analysis of Codon Models Accounting for Protein and Nucleotide Selection.
Davydov II; Salamin N; Robinson-Rechavi M
Mol Biol Evol; 2019 Jun; 36(6):1316-1332. PubMed ID: 30847475
[TBL] [Abstract][Full Text] [Related]
6. A codon model of nucleotide substitution with selection on synonymous codon usage.
Kubatko L; Shah P; Herbei R; Gilchrist MA
Mol Phylogenet Evol; 2016 Jan; 94(Pt A):290-7. PubMed ID: 26358614
[TBL] [Abstract][Full Text] [Related]
7. An analysis of codon usage in mammals: selection or mutation bias?
Eyre-Walker AC
J Mol Evol; 1991 Nov; 33(5):442-9. PubMed ID: 1960741
[TBL] [Abstract][Full Text] [Related]
8. Estimating Gene Expression and Codon-Specific Translational Efficiencies, Mutation Biases, and Selection Coefficients from Genomic Data Alone.
Gilchrist MA; Chen WC; Shah P; Landerer CL; Zaretzki R
Genome Biol Evol; 2015 May; 7(6):1559-79. PubMed ID: 25977456
[TBL] [Abstract][Full Text] [Related]
9. Genes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale.
Latrille T; Rodrigue N; Lartillot N
Proc Natl Acad Sci U S A; 2023 Mar; 120(11):e2214977120. PubMed ID: 36897968
[TBL] [Abstract][Full Text] [Related]
10. Statistical properties of the branch-site test of positive selection.
Yang Z; dos Reis M
Mol Biol Evol; 2011 Mar; 28(3):1217-28. PubMed ID: 21087944
[TBL] [Abstract][Full Text] [Related]
11. Codon Usage Selection Can Bias Estimation of the Fraction of Adaptive Amino Acid Fixations.
Matsumoto T; John A; Baeza-Centurion P; Li B; Akashi H
Mol Biol Evol; 2016 Jun; 33(6):1580-9. PubMed ID: 26873577
[TBL] [Abstract][Full Text] [Related]
12. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level.
Zhang J; Nielsen R; Yang Z
Mol Biol Evol; 2005 Dec; 22(12):2472-9. PubMed ID: 16107592
[TBL] [Abstract][Full Text] [Related]
13. Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion.
Galtier N; Roux C; Rousselle M; Romiguier J; Figuet E; Glémin S; Bierne N; Duret L
Mol Biol Evol; 2018 May; 35(5):1092-1103. PubMed ID: 29390090
[TBL] [Abstract][Full Text] [Related]
14. Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril.
Wisotsky SR; Kosakovsky Pond SL; Shank SD; Muse SV
Mol Biol Evol; 2020 Aug; 37(8):2430-2439. PubMed ID: 32068869
[TBL] [Abstract][Full Text] [Related]
15. The Impact of Selection at the Amino Acid Level on the Usage of Synonymous Codons.
Błażej P; Mackiewicz D; Wnętrzak M; Mackiewicz P
G3 (Bethesda); 2017 Mar; 7(3):967-981. PubMed ID: 28122952
[TBL] [Abstract][Full Text] [Related]
16. Mutations to Less-Preferred Synonymous Codons in a Highly Expressed Gene of Escherichia coli: Fitness and Epistatic Interactions.
Hauber DJ; Grogan DW; DeBry RW
PLoS One; 2016; 11(1):e0146375. PubMed ID: 26727272
[TBL] [Abstract][Full Text] [Related]
17. Large-scale in silico mutagenesis experiments reveal optimization of genetic code and codon usage for protein mutational robustness.
Schwersensky M; Rooman M; Pucci F
BMC Biol; 2020 Oct; 18(1):146. PubMed ID: 33081759
[TBL] [Abstract][Full Text] [Related]
18. Selected codon usage bias in members of the class Mollicutes.
Iriarte A; Baraibar JD; Romero H; Musto H
Gene; 2011 Mar; 473(2):110-8. PubMed ID: 21147204
[TBL] [Abstract][Full Text] [Related]
19. Factors affecting the codon usage bias of SRY gene across mammals.
Chakraborty S; Uddin A; Choudhury MN
Gene; 2017 Sep; 630():13-20. PubMed ID: 28827114
[TBL] [Abstract][Full Text] [Related]
20. Translational selection frequently overcomes genetic drift in shaping synonymous codon usage patterns in vertebrates.
Doherty A; McInerney JO
Mol Biol Evol; 2013 Oct; 30(10):2263-7. PubMed ID: 23883522
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
