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Large-Scale Comparative Analysis of Codon Models Accounting for Protein and Nucleotide Selection

https://doi.org/10.1101/174839
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Drosophila melanogaster recombination rate calculator
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Increased rate of human mutations where DNA and RNA polymerases collide
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Positive diversifying selection is a pervasive adaptive force throughout the Drosophila radiation
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Human SNP variability and mutation rate are higher in regions of high recombination
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Statistical methods for detecting molecular adaptation
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Neutral effect of recombination on base composition in Drosophila
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Impact of translational error‐induced and error‐free misfolding on the rate of protein evolution
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Efficient translation initiation dictates codon usage at gene start
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Evolution of genes and genomes on the Drosophila phylogeny
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Genome-wide measurement of RNA secondary structure in yeast
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Rate of de novo mutations and the importance of father’s age to disease risk
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Comparative population genomics in animals uncovers the determinants of genetic diversity
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Differential DNA mismatch repair underlies mutation rate variation across the human genome
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How sexual selection can drive the evolution of costly sperm ornamentation
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Human mutation rate associated with DNA replication timing
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Fine-scale recombination patterns differ between chimpanzees and humans
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Hearing silence: non-neutral evolution at synonymous sites in mammals
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An integrated view of protein evolution
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Constraints and plasticity in genome and molecular-phenome evolution
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Synonymous but not the same: the causes and consequences of codon bias
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Variation in the mutation rate across mammalian genomes
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Listening to silence and understanding nonsense: exonic mutations that affect splicing
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Wolbachia: master manipulators of invertebrate biology
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Multinucleotide mutations cause false inferences of lineage-specific positive selection
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Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution
inferredcites →https://doi.org/10.1073/pnas.0504070102openalex-snapshot
Why highly expressed proteins evolve slowly
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Conservation and relative importance of residues across protein-protein interfaces
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Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics
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A Neutral Explanation for the Correlation of Diversity with Recombination Rates in Humans
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Molecular Evolution
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Detection and analysis of conservation at synonymous sites
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HyPhy: hypothesis testing using phylogenies
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Robust inference of positive selection from recombining coding sequences
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TimeTree: a public knowledge-base of divergence times among organisms
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Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates
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Bayesian evolutionary model testing in the phylogenomics era: matching model complexity with computational efficiency
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State aggregation for fast likelihood computations in molecular evolution
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The Effect of Variation in the Effective Population Size on the Rate of Adaptive Molecular Evolution in Eukaryotes
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The selection-mutation-drift theory of synonymous codon usage.
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Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites
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Highly Expressed Genes in Yeast Evolve Slowly
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In VivoIntroduction of Unpreferred Synonymous Codons Into the DrosophilaAdhGene Results in Reduced Levels of ADH Protein
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Effect of Recombination on the Accuracy of the Likelihood Method for Detecting Positive Selection at Amino Acid Sites
inferredcites →https://doi.org/10.1093/hmg/ddl046openalex-snapshot
Non-coding RNA
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An Analysis of Determinants of Amino Acids Substitution Rates in Bacterial Proteins
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A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process
inferredcites →https://doi.org/10.1093/molbev/msh134openalex-snapshot
The Genomic Rate of Adaptive Amino Acid Substitution in Drosophila
inferredcites →https://doi.org/10.1093/molbev/msi097openalex-snapshot
Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection
inferredcites →https://doi.org/10.1093/molbev/msi232openalex-snapshot
Site-to-Site Variation of Synonymous Substitution Rates
inferredcites →https://doi.org/10.1093/molbev/msi237openalex-snapshot
Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level
inferredcites →https://doi.org/10.1093/molbev/msq115openalex-snapshot
The Effect of Insertions, Deletions, and Alignment Errors on the Branch-Site Test of Positive Selection
inferredcites →https://doi.org/10.1093/molbev/msq303openalex-snapshot
Statistical Properties of the Branch-Site Test of Positive Selection
inferredcites →https://doi.org/10.1093/molbev/msr125openalex-snapshot
A Random Effects Branch-Site Model for Detecting Episodic Diversifying Selection
inferredcites →https://doi.org/10.1093/molbev/msr162openalex-snapshot
Evolutionary Models Accounting for Layers of Selection in Protein-Coding Genes and their Impact on the Inference of Positive Selection
inferredcites →https://doi.org/10.1093/molbev/mst034openalex-snapshot
CodonPhyML: Fast Maximum Likelihood Phylogeny Estimation under Codon Substitution Models
inferredcites →https://doi.org/10.1093/molbev/mst062openalex-snapshot
The Branch-Site Test of Positive Selection Is Surprisingly Robust but Lacks Power under Synonymous Substitution Saturation and Variation in GC
inferredcites →https://doi.org/10.1093/molbev/msu056openalex-snapshot
The Relation between Recombination Rate and Patterns of Molecular Evolution and Variation in Drosophila melanogaster
inferredcites →https://doi.org/10.1093/molbev/msv035openalex-snapshot
Gene-Wide Identification of Episodic Selection
inferredcites →https://doi.org/10.1093/molbev/msx083openalex-snapshot
Detection of Pathways Affected by Positive Selection in Primate Lineages Ancestral to Humans
inferredcites →https://doi.org/10.1093/molbev/msx199openalex-snapshot
Selective Constraints on Coding Sequences of Nervous System Genes Are a Major Determinant of Duplicate Gene Retention in Vertebrates
inferredcites →https://doi.org/10.1093/molbev/msy164openalex-snapshot
Nearly Neutral Evolution across the Drosophila melanogaster Genome
inferredcites →https://doi.org/10.1093/nar/gkq443openalex-snapshot
GUIDANCE: a web server for assessing alignment confidence scores
inferredcites →https://doi.org/10.1093/nar/gkt1065openalex-snapshot
Selectome update: quality control and computational improvements to a database of positive selection
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a003886openalex-snapshot
Local Rates of Recombination Are Positively Correlated with GC Content in the Human Genome
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a004148openalex-snapshot
Codon-Substitution Models for Detecting Molecular Adaptation at Individual Sites Along Specific Lineages
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026420openalex-snapshot
Cytosine Deamination Plays a Primary Role in the Evolution of Mammalian Isochores
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040152openalex-snapshot
A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome.
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A codon-based model of nucleotide substitution for protein-coding DNA sequences.
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New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
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Detecting positive selection within genomes: the problem of biased gene conversion
inferredcites →https://doi.org/10.1101/gr.074187.107openalex-snapshot
Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals
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Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes
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Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines
inferredcites →https://doi.org/10.1101/gr.115949.110openalex-snapshot
High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes
inferredcites →https://doi.org/10.1101/gr.170100.113openalex-snapshot
Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data
inferredcites →https://doi.org/10.1101/gr.185488.114openalex-snapshot
Quantification of GC-biased gene conversion in the human genome
inferredcites →https://doi.org/10.1101/gr.606402openalex-snapshot
Distribution and Characterization of Regulatory Elements in the Human Genome
inferredcites →https://doi.org/10.1111/ele.12423openalex-snapshot
Fossil‐based comparative analyses reveal ancient marine ancestry erased by extinction in ray‐finned fishes
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Strong Control, Conservative Point Estimation and Simultaneous Conservative Consistency of False Discovery Rates: A Unified Approach
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Phylogenetic analysis and a time tree for a large drosophilid data set (Diptera: Drosophilidae)
inferredcites →https://doi.org/10.1126/science.1170160openalex-snapshot
Coding-Sequence Determinants of Gene Expression in Escherichia coli
inferredcites →https://doi.org/10.1126/science.1234070openalex-snapshot
Multiple Instances of Ancient Balancing Selection Shared Between Humans and Chimpanzees
inferredcites →https://doi.org/10.1126/science.1251385openalex-snapshot
Comparative genomics reveals insights into avian genome evolution and adaptation
inferredcites →https://doi.org/10.1146/annurev-genom-031714-125740openalex-snapshot
Determinants of Mutation Rate Variation in the Human Germline
inferredcites →https://doi.org/10.1146/annurev-genom-082908-150001openalex-snapshot
Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes
inferredcites →https://doi.org/10.12688/f1000research.9973.2openalex-snapshot
BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests
inferredcites →https://doi.org/10.1371/journal.pbio.0030042openalex-snapshot
Evidence for Widespread Degradation of Gene Control Regions in Hominid Genomes
inferredcites →https://doi.org/10.1371/journal.pgen.1000083openalex-snapshot
Assessing the Evolutionary Impact of Amino Acid Mutations in the Human Genome
inferredcites →https://doi.org/10.1371/journal.pgen.1000144openalex-snapshot
Patterns of Positive Selection in Six Mammalian Genomes
inferredcites →https://doi.org/10.1371/journal.pgen.1002905openalex-snapshot
The Many Landscapes of Recombination in Drosophila melanogaster
inferredcites →https://doi.org/10.1371/journal.pgen.1006024openalex-snapshot
Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States
inferredcites →https://doi.org/10.1371/journal.pone.0095034openalex-snapshot
Unraveling Patterns of Site-to-Site Synonymous Rates Variation and Associated Gene Properties of Protein Domains and Families
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Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse
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A Cellular Basis for Wolbachia Recruitment to the Host Germline
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Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation
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Selective and Mutational Patterns Associated With Gene Expression in Humans
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A Comparison of One-Rate and Two-Rate Inference Frameworks for Site-Specific dN/ dS Estimation
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A Heteroskedasticity-Consistent Covariance Matrix Estimator and a Direct Test for Heteroskedasticity
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Letter to the Editor
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AIC model selection using Akaike weights
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Gene Tree Affects Inference of Sites under Selection by the Branch-Site Test of Positive Selection

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1093/molbev/msad150openalex-snapshot
Evolutionary Shortcuts via Multinucleotide Substitutions and Their Impact on Natural Selection Analyses
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Distribuição de espécies e patógenos
inferred← citeshttps://doi.org/10.47749/t/unicamp.2022.1239437openalex-snapshot
Molecular evolution of adaptive immune system genes in aquatic mammals
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