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Mutational Bias and Natural Selection Driving the Synonymous Codon Usage of Single-Exon Genes in Rice (Oryza sativa L.)
The relative abundance of single-exon genes (SEGs) in higher plants is perplexing. Uncovering the synonymous codon usage pattern of SEGs will benefit...
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Multivariate selection and the making and breaking of mutational pleiotropy
The role of mutations have been subject to many controversies since the formation of the Modern Synthesis of evolution in the early 1940ties....
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Transcriptional and mutational signatures of the Drosophila ageing germline
Ageing is a complex biological process that is accompanied by changes in gene expression and mutational load. In many species, including humans,...
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Identification of multiplicatively acting modulatory mutational signatures in cancer
BackgroundA deep understanding of carcinogenesis at the DNA level underpins many advances in cancer prevention and treatment. Mutational signatures...
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The Memory Problem for Neutral Mutational Models of Evolution
Models for the evolution of various phenotypes are sometimes constructed with an assumption that mutational effects will be symmetrically distributed...
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Incorporating mutational heterogeneity to identify genes that are enriched for synonymous mutations in cancer
BackgroundSynonymous mutations, which change the DNA sequence but not the encoded protein sequence, can affect protein structure and function, mRNA...
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Model selection and robust inference of mutational signatures using Negative Binomial non-negative matrix factorization
BackgroundThe spectrum of mutations in a collection of cancer genomes can be described by a mixture of a few mutational signatures. The mutational...
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Integrative analysis of mutated genes and mutational processes reveals novel mutational biomarkers in colorectal cancer
BackgroundColorectal cancer (CRC) is one of the leading causes of cancer-related deaths worldwide. Recent studies have observed causative mutations...
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Spontaneous mutations and mutational responses to penicillin treatment in the bacterial pathogen Streptococcus pneumoniae D39
Bacteria with functional DNA repair systems are expected to have low mutation rates due to strong natural selection for genomic stability. However,...
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Comparative analysis of codon usage bias in chloroplast genomes of ten medicinal species of Rutaceae
Rutaceae family comprises economically important plants due to their extensive applications in spices, food, oil, medicine, etc. The Rutaceae plants...
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Rosace : a robust deep mutational scanning analysis framework employing position and mean-variance shrinkageDeep mutational scanning (DMS) measures the effects of thousands of genetic variants in a protein simultaneously. The small sample size renders...
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The mutational dynamics of short tandem repeats in large, multigenerational families
BackgroundShort tandem repeats (STRs) compose approximately 3% of the genome, and mutations at STR loci have been linked to dozens of human diseases...
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MutationalPatterns: the one stop shop for the analysis of mutational processes
BackgroundThe collective of somatic mutations in a genome represents a record of mutational processes that have been operative in a cell. These...
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Analysis of chloroplast genome characteristics and codon usage bias in 14 species of Annonaceae
For the study of species evolution, chloroplast gene expression, and transformation, the chloroplast genome is an invaluable resource. Codon usage...
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Analysis of codon usage bias of WRKY transcription factors in Helianthus annuus
BackgroundThe phenomenon of codon usage bias is known to exist in many genomes and is mainly determined by mutation and selection. Codon usage bias...
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MSA: reproducible mutational signature attribution with confidence based on simulations
BackgroundMutational signatures proved to be a useful tool for identifying patterns of mutations in genomes, often providing valuable insights about...
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Codon usage bias analysis of mitochondrial protein-coding genes in 12 species of Candida
The incidence of diseases that are caused by fungal infection is gradually increasing, together with antibiotic abuse and the number of patients with...
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Codon usage bias analysis of the gene encoding NAD+-dependent DNA ligase protein of Invertebrate iridescent virus 6
The genome of Invertebrate iridescent virus 6 (IIV6) contains a sequence that shows similarity to eubacterial NAD + -dependent DNA ligases. The...
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Codon usage bias
Codon usage bias is the preferential or non-random use of synonymous codons, a ubiquitous phenomenon observed in bacteria, plants and animals....
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Microfluidic deep mutational scanning of the human executioner caspases reveals differences in structure and regulation
The human caspase family comprises 12 cysteine proteases that are centrally involved in cell death and inflammation responses. The members of this...
