Deletional bias across the three domains of life
Elevated levels of genetic drift are hypothesized to be a dominant factor that influences
genome size evolution across all life-forms. However, increased levels of drift appear to be …
genome size evolution across all life-forms. However, increased levels of drift appear to be …
Identifying novel constrained elements by exploiting biased substitution patterns
Motivation: Comparing the genomes from closely related species provides a powerful tool to
identify functional elements in a reference genome. Many methods have been developed to …
identify functional elements in a reference genome. Many methods have been developed to …
Codon usage pattern and prediction of gene expression level in Bungarus species
S Chakraborty, D Nag, TH Mazumder, A Uddin - Gene, 2017 - Elsevier
Codon bias study in an organism gains significance in understanding the molecular
mechanism as well as the functional conservation of gene expression during the course of …
mechanism as well as the functional conservation of gene expression during the course of …
Genomics and conservation genetics
In large part, the relevance of genetics to conservation rests on the premise that neutral
marker variation in populations reflects levels of detrimental and adaptive genetic variation …
marker variation in populations reflects levels of detrimental and adaptive genetic variation …
scnRCA: a novel method to detect consistent patterns of translational selection in mutationally-biased genomes
PK O'Neill, M Or, I Erill - PLoS One, 2013 - journals.plos.org
Codon usage bias (CUB) results from the complex interplay between translational selection
and mutational biases. Current methods for CUB analysis apply heuristics to integrate both …
and mutational biases. Current methods for CUB analysis apply heuristics to integrate both …
Elevated rates of nonsynonymous substitution in island birds
KP Johnson, J Seger - Molecular biology and evolution, 2001 - academic.oup.com
Slightly deleterious mutations are expected to fix at relatively higher rates in small
populations than in large populations. Support for this prediction of the nearly-neutral theory …
populations than in large populations. Support for this prediction of the nearly-neutral theory …
Studying Patterns of Recent Evolution at Synonymous Sites and Intronic Sites in Drosophila melanogaster
K Zeng, B Charlesworth - Journal of Molecular Evolution, 2010 - Springer
Most previous studies of the evolution of codon usage bias (CUB) and intronic GC content
(iGC) in Drosophila melanogaster were based on between-species comparisons, reflecting …
(iGC) in Drosophila melanogaster were based on between-species comparisons, reflecting …
Correlated selection on amino acid deletion and replacement in mammalian protein sequences
Y Zheng, D Graur, RBR Azevedo - Journal of Molecular Evolution, 2018 - Springer
A low ratio of nonsynonymous and synonymous substitution rates (dN/dS) at a codon is an
indicator of functional constraint caused by purifying selection. Intuitively, the functional …
indicator of functional constraint caused by purifying selection. Intuitively, the functional …
Accuracy and power of the likelihood ratio test for comparing evolutionary rates among genes
JE Aagaard, P Phillips - Journal of molecular evolution, 2005 - Springer
Sequences for multiple protein-coding genes are now commonly available from several,
often closely related species. These data sets offer intriguing opportunities to test …
often closely related species. These data sets offer intriguing opportunities to test …
Analysis of codon usage between different poplar species
M Zhou, C Tong, J Shi - Journal of Genetics and Genomics, 2007 - Elsevier
Codon usage is the selective and nonrandom use of synonymous codons to encode amino
acids in genes for proteins. The analysis of codon usage may improve the understanding of …
acids in genes for proteins. The analysis of codon usage may improve the understanding of …