A detailed overview of immune escape, antibody escape, partial vaccine escape of SARS-CoV-2 and their emerging variants with escape mutations
The infective SARS-CoV-2 is more prone to immune escape. Presently, the significant
variants of SARS-CoV-2 are emerging in due course of time with substantial mutations …
variants of SARS-CoV-2 are emerging in due course of time with substantial mutations …
Causes of evolutionary rate variation among protein sites
It has long been recognized that certain sites within a protein, such as sites in the protein
core or catalytic residues in enzymes, are evolutionarily more conserved than other sites …
core or catalytic residues in enzymes, are evolutionarily more conserved than other sites …
Fitness effects of mutations to SARS-CoV-2 proteins
Abstract Knowledge of the fitness effects of mutations to SARS-CoV-2 can inform
assessment of new variants, design of therapeutics resistant to escape, and understanding …
assessment of new variants, design of therapeutics resistant to escape, and understanding …
Moderating the neutralist–selectionist debate: exactly which propositions are we debating, and which arguments are valid?
Half a century after its foundation, the neutral theory of molecular evolution continues to
attract controversy. The debate has been hampered by the coexistence of different …
attract controversy. The debate has been hampered by the coexistence of different …
Pyvolve: a flexible Python module for simulating sequences along phylogenies
We introduce Pyvolve, a flexible Python module for simulating genetic data along a
phylogeny using continuous-time Markov models of sequence evolution. Easily incorporated …
phylogeny using continuous-time Markov models of sequence evolution. Easily incorporated …
Genes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale
Adaptation in protein-coding sequences can be detected from multiple sequence alignments
across species or alternatively by leveraging polymorphism data within a population. Across …
across species or alternatively by leveraging polymorphism data within a population. Across …
Analysis of selection in protein-coding sequences accounting for common biases
The evolution of protein-coding genes is usually driven by selective processes, which favor
some evolutionary trajectories over others, optimizing the subsequent protein stability and …
some evolutionary trajectories over others, optimizing the subsequent protein stability and …
Connecting the sequence-space of bacterial signaling proteins to phenotypes using coevolutionary landscapes
Two-component signaling (TCS) is the primary means by which bacteria sense and respond
to the environment. TCS involves two partner proteins working in tandem, which interact to …
to the environment. TCS involves two partner proteins working in tandem, which interact to …
Incorporation of transition to transversion ratio and nonsense mutations, improves the estimation of the number of synonymous and non-synonymous sites in codons
A common approach to estimate the strength and direction of selection acting on protein
coding sequences is to calculate the dN/dS ratio. The method to calculate dN/dS has been …
coding sequences is to calculate the dN/dS ratio. The method to calculate dN/dS has been …
Genome evolution in outcrossing vs. selfing vs. asexual species
A major current molecular evolution challenge is to link comparative genomic patterns to
species' biology and ecology. Breeding systems are pivotal because they affect many …
species' biology and ecology. Breeding systems are pivotal because they affect many …