Ancestral sequence reconstruction for protein engineers
In addition to its value in the study of molecular evolution, ancestral sequence reconstruction
(ASR) has emerged as a useful methodology for engineering proteins with enhanced …
(ASR) has emerged as a useful methodology for engineering proteins with enhanced …
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 …
Consequences of substitution model selection on protein ancestral sequence reconstruction
The selection of the best-fitting substitution model of molecular evolution is a traditional step
for phylogenetic inferences, including ancestral sequence reconstruction (ASR). However, a …
for phylogenetic inferences, including ancestral sequence reconstruction (ASR). However, a …
Accuracy of ancestral state reconstruction for non-neutral traits
BR Holland, S Ketelaar-Jones, AR o'Mara… - Scientific Reports, 2020 - nature.com
The assumptions underpinning ancestral state reconstruction are violated in many
evolutionary systems, especially for traits under directional selection. However, the accuracy …
evolutionary systems, especially for traits under directional selection. However, the accuracy …
Ancestral sequence reconstruction: from chemical paleogenetics to maximum likelihood algorithms and beyond
As both a computational and an experimental endeavor, ancestral sequence reconstruction
remains a timely and important technique. Modern approaches to conduct ancestral …
remains a timely and important technique. Modern approaches to conduct ancestral …
The evolution of gene regulatory networks controlling Arabidopsis thaliana L. trichome development
Background The variation in structure and function of gene regulatory networks (GRNs)
participating in organisms development is a key for understanding species-specific …
participating in organisms development is a key for understanding species-specific …
Evolution of protein structure and stability in global warming
S Barik - International Journal of Molecular Sciences, 2020 - mdpi.com
This review focuses on the molecular signatures of protein structures in relation to evolution
and survival in global warming. It is based on the premise that the power of evolutionary …
and survival in global warming. It is based on the premise that the power of evolutionary …
ProtASR2: ancestral reconstruction of protein sequences accounting for folding stability
The ancestral sequence reconstruction (ASR) is a molecular evolution technique that
provides applications to a variety of fields such as biotechnology and biomedicine. To infer …
provides applications to a variety of fields such as biotechnology and biomedicine. To infer …
[HTML][HTML] Ancestral sequence reconstruction-An underused approach to understand the evolution of gene function in plants?
Whilst substantial research effort has been placed on understanding the interactions of plant
proteins with their molecular partners, relatively few studies in plants-by contrast to work in …
proteins with their molecular partners, relatively few studies in plants-by contrast to work in …
Ancestral reconstruction reveals catalytic inactivation of activation-induced cytidine deaminase concomitant with cold water adaption in the Gadiformes bony fish
A Ghorbani, SJ Khataeipour, MH Solbakken… - BMC biology, 2022 - Springer
Background Antibody affinity maturation in vertebrates requires the enzyme activation-
induced cytidine deaminase (AID) which initiates secondary antibody diversification by …
induced cytidine deaminase (AID) which initiates secondary antibody diversification by …