Epistasis and adaptation on fitness landscapes
C Bank - Annual Review of Ecology, Evolution, and Systematics, 2022 - annualreviews.org
Epistasis occurs when the effect of a mutation depends on its carrier's genetic background.
Despite increasing evidence that epistasis for fitness is common, its role during evolution is …
Despite increasing evidence that epistasis for fitness is common, its role during evolution is …
The causes and consequences of genetic interactions (epistasis)
J Domingo, P Baeza-Centurion… - Annual review of …, 2019 - annualreviews.org
The same mutation can have different effects in different individuals. One important reason
for this is that the outcome of a mutation can depend on the genetic context in which it …
for this is that the outcome of a mutation can depend on the genetic context in which it …
Language models enable zero-shot prediction of the effects of mutations on protein function
Modeling the effect of sequence variation on function is a fundamental problem for
understanding and designing proteins. Since evolution encodes information about function …
understanding and designing proteins. Since evolution encodes information about function …
Proteingym: Large-scale benchmarks for protein fitness prediction and design
Predicting the effects of mutations in proteins is critical to many applications, from
understanding genetic disease to designing novel proteins to address our most pressing …
understanding genetic disease to designing novel proteins to address our most pressing …
Protein design and variant prediction using autoregressive generative models
JE Shin, AJ Riesselman, AW Kollasch… - Nature …, 2021 - nature.com
The ability to design functional sequences and predict effects of variation is central to protein
engineering and biotherapeutics. State-of-art computational methods rely on models that …
engineering and biotherapeutics. State-of-art computational methods rely on models that …
Epistatic drift causes gradual decay of predictability in protein evolution
Epistatic interactions can make the outcomes of evolution unpredictable, but no
comprehensive data are available on the extent and temporal dynamics of changes in the …
comprehensive data are available on the extent and temporal dynamics of changes in the …
A combinatorially complete epistatic fitness landscape in an enzyme active site
Protein engineering often targets binding pockets or active sites which are enriched in
epistasis—nonadditive interactions between amino acid substitutions—and where the …
epistasis—nonadditive interactions between amino acid substitutions—and where the …
The simplicity of protein sequence-function relationships
How complex are the rules by which a protein's sequence determines its function? High-
order epistatic interactions among residues are thought to be pervasive, suggesting an …
order epistatic interactions among residues are thought to be pervasive, suggesting an …
Molecular determinants of protein evolvability
The plethora of biological functions that sustain life is rooted in the remarkable evolvability of
proteins. An emerging view highlights the importance of a protein's initial state in dictating …
proteins. An emerging view highlights the importance of a protein's initial state in dictating …
Idiosyncratic epistasis leads to global fitness–correlated trends
Epistasis can markedly affect evolutionary trajectories. In recent decades, protein-level
fitness landscapes have revealed extensive idiosyncratic epistasis among specific …
fitness landscapes have revealed extensive idiosyncratic epistasis among specific …