Epistasis as the primary factor in molecular evolution

By M. Breen, Carsten Kemena, P. Vlasov, Cédric Notredame, Fyodor A. Kondrashov. 2012

379 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Computational Biology & Bioinformatics

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Citations in the corpus

Evolutionary context-integrated deep sequence modeling for protein engineering (2020, background): “Evidence has shown that mutations within the sequence can have non-independent effects (epistasis) on fitness [43,55] .”
Low-N protein engineering with data-efficient deep learning (2020, background): “Not only is this an arduous task due to the essential role of epistasis in proteins 49,50 , but also TEM-1 β -lactamase is dissimilar to avGFP both evolutionarily (Eukaryotic vs. Prokaryotic) and functionally (fluorescence vs. hydrolysis).”
Epistasis and the Dynamics of Reversion in Molecular Evolution (2016, methodology): “This example is motivated by the model used by Kondrashov and colleagues to study long-term purifying selection (Breen et al. 2012; Usmanova et al. 2015).”
A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness (2014, background): “The remainder of the context-dependence should reside in higher order terms that explicitly represent epistatic interactions with other mutations (Breen et al. 2012).”
Patterns of Epistasis between Beneficial Mutations in an Antibiotic Resistance Gene (2013, background): “The relatively slow rate of expansion of the “protein universe” (Povoltskaya and Kondrashov 2010) and discrepancy between long and short-term amino acid substitution rates (Breen et al. 2012) also suggest constraints from sign epistasis in protein evolution.”
DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment (2015, background): “A multiple sequence alignment may reveal many aspects about a gene: which regions are constrained, which sites undergo positive selection [5], and potentially the structure of its gene product [6].”
Systematic Mapping of Protein Mutational Space by Prolonged Drift Reveals the Deleterious Effects of Seemingly Neutral Mutations (2015, background): “Exchanges in highly diverged orthologs are tolerated by virtue of being compensated by exchanges at other positions [41, 45, 67] and therefore tend to be context-specific.”