Mechanistic approaches to the study of evolution: the functional synthesis

By A. Dean, Joseph W. Thornton. 2007

346 citations recorded by the source corpus.

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Citations in the corpus

Exploring protein fitness landscapes by directed evolution (2009, positive): “These experimental results allow us to look at sequence data in a functional context, providing a bridge between long-separated fields of evolutionary and molecular biolog”
Systematic exploration of ubiquitin sequence, E1 activation efficiency, and experimental fitness in yeast (2014, background): “…deciphering how this blueprint leads to biological function is challenging due in large part to Systematic investigations of the relationships between gene or protein sequence, function and fitness provide new opportunities to bridge molecular, systems, and evolutionary biology 15; 16; 17; 18 .”
Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution (2008, positive): “Recent work has revealed the molecular basis of organism-level adaptations by drawing upon phylogenetic information to infer, recreate, and functionally interrogate the sequences of evolving proteins (Dean and Thornton, 2007), such as receptors bound by distinct ligands (Bridgham et al.”
Constraints Evolve: Context Dependency of Gene Effects Allows Evolution of Pleiotropy (2015, background): “We think that the next big challenge in evolutionary biology is the integration of well-studied variational concepts with mechanistic detail, in a systems-oriented approach (Dean & Thornton 2007).”
Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding (2020, neutral): “Fitness ultimately arises from the concerted action of biochemical phenotypes, which are in turn determined by genotype (Dean and Thornton, 2007; Harms and Thornton, 2013; Russell et al., 2014).”
Neutralism and selectionism: a network-based reconciliation (2008, background): “L111Q followed by S106P yields a receptor that is still sensitive to cortisol but that is 1,000-fold less sensitive to aldosteron”
Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding (2020, neutral): “Furthermore, fitness ultimately arises from the concerted action of biochemical phenotypes, which are in turn determined by genotype (Dean and Thornton, 2007; Harms and Thornton, 2013; Russell et al., 2014).”
Should evolutionary geneticists worry about higher-order epistasis? (2013, background): “This work has further stimulated study of the underlying molecular mechanisms of epistasis [32,34,35,36 ] as well as epistasis across environments [37 ,38] and epistatic opportunities for evolutionary reversions [32,37 ].”
Capturing the mutational landscape of the beta-lactamase TEM-1 (2013, background): “For population genetics purposes, the shape of the DFE is in itself fully informative, yet from a genetics point of view, the large-scale analysis of mutants required to compute a DFE may also be used to uncover the mechanistic determinants of mutation effects on fitness (6, 7).”