Empirical fitness landscapes and the predictability of evolution

JAGM De Visser, J Krug - Nature Reviews Genetics, 2014 - nature.com
The genotype–fitness map (that is, the fitness landscape) is a key determinant of evolution,
yet it has mostly been used as a superficial metaphor because we know little about its …

The causes of evolvability and their evolution

JL Payne, A Wagner - Nature Reviews Genetics, 2019 - nature.com
Evolvability is the ability of a biological system to produce phenotypic variation that is both
heritable and adaptive. It has long been the subject of anecdotal observations and …

Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

A Currin, N Swainston, PJ Day, DB Kell - Chemical Society Reviews, 2015 - pubs.rsc.org
The amino acid sequence of a protein affects both its structure and its function. Thus, the
ability to modify the sequence, and hence the structure and activity, of individual proteins in …

Specificity and nonspecificity in RNA–protein interactions

E Jankowsky, ME Harris - Nature reviews Molecular cell biology, 2015 - nature.com
To fully understand the regulation of gene expression, it is critical to quantitatively define
whether and how RNA-binding proteins (RBPs) discriminate between alternative binding …

Methods for improving aptamer binding affinity

H Hasegawa, N Savory, K Abe, K Ikebukuro - Molecules, 2016 - mdpi.com
Aptamers are single stranded oligonucleotides that bind a wide range of biological targets.
Although aptamers can be isolated from pools of random sequence oligonucleotides using …

Towards a unifying, systems biology understanding of large-scale cellular death and destruction caused by poorly liganded iron: Parkinson's, Huntington's …

DB Kell - Archives of toxicology, 2010 - Springer
Exposure to a variety of toxins and/or infectious agents leads to disease, degeneration and
death, often characterised by circumstances in which cells or tissues do not merely die and …

A rugged yet easily navigable fitness landscape

A Papkou, L Garcia-Pastor, JA Escudero, A Wagner - Science, 2023 - science.org
Fitness landscape theory predicts that rugged landscapes with multiple peaks impair
Darwinian evolution, but experimental evidence is limited. In this study, we used genome …

[HTML][HTML] From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics

S Manrubia, JA Cuesta, J Aguirre, SE Ahnert… - Physics of Life …, 2021 - Elsevier
Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is
arguably the next major missing piece in a fully predictive theory of evolution. We refer to this …

Evolutionary accessibility of mutational pathways

J Franke, A Klözer, JAGM de Visser… - PLoS computational …, 2011 - journals.plos.org
Functional effects of different mutations are known to combine to the total effect in highly
nontrivial ways. For the trait under evolutionary selection ('fitness'), measured values over all …

The robustness and evolvability of transcription factor binding sites

JL Payne, A Wagner - Science, 2014 - science.org
Robustness, the maintenance of a character in the presence of genetic change, can help
preserve adaptive traits but also may hinder evolvability, the ability to bring forth novel …