The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology

TE Sandberg, MJ Salazar, LL Weng, BO Palsson… - Metabolic …, 2019‏ - Elsevier
Harnessing the process of natural selection to obtain and understand new microbial
phenotypes has become increasingly possible due to advances in culturing techniques …

Mechanisms and concepts in RNA virus population dynamics and evolution

PT Dolan, ZJ Whitfield, R Andino - Annual Review of Virology, 2018‏ - annualreviews.org
RNA viruses are unique in their evolutionary capacity, exhibiting high mutation rates and
frequent recombination. They rapidly adapt to environmental changes, such as shifts in …

[HTML][HTML] Population immunity predicts evolutionary trajectories of SARS-CoV-2

M Meijers, D Ruchnewitz, J Eberhardt, M Łuksza… - Cell, 2023‏ - cell.com
The large-scale evolution of the SARS-CoV-2 virus has been marked by rapid turnover of
genetic clades. New variants show intrinsic changes, notably increased transmissibility, and …

The landscape of antibody binding affinity in SARS-CoV-2 Omicron BA. 1 evolution

A Moulana, T Dupic, AM Phillips, J Chang, AA Roffler… - Elife, 2023‏ - elifesciences.org
The Omicron BA. 1 variant of SARS-CoV-2 escapes convalescent sera and monoclonal
antibodies that are effective against earlier strains of the virus. This immune evasion is …

Steering and controlling evolution—from bioengineering to fighting pathogens

M Lässig, V Mustonen, A Nourmohammad - Nature Reviews Genetics, 2023‏ - nature.com
Control interventions steer the evolution of molecules, viruses, microorganisms or other cells
towards a desired outcome. Applications range from engineering biomolecules and …

Binding affinity landscapes constrain the evolution of broadly neutralizing anti-influenza antibodies

AM Phillips, KR Lawrence, A Moulana, T Dupic… - Elife, 2021‏ - elifesciences.org
Over the past two decades, several broadly neutralizing antibodies (bnAbs) that confer
protection against diverse influenza strains have been isolated. Structural and biochemical …

Protein ensembles link genotype to phenotype

R Nussinov, CJ Tsai, H Jang - PLoS computational biology, 2019‏ - journals.plos.org
Classically, phenotype is what is observed, and genotype is the genetic makeup. Statistical
studies aim to project phenotypic likelihoods of genotypic patterns. The traditional genotype …

Mutational biases favor complexity increases in protein interaction networks after gene duplication

AF Cisneros, L Nielly-Thibault, S Mallik… - Molecular Systems …, 2024‏ - embopress.org
Biological systems can gain complexity over time. While some of these transitions are likely
driven by natural selection, the extent to which they occur without providing an adaptive …

[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 …

Viral evolution shaped by host proteostasis networks

J Yoon, JE Patrick, CB Ogbunugafor… - Annual review of …, 2023‏ - annualreviews.org
Understanding the factors that shape viral evolution is critical for develo** effective
antiviral strategies, accurately predicting viral evolution, and preventing pandemics. One …