Epistasis

Fitness landscapes largely shape the dynamics of evolution, but it is unclear how they shift upon ecological diversification. By engineering genome-wide knockout libraries of a nascent bacterial community, Ascensao et al. show how ecological and epistatic patterns combine to shape adaptive landscapes.

An open-source framework combines deep learning and permutations of gene interaction neural networks to detect complex gene–gene interactions and their significance in contributions to phenotypes.

Pan-genome analyses of clinical pneumococcal strains identify categories of essential genes and show that gene essentiality depends on strain genetic background.

The bacterium E. coli has around 300 transcriptional factors, but the functions of many of them, and the interactions between their respective regulatory networks, are unclear. Here, the authors study genetic interactions among all transcription factor genes in E. coli, revealing condition-dependent interactions and roles for uncharacterized transcription factors.

Epistasis can lead to different phenotypic consequences from the same mutation. Here the authors carry out a genome-wide analysis of conditionally essential genes in yeast, finding that gene essentiality changes tend to occur concordantly among components of the same protein complex or metabolic pathway.