Compensatory epistasis maintains ACE2 affinity in SARS-CoV-2 Omicron BA. 1
The Omicron BA. 1 variant emerged in late 2021 and quickly spread across the world.
Compared to the earlier SARS-CoV-2 variants, BA. 1 has many mutations, some of which …
Compared to the earlier SARS-CoV-2 variants, BA. 1 has many mutations, some of which …
[HTML][HTML] From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics
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 …
arguably the next major missing piece in a fully predictive theory of evolution. We refer to this …
Statistically learning the functional landscape of microbial communities
Microbial consortia exhibit complex functional properties in contexts ranging from soils to
bioreactors to human hosts. Understanding how community composition determines …
bioreactors to human hosts. Understanding how community composition determines …
Evolution of high-level resistance during low-level antibiotic exposure
E Wistrand-Yuen, M Knopp, K Hjort… - Nature …, 2018 - nature.com
It has become increasingly clear that low levels of antibiotics present in many environments
can select for resistant bacteria, yet the evolutionary pathways for resistance development …
can select for resistant bacteria, yet the evolutionary pathways for resistance development …
High throughput and quantitative enzymology in the genomic era
Accurate predictions from models based on physical principles are the ultimate metric of our
biophysical understanding. Although there has been stunning progress toward structure …
biophysical understanding. Although there has been stunning progress toward structure …
The simplicity of protein sequence-function relationships
How complex are the rules by which a protein's sequence determines its function? High-
order epistatic interactions among residues are thought to be pervasive, suggesting an …
order epistatic interactions among residues are thought to be pervasive, suggesting an …
Learning the pattern of epistasis linking genotype and phenotype in a protein
FJ Poelwijk, M Socolich, R Ranganathan - Nature communications, 2019 - nature.com
Understanding the pattern of epistasis—the non-independence of mutations—is critical for
relating genotype and phenotype. However, the combinatorial complexity of potential …
relating genotype and phenotype. However, the combinatorial complexity of potential …
Pervasive epistasis exposes intramolecular networks in adaptive enzyme evolution
Enzyme evolution is characterized by constant alterations of the intramolecular residue
networks supporting their functions. The rewiring of these network interactions can give rise …
networks supporting their functions. The rewiring of these network interactions can give rise …
Interpreting cis-regulatory mechanisms from genomic deep neural networks using surrogate models
Deep neural networks (DNNs) have greatly advanced the ability to predict genome function
from sequence. However, elucidating underlying biological mechanisms from genomic …
from sequence. However, elucidating underlying biological mechanisms from genomic …
Evolution-based functional decomposition of proteins
O Rivoire, KA Reynolds… - PLoS computational …, 2016 - journals.plos.org
The essential biological properties of proteins—folding, biochemical activities, and the
capacity to adapt—arise from the global pattern of interactions between amino acid …
capacity to adapt—arise from the global pattern of interactions between amino acid …