Juannan Zhou

Abstract Protein sequence-function relationships are inherently complex, as amino acids at different positions can interact in highly unpredictable ways. A key question for protein evolution and engineering is how often epistasis extends beyond pairwise interactions to involve three or more positions.

Results In this section we review how gauge freedoms arise in commonly used models of sequence-function relationships, as well as strategies commonly used to fix the gauge. In doing so, we establish notation and concepts that are used in subsequent sections. Linear models. We define quantitative models of sequence-function relationships as follows.

Abstract Unraveling complex gene interactions and understanding their functions in the genomes of bacteria will provide critical advancements in fields including bacterial genome evolution, microbiome studies, as well as drug and natural product discovery. This is a challenging problem due to the structural and functional complexity of bacterial genomes, and issues including poor gene annotation in non-model species.