The design and optimization of biological systems is an inherently complex undertaking that
requires careful balancing of myriad synergistic and antagonistic variables. However …

Abstract Design of de novo synthetic regulatory DNA is a promising avenue to control gene
expression in biotechnology and medicine. Using mutagenesis typically requires screening …

Degeneracy in the genetic code allows multiple codon sequences to encode the same
protein. Codon usage bias in genes is the term given to the preferred use of particular …

Comparative analyses of natural and mutated sequences have been used to probe
mechanisms of gene expression, but small sample sizes may produce biased outcomes. We …

Synthetic biology often involves engineering microbial strains to express high-value
proteins. Thanks to progress in rapid DNA synthesis and sequencing, deep learning has …

Advances in DNA synthesis have enabled the construction of artificial genes, gene circuits,
and genomes of bacterial scale. Freedom in de novo design of synthetic constructs provides …

Over the past few decades, Escherichia coli (E. coli) remains the most favorable host among
the microbial cell factories for the production of soluble recombinant proteins. Recombinant …

Motivation Accounting for biological and practical requirements in DNA sequence design
often results in challenging optimization problems. Current software solutions are problem …

Recombinant multiepitope proteins (RMPs) are a promising alternative for application in
diagnostic tests and, given their wide application in the most diverse diseases, this review …

The integration of multiple genes to maximize protein expression levels represents an
important challenge in synthetic biology. This task relies on the definition of multiple protein …