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Codon usage bias
Codon usage bias is the preferential or non-random use of synonymous codons, a
ubiquitous phenomenon observed in bacteria, plants and animals. Different species have …
ubiquitous phenomenon observed in bacteria, plants and animals. Different species have …
Translational regulation by uORFs and start codon selection stringency
In addition to the main, protein-coding, open reading frame (mORF), many eukaryotic
mRNAs contain upstream ORFs (uORFs) initiated at AUG or near-cognate codons residing …
mRNAs contain upstream ORFs (uORFs) initiated at AUG or near-cognate codons residing …
DNA language models are powerful predictors of genome-wide variant effects
The expanding catalog of genome-wide association studies (GWAS) provides biological
insights across a variety of species, but identifying the causal variants behind these …
insights across a variety of species, but identifying the causal variants behind these …
Controlling gene expression with deep generative design of regulatory DNA
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 …
expression in biotechnology and medicine. Using mutagenesis typically requires screening …
Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure
Understanding the genetic regulatory code governing gene expression is an important
challenge in molecular biology. However, how individual coding and non-coding regions of …
challenge in molecular biology. However, how individual coding and non-coding regions of …
Orthotopic replacement of T-cell receptor α-and β-chains with preservation of near-physiological T-cell function
Therapeutic T cells with desired specificity can be engineered by introducing T-cell
receptors (TCRs) specific for antigens of interest, such as those from pathogens or tumour …
receptors (TCRs) specific for antigens of interest, such as those from pathogens or tumour …
Non-canonical translation in RNA viruses
Viral protein synthesis is completely dependent upon the translational machinery of the host
cell. However, many RNA virus transcripts have marked structural differences from cellular …
cell. However, many RNA virus transcripts have marked structural differences from cellular …
Deep learning of the regulatory grammar of yeast 5′ untranslated regions from 500,000 random sequences
Our ability to predict protein expression from DNA sequence alone remains poor, reflecting
our limited understanding of cis-regulatory grammar and hampering the design of …
our limited understanding of cis-regulatory grammar and hampering the design of …
EasyClone: method for iterative chromosomal integration of multiple genes Saccharomyces cerevisiae
Abstract Development of strains for efficient production of chemicals and pharmaceuticals
requires multiple rounds of genetic engineering. In this study, we describe construction and …
requires multiple rounds of genetic engineering. In this study, we describe construction and …
What, where, and how: regulation of translation and the translational landscape in plants
Translation is a crucial step in gene expression and plays a vital role in regulating various
aspects of plant development and environmental responses. It is a dynamic and complex …
aspects of plant development and environmental responses. It is a dynamic and complex …