Codon usage bias

ST Parvathy, V Udayasuriyan, V Bhadana - Molecular biology reports, 2022 - Springer
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 …

Translational regulation by uORFs and start codon selection stringency

TE Dever, IP Ivanov, AG Hinnebusch - Genes & development, 2023 - genesdev.cshlp.org
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 …

DNA language models are powerful predictors of genome-wide variant effects

G Benegas, SS Batra, YS Song - Proceedings of the National Academy of …, 2023 - pnas.org
The expanding catalog of genome-wide association studies (GWAS) provides biological
insights across a variety of species, but identifying the causal variants behind these …

Controlling gene expression with deep generative design of regulatory DNA

J Zrimec, X Fu, AS Muhammad, C Skrekas… - Nature …, 2022 - nature.com
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 …

Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure

J Zrimec, CS Börlin, F Buric, AS Muhammad… - Nature …, 2020 - nature.com
Understanding the genetic regulatory code governing gene expression is an important
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

K Schober, TR Müller, F Gökmen… - Nature biomedical …, 2019 - nature.com
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 …

Non-canonical translation in RNA viruses

AE Firth, I Brierley - Journal of General Virology, 2012 - microbiologyresearch.org
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 …

Deep learning of the regulatory grammar of yeast 5′ untranslated regions from 500,000 random sequences

JT Cuperus, B Groves, A Kuchina… - Genome …, 2017 - genome.cshlp.org
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 …

EasyClone: method for iterative chromosomal integration of multiple genes Saccharomyces cerevisiae

NB Jensen, T Strucko, KR Kildegaard… - FEMS yeast …, 2014 - academic.oup.com
Abstract Development of strains for efficient production of chemicals and pharmaceuticals
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

HYL Wu, J Jen, PY Hsu - The Plant Cell, 2024 - academic.oup.com
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 …