RNA and protein synthesis mechanisms

This paper applies directed evolution to codon space, improving recombinant expression of 74% of tested therapeutics without altering protein sequence.

This paper investigates the role of the β-hairpin loop in the SUI1 domain of DENR/Tma22p in yeast, showing its critical function in ribosome recycling and reinitiation.

The paper shows that synthesis cost minimization drives convergent amino acid changes in plastid ribosomal proteins across plant lineages with relaxed selection.

The paper identifies hidden open reading frames in plasmids using eGFP as a model, finding 6% of constructs contain hidden ORFs, mostly in the +2 frame.

This study shows that the eIF4B RRM regulates stress granule assembly and translational repression during oxidative stress.

This study investigates how different tRNA mutations lead to varied toxic phenotypes across organisms, finding that amino acid property changes and mistranslation frequency are key factors.

The paper develops a hydrogen-bond correction to improve RNA force fields' accuracy in modeling noncanonical motifs like the MAPT A-bulge.

The paper identifies isoaspartate modification of ribosomal protein uS11 as essential for ribosome biogenesis and function across all domains of life.

The paper shows that timing of metabolomics-driven supplementation in E. coli-based cell-free systems affects protein expression, with optimal timing after the inflection point of metabolic activity.

This study identifies SERBP1 as a regulator of ribosome interactions, showing its role in modulating factors involved in mRNA degradation, translational control, and ribosome quality control.

The paper identifies an enzymatic pathway for isoaspartate formation in bacterial ribosomal protein uS11, showing its conservation and structural importance.

This paper develops a method to control gene expression by selectively caging mRNAs with glyoxal, enabling tunable and time-dependent regulation.

The paper identifies DCP2 as an ISR-induced transcript whose translation is regulated by an overlapping ORF that acts as an inhibitory element, which is relieved during stress.

UTR-Diffusion is a diffusion model for designing 5-prime UTR and UTR-CDS junctions that optimizes translation efficiency, RNA stability, and codon adaptation while preserving sequence constraints.

The paper compares codon usage bias between oncogenes and tumor suppressor genes in humans and mice, finding distinct patterns in humans and less distinct in mice.

The paper develops a generalized growth law to predict antibiotic interactions by integrating single-drug responses and showing how different antibiotics affect ribosome levels and growth.

CodonMamba is a foundation model for mRNA coding sequence design that achieves state-of-the-art performance and enables programmable codon optimization through inference-time steering.

The paper shows that mRNA concentration-dependent translation allows Drosophila embryos to create sharp protein patterns despite limited resources.

The paper introduces a method to quantify tRNA in low-input samples using RNA-dependent RNA amplification with T7 polymerase, showing reproducible and quantitative results.

This study identifies NEDDylation as a mechanism stabilizing eIF3g and eIF3i during stress, linking the NEDD8 pathway to SG localization and translation reinitiation.

This study compares enhanced sampling methods for RNA conformational sampling, finding T-REMD provides the most accurate ensembles and improves virtual screening.

The paper introduces Mountain Centroid, a method for representing RNA structural ensembles as single secondary structures, showing improved performance over existing methods in certain metrics.

This study identifies RTTN's role in ribosome biogenesis and tRNA modification in human brain organoids, showing mutations disrupt translation and cause cortical malformations.

The paper identifies translation-restricted uORFs in the human genome that act as sequence-intrinsic barriers to protein production, showing they are under purifying selection as cis-regulatory elements.

RIFT-VAE improves RNA inverse folding by combining grammar-conditioned pretraining with latent-space optimization, achieving high structural recovery on benchmark datasets.

NACraft generates high-confidence nucleic-acid aptamers for diverse protein targets using a programmatic framework with structure-model feedback, outperforming existing methods in several evaluations.

The paper uses statistical analysis to uncover growth tradeoffs in E. coli and S. pombe by identifying gene sectors and modeling transcription-translation constraints.

This paper introduces DuetRNA, a dual-frame flow matching model for RNA co-design that improves sequence-structure generation by jointly modeling base-and-sugar frames.

The paper uses sparse autoencoders to analyze BiRNA-BERT, revealing biologically meaningful features and improving RNA-type classification.

The paper identifies the Trl1 sealing domain as a promising drug target for antifungal and anti-trypanosomal therapies by analyzing its essentiality in pathogenic fungi and trypanosomes.