相关论文: A model for codon position bias in RNA editing

The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting…

Large language models (LLMs) exhibit cognitive biases -- systematic tendencies of irrational decision-making, similar to those seen in humans. Prior work has found that these biases vary across models and can be amplified by instruction…

Synthesis of DNA molecules offers unprecedented advances in storage technology. Yet, the microscopic world in which these molecules reside induces error patterns that are fundamentally different from their digital counterparts. Hence, to…

A single gene can encode for different protein versions through a process called alternative splicing. Since proteins play major roles in cellular functions, aberrant splicing profiles can result in a variety of diseases, including cancers.…

Predictive biomarkers are playing an essential role in precision medicine. Identifying an optimal cutoff to select patient subsets with greater benefit from treatment is critical and more challenging for predictive biomarkers measured with…

In eukaryotic genomes, nucleosomes function to compact DNA and to regulate access to it both by simple physical occlusion and by providing the substrate for numerous covalent epigenetic tags. While nucleosome positions in vitro are…

A-To-I RNA editing is common to all eukaryotes, associated with various neurological functions. Recently, A-to-I editing was found to occur abundantly in the human transcriptome. Here we show that the frequency of A-to-I editing in humans…

Cotranslational folding depends on the folding speed and stability of the nascent protein. It remains difficult, however, to predict which proteins cotranslationally fold. Here, we simulate evolution of model proteins to investigate how…

Mitochondrial DNA (mtDNA) mutations cause severe congenital diseases but may also be associated with healthy aging. MtDNA is stochastically replicated and degraded, and exists within organelles which undergo dynamic fusion and fission. The…

The intrinsic stochasticity of gene expression can lead to large variability of protein levels across a population of cells. Variability (or noise) in protein distributions can be modulated by cellular mechanisms of gene regulation; in…

Motivation: DNA methylation is an intensely studied epigenetic mark, yet its functional role is incompletely understood. Attempts to quantitatively associate average DNA methylation to gene expression yield poor correlations outside of the…

The new dynamical game theoretic model of sex ratio evolution emphasizes the role of males as passive carriers of sex ratio genes. This shows inconsistency between population genetic models of sex ratio evolution and classical strategic…

X-ray data indicate that complexes of ribosomes with cognate and near cognate tRNAs are very similar structurally, and this was the ground for a suggestion that the ribosome discriminates correct codon-anticodon pair because of its higher…

Positional bias in binary question answering occurs when a model systematically favors one choice over another based solely on the ordering of presented options. In this study, we quantify and analyze positional bias across five large…

RNA sequencing (RNA-seq) is the conventional genome-scale approach used to capture the expression levels of all detectable genes in a biological sample. This is now regularly used for population-based studies designed to identify genetic…

Large language models (LLMs) often exhibit gender bias, posing challenges for their safe deployment. Existing methods to mitigate bias lack a comprehensive understanding of its mechanisms or compromise the model's core capabilities. To…

Positioning of nucleosomes along eukaryotic genomes plays an important role in their organization and regulation. There are many different factors affecting the location of nucleosomes. Some can be viewed as preferential binding of a single…

Secondary structure plays an important role in determining the function of non-coding RNAs. Hence, identifying RNA secondary structures is of great value to research. Computational prediction is a mainstream approach for predicting RNA…

Designing RNA molecules has garnered recent interest in medicine, synthetic biology, biotechnology and bioinformatics since many functional RNA molecules were shown to be involved in regulatory processes for transcription, epigenetics and…

The prevalence of neutral mutations implies that biological systems typically have many more genotypes than phenotypes. But can the way that genotypes are distributed over phenotypes determine evolutionary outcomes? Answering such questions…