Related papers: Is there any sense in antisense editing?
Despite the greater functional importance of protein levels, our knowledge of gene expression evolution is based almost entirely on studies of mRNA levels. In contrast, our understanding of how translational regulation evolves has lagged…
The observation that, through a titration mechanism, microRNAs (miRNAs) can act as mediators of effective interactions among their common targets (competing endogenous RNAs or ceRNAs) has brought forward the idea ('ceRNA hypothesis') that…
We live in a period where bio-informatics is rapidly expanding, a significant quantity of genomic data has been produced as a result of the advancement of high-throughput genome sequencing technology, raising concerns about the costs…
Recent progress in text-to-image diffusion models has transformed image editing via text prompts, yet this also introduces significant ethical challenges from potential misuse in creating deceptive or harmful content. While current defenses…
The nucleotide composition of human genes with a special emphasis on transcription-related strand asymmetries is analyzed. Such asymmetries may be associated with different mutational rates in two principal factors. The first one is…
Single cell experiments of simple regulatory networks can markedly differ from cell population experiments. Such differences arise from stochastic events in individual cells that are averaged out in cell populations. For instance, while…
The Transformer model has a tendency to overfit various aspects of the training data, such as the overall sequence length. We study elementary string edit functions using a defined set of error indicators to interpret the behaviour of the…
AI technology has enabled the creation of deepfakes: hyper-realistic synthetic media. We surveyed 315 individuals in the U.S. on their views regarding the hypothetical non-consensual creation of deepfakes depicting them, including deepfakes…
In the context of AI-based decision support systems, explanations can help users to judge when to trust the AI's suggestion, and when to question it. In this way, human oversight can prevent AI errors and biased decision-making. However,…
Probabilistic text generators have been used to produce fake scientific papers for more than a decade. Such nonsensical papers are easily detected by both human and machine. Now more complex AI-powered generation techniques produce texts…
Several recent experiments suggest that sharply bent DNA has a surprisingly high bending flexibility, but the cause of this flexibility is poorly understood. Although excitation of flexible defects can explain these results, whether such…
RNA editing can be crucial for the expression of genetic information via inserting, deleting, or substituting a few nucleotides at specific positions in an RNA sequence. Within coding regions in an RNA sequence, editing usually occurs with…
The question of whether DNA is intrinsically conducting or not is still a challenge. The ongoing debate on DNA molecules as an electronic material has so far underestimated a key distinction of the system: the role of base pairing (inter…
In recent years, several studies have provided insight on the functioning of the brain which consists of neurons and form networks via interconnection among them by synapses. Neural networks are formed by interconnected systems of neurons,…
Solving the RNA inverse folding problem is a critical prerequisite to RNA design, an emerging field in bioengineering with a broad range of applications from reaction catalysis to cancer therapy. Although significant progress has been made…
Biological AI models increasingly predict complex cellular responses, yet their learned representations remain disconnected from the molecular processes they aim to capture. We present CDT-III, which extends mechanism-oriented AI across the…
A double stranded DNA molecule under the stress of a pulling force acting on the strand terminals exhibits a partially denatured structure or can be completely unzipped depending the magnitude of the pulling force. A scaling argument for…
A simple stochastic model of a self regulating gene that displays bistable switching is analyzed. While on, a gene transcribes mRNA at a constant rate. Transcription factors can bind to the DNA and affect the gene's transcription rate.…
Dual graphs have been applied to model RNA secondary structures. The purpose of the paper is two-fold: we present new graph-theoretic properties of dual graphs to validate the further analysis and classification of RNAs using these…
Do reasoning models have "Aha!" moments? Prior work suggests that models like DeepSeek-R1-Zero undergo sudden mid-trace realizations that lead to accurate outputs, implying an intrinsic capacity for self-correction. Yet, it remains unclear…