Related papers: A Model for Competition for Ribosomes in the Cell
Modeling biological sequences such as DNA, RNA, and proteins is crucial for understanding complex processes like gene regulation and protein synthesis. However, most current models either focus on a single type or treat multiple types of…
The evolution of various competing cell types in tissues, and the resulting persistent tissue population, is studied numerically and analytically in a particle-based model of active tissues. Mutations change the properties of cells in…
Biomolecular communication demands that interactions between parts of a molecular system act as scaffolds for message transmission. It also requires an evolving and organized system of signs - a communicative agency - for creating and…
Leveraging large language models for machine translation has demonstrated promising results. However, it does require the large language models to possess the capability of handling both the source and target languages in machine…
Pre-training large-scale language models (LMs) requires huge amounts of text corpora. LMs for English enjoy ever growing corpora of diverse language resources. However, less resourced languages and their mono- and multilingual LMs often…
With the rise in engineered biomolecular devices, there is an increased need for tailor-made biological sequences. Often, many similar biological sequences need to be made for a specific application meaning numerous, sometimes prohibitively…
Even though sequence-to-sequence neural machine translation (NMT) model have achieved state-of-art performance in the recent fewer years, but it is widely concerned that the recurrent neural network (RNN) units are very hard to capture the…
Multiple sclerosis is a disease that affects the brain and spinal cord, it can lead to severe disability and has no known cure. The majority of prior work in machine learning for multiple sclerosis has been centered around using Magnetic…
Homeostasis of protein concentrations in cells is crucial for their proper functioning, and this requires concentrations (at their steady-state levels) to be stable to fluctuations. Since gene expression is regulated by proteins such as…
Recent studies reported complex post-transcriptional interplay among targets of a common pool of microRNAs, a class of small non-coding downregulators of gene expression. Behaving as microRNA-sponges, distinct RNA species may compete for…
With the wealth of high-throughput sequencing data generated by recent large-scale consortia, predictive gene expression modelling has become an important tool for integrative analysis of transcriptomic and epigenetic data. However,…
It has been reported that the number of transcription factors encoded in prokaryotic genomes scales approximately quadratically with their total number of genes. We propose a conceptual explanation of this finding and illustrate it using a…
Genes with similar transcriptional activation kinetics can display very different temporal mRNA profiles due to differences in transcription time, degradation rate and RNA processing kinetics. Recent studies have shown that a…
In this article, we quantitatively study, through stochastic models, the efects of several intracellular phenomena, such as cell volume growth, cell division, gene replication as well as fuctuations of available RNA polymerases and…
This work applies the methods of signal processing and the concepts of control system design to model the maintenance and modulation of reading frame in the process of protein synthesis. The model shows how translational speed can modulate…
Recent studies have highlighted the potential of exploiting parallel corpora to enhance multilingual large language models, improving performance in both bilingual tasks, e.g., machine translation, and general-purpose tasks, e.g., text…
The sequence of amino acid monomers in the primary structure of a protein is decided by the corresponding sequence of codons (triplets of nucleic acid monomers) on the template messenger RNA (mRNA). The polymerization of a protein, by…
Prion and prion-like molecules are a type of self replicating aggregate protein that have been implicated in a variety of neurodegenerative diseases. Over recent decades the molecular dynamics of prions have been characterized both…
This paper presents a real-time simulation involving ''protozoan-like'' cells that evolve by natural selection in a physical 2D ecosystem. Selection pressure is exerted via the requirements to collect mass and energy from the surroundings…
Tight regulation of messenger RNA (mRNA) stability is essential to ensure accurate gene expression in response to developmental and environmental cues. mRNA stability is controlled by mRNA decay pathways, which have traditionally been…