Related papers: Units of genetic transfer in prokaryotes
In eukaryotic genes the protein coding sequence is split into several fragments, the exons, separated by non-coding DNA stretches, the introns. Prokaryotes do not have introns in their genome. We report the calculations of stability domains…
During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain…
The remarkable success of foundation models has sparked growing interest in their application to single-cell biology. Models like Geneformer and scGPT promise to serve as versatile tools in this specialized field. However, representing a…
Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding complexity and the functional components of the genome is an untapped wealth…
Statistical physics can describe the behavior of microbial populations consisting of many heterogeneous individuals. A direct consequence is the existence of phase transitions, where the behavior of a population changes discontinuously upon…
Transfer learning on tabular data is challenging due to disparate feature spaces across domains, in contrast to the homogeneous structures of image and text. Large language models (LLMs) offer a knowledge base to improve the limited…
This work analyzed genome-wide nucleotide distribution patterns in ten insect genomes. Two internal measures were applied: (i) GC variation and (ii) third codon nucleotide preference. Although the genome size and overall GC level did not…
This paper presents a parameter-lite transfer learning approach of pretrained language models (LM) for knowledge graph (KG) completion. Instead of finetuning, which modifies all LM parameters, we only tune a few new parameters while keeping…
DNA strand displacement, where a single-stranded nucleic acid invades a DNA duplex, is pervasive in genomic processes and DNA engineering applications. The kinetics of strand displacement have been studied in bulk; however, the kinetics of…
We study the electronic properties of DNA by way of a tight-binding model applied to four particular DNA sequences. The charge transfer properties are presented in terms of localisation lengths, crudely speaking the length over which…
Heritable differences in gene expression between individuals are an important source of phenotypic variation. The question of how closely the effects of genetic variation on protein levels mirror those on mRNA levels remains open. Here, we…
We study the existence of state transfer with respect to the $q$-Laplacian matrix of a graph equipped with a non-trivial involution. We show that the occurrence of perfect state transfer between certain pair (or plus) states in such a graph…
In recent years, the sequencing, assembling and annotation of prokaryotic genomes has become increasingly easy and cheap. Thus it becomes increasingly feasible and interesting to perform comparative genomics analyses of new genomes to those…
Genetic interaction measures how different genes collectively contribute to a phenotype, and can reveal functional compensation and buffering between pathways under genetic perturbations. Recently, genome-wide screening for genetic…
The number of the non-shared edges of two phylogenies is a basic measure of the dissimilarity between the phylogenies. The non-shared edges are also the building block for approximating a more sophisticated metric called the nearest…
The question of what determines genetic diversity both between and within species has long remained unsolved by the modern evolutionary theory (MET). However, it has not deterred researchers from producing interpretations of genetic…
The evolution of the full repertoire of proteins encoded in a given genome is mostly driven by gene duplications, deletions, and sequence modifications of existing proteins. Indirect information about relative rates and other intrinsic…
Genomic language models (gLMs) have shown mostly modest success in identifying evolutionarily constrained elements in mammalian genomes. To address this issue, we introduce a novel framework for training gLMs that explicitly models…
Perfect quantum state transfer is achievable in different settings, including linear qubit chains, bi-dimensional arrays, ladders, etc. The most studied case contemplates transferring arbitrary one-qubit pure states in systems with…
Phylogenetic networks describe the evolution of a set of taxa for which reticulate events have occurred at some point in their evolutionary history. Of particular interest is when the evolutionary history between a set of just three taxa…