Related papers: Units of genetic transfer in prokaryotes
Gene expression datasets offer insights into gene regulation mechanisms, biochemical pathways, and cellular functions. Additionally, comparing gene expression profiles between disease and control patients can deepen the understanding of…
In recent years, pre-trained Multilingual Language Models (MLLMs) have shown a strong ability to transfer knowledge across different languages. However, given that the aspiration for such an ability has not been explicitly incorporated in…
Gene assembly in ciliates is one of the most involved DNA processings going on in any organism. This process transforms one nucleus (the micronucleus) into another functionally different nucleus (the macronucleus). We continue the…
A theoretical study is presented to quantitatively analyze the transport experiment through individual DNA molecules reported recently by Porath {\it et al.} [Nature {\bf 403}, 635 (2000)]. A variety of valuable quantities are identified by…
Hybrid evolution and horizontal gene transfer (HGT) are processes where evolutionary relationships may more accurately be described by a reticulated network than by a tree. In such a network, there will often be several paths between any…
Gene-sharing networks provide a powerful framework to study the evolution of viruses and mobile genetic elements. These bipartite networks, which link genes to the genomes that contain them, exhibit characteristic degree distributions: a…
We investigate theoretically the energy transfer phenomenon in a double-layer graphene (DLG) system in which two layers are coupled due to the Coulomb interlayer interaction without appreciable interlayer tunneling. We use the balance…
A multi-layered structure consisting of alternate right-handed material (RHM) and left-handed material (LHM)is considered and the unusual narrow transmission bands are explained as the competitive results of the Bragg condition and the…
Conjugation is the primary mechanism of horizontal gene transfer that spreads antibiotic resistance among bacteria. Although conjugation normally occurs in surface-associated growth (e.g., biofilms), it has been traditionally studied in…
We consider how transfer of genetic information between individuals influences the phase diagram and mean fitness of both the Eigen and the parallel, or Crow-Kimura, models of evolution. In the absence of genetic transfer, these physical…
The wavefront dislocation is an important and ubiquitous phenomenon in wave fields. It is closely related to the phase singularity in a wave function. Some recent studies have verified that the wavefront dislocations in the local density of…
Bacterial genomes and large-scale computer software projects both consist of a large number of components (genes or software packages) connected via a network of mutual dependencies. Components can be easily added or removed from individual…
Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced…
Coarse-grained simulations are often employed to study the translocation of DNA through a nanopore. The majority of these studies investigate the translocation process in a relatively generic sense and do not endeavour to match any…
We evolve binary mux-6 trees for up to 100000 generations evolving some programs with more than a hundred million nodes. Our unbounded Long-Term Evolution Experiment LTEE GP appears not to evolve building blocks but does suggests a limit to…
We address the question, related with the origin of the genetic code, of why are there three bases per codon in the translation to protein process. As a followup to our previous work, we approach this problem by considering the…
The periodic transference of nucleotide strings in bacterial and archaeal complete genomes is investigated by using the metric representation and the recurrence plot method. The generated periodic correlation structures exhibit four kinds…
Transfer learning is a key component of modern machine learning, enhancing the performance of target tasks by leveraging diverse data sources. Simultaneously, overparameterized models such as the minimum-$\ell_2$-norm interpolator (MNI) in…
Large Language Models (LLMs) offer a transparent brain with accessible parameters that encode extensive knowledge, which can be analyzed, located and transferred. Consequently, a key research challenge is to transcend traditional knowledge…
Prokaryotic gene prediction plays an important role in understanding the biology of organisms and their function with applications in medicine and biotechnology. Although the current gene finders are highly sensitive in finding long genes,…