Related papers: Units of genetic transfer in prokaryotes
The theory of lithopanspermia proposes the natural exchange of organisms between solar system bodies through meteorites. The focus of this theory comprises three distinct stages: planetary ejection, interplanetary transit and planetary…
In this work we present a computational study of the Kinetoplast genome, modelled as a large number of semiflexible unknotted loops, which are allowed to link with each other. As the DNA density increases, the systems shows a percolation…
Large language models (LLMs) demonstrate impressive results in natural language processing tasks but require a significant amount of computational and memory resources. Structured matrix representations are a promising way for reducing the…
How does the interplay between selection, mutation and horizontal gene transfer modify the phenotypic distribution of a bacterial or cell population? While horizontal gene transfer, which corresponds to the exchange of genetic material…
This study presents the first global, 1 Mbp level analysis of patterns of nucleotide substitutions along the human lineage. The study is based on the analysis of a large amount of repetitive elements deposited into the human genome since…
A Linear Boltzmann Transport (LBT) model has been developed for the study of jet propagation inside a quark-gluon plasma. Both leading and thermal recoiled partons are transported according to the Boltzmann equations to account for…
Plasmids are major players in Horizontal Gene Transfer mechanisms, hence they are highly variable in their gene content and length. We propose a model for the fitness of a plasmid as a function of its length, which predicts diminishing…
Genotype imputation enables dense variant coverage for genome-wide association and risk-prediction studies, yet conventional reference-panel methods remain limited by ancestry bias and reduced rare-variant accuracy. We present Genotype…
Substantial progress has been made in identifying single genetic variants predisposing to common complex diseases. Nonetheless, the genetic etiology of human diseases remains largely unknown. Human complex diseases are likely influenced by…
In previous papers we have described with strong experimental support, the organising role that CoHSI (Conservation of Hartley-Shannon Information) plays in determining important global properties of all known proteins, from defining the…
This work illustrates potentials for recognition within {\em ad hoc} sensor networks if their nodes possess individual inter-related biologically inspired genetic codes. The work takes ideas from natural immune systems protecting organisms…
A common theme among the proposed models for network epidemics is the assumption that the propagating object, i.e., a virus or a piece of information, is transferred across the nodes without going through any modification or evolution.…
Large language models are increasingly deployed across diverse applications. This often includes tasks LLMs have not encountered during training. This implies that enumerating and obtaining the high-quality training data for all tasks is…
Following genetic ancestry in eukaryote populations poses several open problems due to sexual reproduction and recombination. The history of extant genetic material is usually modeled backwards in time, but tracking chromosomes at a large…
Summary: BGT is a compact format, a fast command line tool and a simple web application for efficient and convenient query of whole-genome genotypes and frequencies across tens to hundreds of thousands of samples. On real data, it encodes…
Diffusion-driven processes are important phenomena of materials science in the field of energy conversion and transmission. During the conversion from chemical energy to electrical energy, the species diffusion is generally linked to the…
During evolution of microorganisms genomes underwork have different changes in their lengths, gene orders, and gene contents. Investigating these structural rearrangements helps to understand how genomes have been modified over time. Some…
Recent experiments and simulations have demonstrated that proteins can fold on the ribosome. However, the extent and generality of fitness effects resulting from co-translational folding remain open questions. Here we report a genome-wide…
Human mobility and activity patterns mediate contagion on many levels, including the spatial spread of infectious diseases, diffusion of rumors, and emergence of consensus. These patterns however are often dominated by specific locations…
Most of the physical information about astrophysical objects is obtained via the analysis of their electromagnetic spectra. Observed data coupled with radiation transfer models in physical conditions representative of stars, planets,…