相关论文: A mathematical model for gene evolution after whol…

Replication of genetic material is an important process for all living organisms. Origins of replication initiate the copying of DNA at many points on a chromosome, and it is the distribution of these points that is relevant here, as it…

Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of…

Horizontal gene transfer is an important factor in bacterial evolution that can act across species boundaries. Yet, we know little about rate and genomic targets of cross-lineage gene transfer, and about its effects on the recipient…

This paper introduces a continuous model for Multi-cellular Developmental Design. The cells are fixed on a 2D grid and exchange "chemicals" with their neighbors during the growth process. The quantity of chemicals that a cell produces, as…

The number of extant individuals within a lineage, as exemplified by counts of species numbers across genera in a higher taxonomic category, is known to be a highly skewed distribution. Because the sublineages (such as genera in a clade)…

We created the APOGEE-GALEX-\emph{Gaia} catalog to study white dwarfs binaries. This database aims to create a minimally biased sample of WD binary systems identified from a combination of GALEX, {\it Gaia}, and APOGEE data to increase the…

A quantitative theory on the construction and the evolution of the genetic code is proposed. Through introducing the concept of mutational deterioration (MD) and developing a theoretical formalism on MD minimization we have proved: 1, the…

Gene duplication is believed to play a major role in the evolution of genomic complexity. The presence of a duplicate removes the constraint of natural selection upon the gene, leading to its likely loss of function or, occasionally, the…

In many situations, the gene expression signature is a unique marker of the biological state. We study the modification of the gene expression distribution function when the biological state of a system experiences a change. This change may…

Graph Edit Distance (GED) is a widely used measure of graph similarity, valued for its flexibility in encoding domain knowledge through operation costs. However, existing learning-based approximation methods follow a modeling paradigm that…

Galaxy evolution can be studied observationally by linking progenitor and descendant galaxies through an evolving cumulative number density selection. This procedure can reproduce the expected evolution of the median stellar mass from…

Regulatory networks consist of interacting molecules with a high degree of mutual chemical specificity. How can these molecules evolve when their function depends on maintenance of interactions with cognate partners and simultaneous…

We study the iterated Galton-Watson process (IGW), possibly with thinning, introduced by Gawe{\l}and Kimmel to model the number of repeats of DNA triplets during some genetic disorders. If the process involves some thinning, then extinction…

We analyze models of genome evolution based on both restricted and unrestricted double-cut-and-join (DCJ) operations. We compare the number of operations along the evolutionary trajectory to the DCJ distance of the genome from its ancestor…

We consider the bifurcating Markov chain model introduced by Guyon to detect cellular aging from cell lineage. To take into account the possibility for a cell to die, we use an underlying Galton-Watson process to describe the evolution of…

This paper develops a point-mutation model describing the evolutionary dynamics of a population of adult stem cells. Such a model may prove useful for quantitative studies of tissue aging and the emergence of cancer. We consider two modes…

When a biological population expands into new territory, genetic drift develops an enormous influence on evolution at the propagating front. In such range expansion processes, fluctuations in allele frequencies occur through stochastic…

Agent-based simulation platforms play a key role in enabling fast-to-run evolution experiments that can be precisely controlled and observed in detail. Availability of high-resolution snapshots of lineage ancestries from digital…

Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between two input sequences. Haubold {\em et al.} (2009) showed how the average number of substitutions between two DNA…

Likelihood-based, or explicit, deep generative models use neural networks to construct flexible high-dimensional densities. This formulation directly contradicts the manifold hypothesis, which states that observed data lies on a…