相关论文: Revisiting Waiting Times in DNA evolution

We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions and insertion of random segments. These processes are found to generate long-range correlations…

We introduce a family of models incorporating random segmental substitutions and point mutations and demonstrate that such models reproduce algebraic length distributions of exact matches with the slope $-4$ observed earlier in pairwise…

Given a set of aligned sequences of independent noisy observations, we are concerned with detecting intervals where the mean values of the observations change simultaneously in a subset of the sequences. The intervals of changed means are…

In this paper, we study the Random Access Problem in DNA storage, which addresses the challenge of retrieving a specific information strand from a DNA-based storage system. In this framework, the data is represented by $k$ information…

We study the random sequential adsorption of $k$-mers on the fully-connected lattice with $N=kn$ sites. The probability distribution $T_n(s,t)$ of the time $t$ needed to cover the lattice with $s$ $k$-mers is obtained using a generating…

The typical process for classifying and submitting a newly sequenced virus to the NCBI database involves two steps. First, a BLAST search is performed to determine likely family candidates. That is followed by checking the candidate…

The goal of cancer genome sequencing projects is to determine the genetic alterations that cause common cancers. Many malignancies arise during the clonal expansion of a benign tumor which motivates the study of recurrent selective sweeps…

DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes, and DNA…

We introduce a stochastic model of a population with overlapping generations and arbitrary levels of self-fertilization versus outcrossing. We study how the global graph of reproductive relationships, or population pedigree, influences the…

Parent selection methods are widely used in evolutionary computation to accelerate the optimization process, yet their theoretical benefits are still poorly understood. In this paper, we address this gap by proposing a parent selection…

Frequencies of $k$-mers in sequences are sometimes used as a basis for inferring phylogenetic trees without first obtaining a multiple sequence alignment. We show that a standard approach of using the squared-Euclidean distance between…

Genetic algorithms are heuristic optimization techniques inspired by Darwinian evolution, which are characterized by successfully finding robust solutions for optimization problems. Here, we propose a subroutine-based quantum genetic…

In this work we implement the so-called matching time estimators for estimating the entropy rate as well as the entropy production rate for symbolic sequences. These estimators are based on recurrence properties of the system, which have…

The wide array of currently available genomes display a wonderful diversity in size, composition and structure with many more to come thanks to several global biodiversity genomics initiatives starting in recent years. However, sequencing…

Given an evolutionary model, such as Wright--Fisher (WF) or Moran, the n-coalescent problem consists of going backward in time to find for example the time to the most recent common ancestor (MRCA) and the topology of the tree. In the…

Emergence is a fascinating property of large language models and neural networks more broadly: as models scale and train for longer, they sometimes develop new abilities in sudden ways. Despite initial studies, we still lack a comprehensive…

Given a string $s$ of length $n$ over a general alphabet and an integer $k$, the problem is to decide whether $s$ is a concatenation of $k$ nonempty palindromes. Two previously known solutions for this problem work in time $O(kn)$ and…

This report explores the application of machine learning techniques on short timeseries gene expression data. Although standard machine learning algorithms work well on longer time-series', they often fail to find meaningful insights from…

The simplest possible informational heteropolymer requires only a two-letter alphabet to be able to store information. The evolutionary choice of four monomers in the informational biomolecules RNA/DNA or their progenitors is intriguing,…

The problem of assembling DNA fragments starting from imperfect strings given by a sequencer, classified as NP hard when trying to get perfect answers, has a huge importance in several fields, because of its relation with the possibility of…