相关论文: Computing the Inversion-Indel Distance

A "genome structure" is a labeled directed graph with vertices of degree 1 or 2. A set of operations over such graphs is fixed, and each of the operations has a certain cost, a strictly positive number. The transformation problem consists…

The variation in genome arrangements among bacterial taxa is largely due to the process of inversion. Recent studies indicate that not all inversions are equally probable, suggesting, for instance, that shorter inversions are more frequent…

An indel refers to a single insertion or deletion, while an edit refers to a single insertion, deletion or substitution. In this paper, we investigate codes that combat either a single indel or a single edit and provide linear-time…

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…

This paper introduces the Gene Mover's Distance, a measure of similarity between a pair of cells based on their gene expression profiles obtained via single-cell RNA sequencing. The underlying idea of the proposed distance is to interpret…

Computing the similarity between two DNA sequences is of vital importance in bioscience, yet it can be computationally expensive on classical hardware. For example, the edit distance with move operations (EDM), a DNA similarity measure of…

Reconstructing ancestral gene orders is an important step towards understanding genome evolution. The Small Parsimony Problem (SPP) has been extensively studied in this regard. The problem aims at finding the gene orders at internal nodes…

Inversion sequences are integer sequences $(\sigma_1, \dots, \sigma_n)$ such that $0 \leqslant \sigma_i < i$ for all $1 \leqslant i \leqslant n$. The study of pattern-avoiding inversion sequences began in two independent articles by…

In this paper, we consider a tree inference problem motivated by the critical problem in single-cell genomics of reconstructing dynamic cellular processes from sequencing data. In particular, given a population of cells sampled from such a…

We propose local segmentation of multiple sequences sharing a common time- or location-index, building upon the single sequence local segmentation methods of Niu and Zhang (2012) and Fang, Li and Siegmund (2016). We also propose reverse…

Aims. Recent studies showed that time--distance inversions for flows start to be dominated by a random noise at a depth of only a few Mm. It was proposed that the ensemble averaging might be a solution to learn about the structure of the…

Given a set of sequences, the distance between pairs of them helps us to find their similarity and derive structural relationship amongst them. For genomic sequences such measures make it possible to construct the evolution tree of…

Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of…

Motivation: Genome rearrangement plays an important role in evolutionary biology and has profound impacts on phenotype in organisms ranging from microbes to humans. The mechanisms for genome rearrangement events remain unclear. Lots of…

We consider the problem of identifying jointly the ancestral sequence, the phylogeny and the parameters in models of DNA sequence evolution with insertion and deletion (indel). Under the classical TKF91 model of sequence evolution, we…

The classification of DNA sequences is a key research area in bioinformatics as it enables researchers to conduct genomic analysis and detect possible diseases. In this paper, three state-of-the-art algorithms, namely Convolutional Neural…

In an oriented graph, the inversion of a subset of vertices X is the operation reversing the direction of every arc with both endpoints in X. Given a graph G, the inversion distance between two orientations G is the minimum number of…

The process of DNA-based data storage (DNA storage for short) can be mathematically modelled as a communication channel, termed DNA storage channel, whose inputs and outputs are sets of unordered sequences. To design error correcting codes…

We propose a computational method to measure and visualize interrelationships among any number of DNA sequences allowing, for example, the examination of hundreds or thousands of complete mitochondrial genomes. An "image distance" is…

Phase retrieval, or the process of recovering phase information in reciprocal space to reconstruct images from measured intensity alone, is the underlying basis to a variety of imaging applications including coherent diffraction imaging…