相关论文: Computing the Inversion-Indel Distance

The last decade brought a significant increase in the amount of data and a variety of new inference methods for reconstructing the detailed evolutionary history of various cancers. This brings the need of designing efficient procedures for…

Genome rearrangements are events where large blocks of DNA exchange places during evolution. The analysis of these events is a promising tool for understanding evolutionary genomics, providing data for phylogenetic reconstruction based on…

In this work, we explore heuristics for the Adjacency Graph Packing problem, which can be applied to the Double Cut and Join (DCJ) Distance Problem. The DCJ is a rearrangement operation and the distance problem considering it is a well…

The study of genome rearrangement has many flavours, but they all are somehow tied to edit distances on variations of a multi-graph called the breakpoint graph. We study a weighted 2-break distance on Eulerian 2-edge-colored multi-graphs,…

Radon transform is widely used in physical and life sciences and one of its major applications is the X-ray computed tomography (X-ray CT), which is significant in modern health examination. The Radon inversion or image reconstruction is…

Dendrograms are a way to represent evolutionary relationships between organisms. Nowadays, these are inferred based on the comparison of genes or protein sequences by taking into account their differences and similarities. The genetic…

A tandem duplication denotes the process of inserting a copy of a segment of DNA adjacent to its original position. More formally, a tandem duplication can be thought of as an operation that converts a string $S = AXB$ into a string $T =…

Motivated by the problem of classifying individuals with a disease versus controls using functional genomic attributes as input, we encode the input as a string of 1s (presence) or 0s (absence) of the genomic attribute across the genome.…

Genomic data I used in many fields but, it has become known that most of the platforms used in the sequencing process produce significant errors. This means that the analysis and inferences generated from these data may have some errors…

Breakpoint graphs are ubiquitous structures in the field of genome rearrangements. Their cycle decomposition has proved useful in computing and bounding many measures of (dis)similarity between genomes, and studying the distribution of…

We apply deep learning for retrieval of the time-dependent bond length in the dissociating two-dimensional H$_2^{+}$ molecule using photoelectron momentum distributions. We consider a pump-probe scheme and calculate electron momentum…

This paper presents a novel Direct Integration Theorem (DIT), derived as a non-trivial corollary of the classical Central Slice Theorem (CST). The DIT provides a mathematically consistent transition from the continuous to the discrete…

Given a sequence $s_1$ of $n$ letters drawn i.i.d. from an alphabet of size $\sigma$ and a mutated substring $s_2$ of length $m < n$, we often want to recover the mutation history that generated $s_2$ from $s_1$. Modern sequence aligners…

This paper provides a short and transparent solution for the covering cost of white-grey trees which play a crucial role in the algorithm of Bergeron {\it et al.}\ to compute the rearrangement distance between two multichromosomal genomes…

In computational biology, tandem duplication is an important biological phenomenon which can occur either at the genome or at the DNA level. A tandem duplication takes a copy of a genome segment and inserts it right after the segment - this…

Kondo et al. (DS 2014) proposed methods for computing distances between unordered rooted trees by transforming an instance of the distance computing problem into an instance of the integer programming problem. They showed that the tree edit…

String edit distances have been used for decades in applications ranging from spelling correction and web search suggestions to DNA analysis. Most string edit distances are variations of the Levenshtein distance and consider only…

The ability to estimate the evolutionary distance between extant genomes plays a crucial role in many phylogenomic studies. Often such estimation is based on the parsimony assumption, implying that the distance between two genomes can be…

We provide, on an extensive dataset and using several different distances, confirmation of the hypothesis that CGR patterns are preserved along a genomic DNA sequence, and are different for DNA sequences originating from genomes of…

In Electrical Impedance Tomography (EIT) one wants to image the conductivity distribution of a body from current and voltage measurements carried out on its boundary. In this paper we consider the underlying mathematical model, the inverse…