相关论文: Safe and complete contig assembly via omnitigs

The coherent radiation emitted by an electron bunch provides a diagnostic signal that can be used to estimate its longitudinal distribution. Commonly only the amplitude of the intensity spectrum can be measured and the associated phase must…

Here we study the complexity of string problems as a function of the size of a program that generates input. We consider straight-line programs (SLP), since all algorithms on SLP-generated strings could be applied to processing…

Current metagenome assemblers developed for short sequence reads or noisy long readswere not optimized for accurate long reads. Here we describe hifiasm-meta, a new metagenome assembler that exploits the high accuracy of recent data.…

Background: Significance analysis plays a major role in identifying and ranking genes, transcription factor binding sites, DNA methylation regions, and other high-throughput features for association with disease. We propose a new approach,…

We prove that deciding whether a given input word contains as subsequence every possible permutation of integers $\{1,2,\ldots,n\}$ is coNP-complete. The coNP-completeness holds even when given the guarantee that the input word contains as…

DNA self-assembly is an important tool that has a wide range of applications such as building nanostructures, the transport of target virotherapies, and nano-circuitry. Tools from graph theory can be used to encode the biological process of…

Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art…

In this paper, we study the problem of sorting unichromosomal linear genomes by prefix double-cut-and-joins (or DCJs) in both the signed and the unsigned settings. Prefix DCJs cut the leftmost segment of a genome and any other segment, and…

Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly…

The Consecutive-Ones Property (C1P) is a classical concept in discrete mathematics that has been used in several genomics applications, from physical mapping of contemporary genomes to the assembly of ancient genomes. A common issue in…

Given a graph G and an integer k, the objective of the $\Pi$-Contraction problem is to check whether there exists at most k edges in G such that contracting them in G results in a graph satisfying the property $\Pi$. We investigate the…

The biological process of gene assembly has been modeled based on three types of string rewriting rules, called string pointer rules, defined on so-called legal strings. It has been shown that reduction graphs, graphs that are based on the…

Within biology, it is of interest to construct DNA complexes of a certain shape. These complexes can be represented through graph theory, using edges to model strands of DNA joined at junctions, represented by vertices. Because guided…

The biggest challenge when using DNA as a storage medium is maintaining its stability. The relative occurrence of Guanine (G) and Cytosine (C) is essential for the longevity of DNA. In addition to that, reverse complementary base pairs…

We formulate genome assembly problem as an optimization problem in which the objective function is the likelihood of the assembly given the reads.

Sumsets are central objects in additive combinatorics. In 2007, Granville asked whether one can efficiently recognize whether a given set $S$ is a sumset, i.e. whether there is a set $A$ such that $A+A=S$. Granville suggested an algorithm…

Given $n$ points in the plane, we propose algorithms to compile connected crossing-free geometric graphs into directed acyclic graphs (DAGs). The DAGs allow efficient counting, enumeration, random sampling, and optimization. Our algorithms…

This paper investigates the number of quantum queries made to solve the problem of reconstructing an unknown string from its substrings in a certain query model. More concretely, the goal of the problem is to identify an unknown string $S$…

An \emph{indeterminate string} $x = x[1..n]$ on an alphabet $\Sigma$ is a sequence of nonempty subsets of $\Sigma$; $x$ is said to be \emph{regular} if every subset is of size one. A proper substring $u$ of regular $x$ is said to be a…

The problem of reconstructing strings from their substring spectra has a long history and in its most simple incarnation asks for determining under which conditions the spectrum uniquely determines the string. We study the problem of coded…