相关论文: Safe and complete contig assembly via omnitigs

Let a text $T[1..n]$ be the only string generated by a context-free grammar with $g$ (terminal and nonterminal) symbols, and of size $G$ (measured as the sum of the lengths of the right-hand sides of the rules). Such a grammar, called a…

Metagenomic studies have primarily relied on de novo assembly for reconstructing genes and genomes from microbial mixtures. While reference-guided approaches have been employed in the assembly of single organisms, they have not been used in…

We present a data structure called a history graph that offers a practical basis for the analysis of genome evolution. It conceptually simplifies the study of parsimonious evolutionary histories by representing both substitutions and double…

It is shown that metric representation of DNA sequences is one-to-one. By using the metric representation method, suppression of nucleotide strings in the DNA sequences is determined. For a DNA sequence, an optimal string length to display…

The complex correlation structure of a collection of orthologous DNA sequences is uniquely captured by the "ancestral recombination graph" (ARG), a complete record of coalescence and recombination events in the history of the sample.…

Microbes are essentially yet convolutedly linked with human lives on the earth. They critically interfere in different physiological processes and thus influence overall health status. Studying microbial species is used to be constrained to…

Datalogo is an extension of Datalog that allows for aggregation and recursion over an arbitrary commutative semiring. Like Datalog, Datalogo programs can be evaluated via the natural iterative algorithm until a fixed point is reached.…

We address the satisfiability problem for string constraints that combine relational constraints represented by transducers, word equations, and string length constraints. This problem is undecidable in general. Therefore, we propose a new…

Self-assembly is a process found everywhere in the Nature. In particular, it is known that DNA self-assembly is Turing universal. Thus one can do arbitrary computations or build nano-structures using DNA self-assembly. In order to…

We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…

A crucial problem in genome assembly is the discovery and correction of misassembly errors in draft genomes. We develop a method that will enhance the quality of draft genomes by identifying and removing misassembly errors using paired…

DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are…

The spectrum $\omega(G)$ of a finite group $G$ is the set of orders of elements of $G$. We present a polynomial-time algorithm that, given a finite set $\mathcal M$ of positive integers, outputs either an empty set or a finite simple group…

It remains a challenging task to generate a vast variety of novel compounds with desirable pharmacological properties. In this work, a generative network complex (GNC) is proposed as a new platform for designing novel compounds, predicting…

The tremdendous advances in high-throughput sequencing technologies have made population-scale sequencing as performed in the 1000 Genomes project and the Genome of the Netherlands project possible. Next-generation sequencing has allowed…

In 2015, Guth proved that if $S$ is a collection of $n$ $g$-dimensional semi-algebraic sets in $\mathbb{R}^d$ and if $D\geq 1$ is an integer, then there is a $d$-variate polynomial $P$ of degree at most $D$ so that each connected component…

In the recent research of data mining, frequent structures in a sequence of graphs have been studied intensively, and one of the main concern is changing structures along a sequence of graphs that can capture dynamic properties of data. On…

A consensus tree is a phylogenetic tree that synthesizes a given collection of phylogenetic trees, all of which share the same leaf labels but may have different topologies, typically obtained through bootstrapping. Our research focuses on…

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…

Longest Run Subsequence is a problem introduced recently in the context of the scaffolding phase of genome assembly (Schrinner et al., WABI 2020). The problem asks for a maximum length subsequence of a given string that contains at most one…