Related papers: On the Coverage Required for Diploid Genome Assemb…
Affordable, high-quality whole-genome assemblies have made it possible to construct rich pangenomes that capture haplotype diversity across many species. As these datasets grow, they motivate the development of specialized techniques…
This paper examines the effect of mimicking discontinuous heredity caused by carrying more than one chromosome in some living organisms cells in Evolutionary Multi-Objective Optimization algorithms. In this representation, the phenotype may…
Defect-free single atom array in optical tweezers is a promising platform for scalable quantum computing, quantum simulation, and quantum metrology. Extending single-species array to mixed-species one promise to offer new possibilities. In…
It is known that the majority of the human genome consists of repeated sequences. Furthermore, it is believed that a significant part of the rest of the genome also originated from repeated sequences and has mutated to its current form. In…
The line coverage problem involves finding efficient routes for the coverage of linear features by one or more resource-constrained robots. Linear features model environments like road networks, power lines, and oil and gas pipelines. Two…
In the post-genome era, biologists have sought to measure the complete complement of proteins, termed proteomics. Currently, the most effective method to measure the proteome is with shotgun, or bottom-up, proteomics, in which the proteome…
Extracting associations that recur across multiple studies while controlling the false discovery rate is a fundamental challenge. Here, we consider an extension of Efron's single-study two-groups model to allow joint analysis of multiple…
Linkage maps are used to identify the location of genes responsible for traits and diseases. New sequencing techniques have created opportunities to substantially increase the density of genetic markers. Such revolutionary advances in…
In the past several years, the problem of genome assembly has received considerable attention from both biologists and computer scientists. An important component of current assembly methods is the scaffolding process. This process involves…
We study the problem of generating a test sequence that achieves maximal coverage for a reactive system under test. We formulate the problem as a repeated game between the tester and the system, where the system state space is partitioned…
Motivation: Intimately tied to assembly quality is the complexity of the de Bruijn graph built by the assembler. Thus, there have been many paradigms developed to decrease the complexity of the de Bruijn graph. One obvious combinatorial…
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…
In this article, we show how to transform a colored de Bruijn graph (dBG) into a practical index for processing massive sets of sequencing reads. Similar to previous works, we encode an instance of a colored dBG of the set using BOSS and a…
We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…
The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fibre is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors…
An exact-match overlap graph of $n$ given strings of length $\ell$ is an edge-weighted graph in which each vertex is associated with a string and there is an edge $(x,y)$ of weight $\omega = \ell - |ov_{max}(x,y)|$ if and only if $\omega…
Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…
Efficient marketing or awareness-raising campaigns seek to recruit $n$ influential individuals -- where $n$ is the campaign budget -- that are able to cover a large target audience through their social connections. So far most of the…
Sequencing errors and biases in metagenomic datasets affect coverage-based assemblies and are often ignored during analysis. Here, we analyze read connectivity in metagenomes and identify the presence of problematic and likely a-biological…
We investigate the structure of graphs of twin-width at most $1$, and obtain the following results: - Graphs of twin-width at most $1$ are permutation graphs. In particular they have an intersection model and a linear structure. - There is…